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Brepoels P, De Wit G, Lories B, Belpaire TER, Steenackers HP. Selective pressures for public antibiotic resistance. Crit Rev Microbiol 2024:1-10. [PMID: 39158370 DOI: 10.1080/1040841x.2024.2367666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/25/2024] [Indexed: 08/20/2024]
Abstract
The rapid increase of antibiotic-resistant pathogens is severely limiting our current treatment possibilities. An important subset of the resistance mechanisms conferring antibiotic resistance have public effects, allowing otherwise susceptible bacteria to also survive antibiotic treatment. As susceptible bacteria can survive treatment without bearing the metabolic cost of producing the resistance mechanism, there is potential to increase their relative frequency in the population and, as such, select against resistant bacteria. Multiple studies showed that this altered selection for resistance is dependent on various environmental and treatment parameters. In this review, we provide a comprehensive overview of their most important findings and describe the main factors impacting the selection for resistance. In-depth understanding of the driving forces behind selection can aid in the design and implementation of alternative treatments which limit the risk of resistance development.
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Affiliation(s)
- Pauline Brepoels
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Gitta De Wit
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Bram Lories
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Tom E R Belpaire
- Centre for Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, Leuven, Belgium
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2
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Jia X, Zhu Y, Jia P, Li C, Chu X, Sun T, Liu X, Yu W, Chen F, Xu Y, Yang Q. The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China. Drug Resist Updat 2024; 77:101137. [PMID: 39178714 DOI: 10.1016/j.drup.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
AIMS Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP), coharboring hypervirulence and carbapenem-resistance genes mediated by plasmids, causes infections with extremely high mortality and seriously impacts public health. Exploring the transfer mechanisms of virulence/carbapenem-resistance plasmids, as well as the formation and evolution pathway of hv-CRKP is of great significance to the control of hv-CRKP infections. METHODS In this study, we identified the predominant clone of hv-CRKP in China and elucidated its genomic characteristics and formation route based on 239 multicenter clinical K. pneumoniae isolates and 1014 GenBank genomes by using comparative genomic analysis. Further, we revealed the factors affecting the transfer of virulence plasmids, and explained the genetic foundation for the prevalence of Chinese predominant hv-CRKP clone. RESULTS ST11-KL64 is the predominant clone of hv-CRKP in China and primarily evolved from ST11-KL64 CRKP by acquiring the pLVPK-like virulence plasmid from hvKP. Significantly, the virulence gene cluster iroBCDN was lost in the virulence plasmid of ST11-KL64 hv-CRKP but existed in that of hvKP. Moreover, the absence of iroBCDN didn't decrease the virulence of hv-CRKP, which was proved by bacterial test, cell-interaction test and mice infection model. On the contrary, loss of iroBCDN was observed to regulate virulence/carbapenem-resistance plasmid transfer and oxidative stress-related genes in strains and thus promoted the mobilization of nonconjugative virulence plasmid from hvKP into ST11-KL64 CRKP, forming hv-CRKP which finally had elevated antioxidant capacity and enhanced survival capacity in macrophages. The loss of iroBCDN increased the survival ability of hv-CRKP without decreasing its virulence, endowing it with an evolutionary advantage. CONCLUSIONS Our work provides new insights into the key role of iroBCDN loss in convergence of CRKP and hvKP, and the genetic and biological foundation for the widespread prevalence of ST11-KL64 hv-CRKP in China.
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Affiliation(s)
- Xinmiao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cuidan Li
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Chu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Clinical Biobank, Center for Biomedical Technology, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Chen
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
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3
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He W, Russel J, Klincke F, Nesme J, Sørensen SJ. Insights into the ecology of the infant gut plasmidome. Nat Commun 2024; 15:6924. [PMID: 39138199 PMCID: PMC11322291 DOI: 10.1038/s41467-024-51398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Plasmids are small DNA molecules that enable bacteria to share beneficial traits, influencing microbial communities. However, their role within the human gut microbiome remains largely unknown. In this study, we investigate the gut microbiomes of 34 mother-child cohorts, employing a plasmid analysis workflow to understand the impact of plasmids on the gut microbiome. We create a plasmid phylogenetic tree, devise a method for assigning plasmid hosts, and examine potential plasmid transfer networks. Our research discovers a wide variety of previously unidentified plasmid sequences, indicating that current databases do not fully represent the gut plasmidome. Interestingly, infants display greater plasmid diversity compared to mothers and other healthy adults. We find that Bacteroidota, a major bacterial phylum, serves as the primary host for gut plasmids and plays a dominant role in gut plasmid transfer events. Additionally, plasmids broaden the genetic capabilities of bacteria, with their influence on bacterial function becoming more apparent as children's gut microbiomes develop. This study sheds light on the role of plasmids in the infant gut microbiome, making a significant contribution to our understanding of plasmid biology.
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Affiliation(s)
- Wanli He
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Franziska Klincke
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
| | - Søren Johannes Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark.
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Sendra E, Fernández-Muñoz A, Zamorano L, Oliver A, Horcajada JP, Juan C, Gómez-Zorrilla S. Impact of multidrug resistance on the virulence and fitness of Pseudomonas aeruginosa: a microbiological and clinical perspective. Infection 2024; 52:1235-1268. [PMID: 38954392 PMCID: PMC11289218 DOI: 10.1007/s15010-024-02313-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
Pseudomonas aeruginosa is one of the most common nosocomial pathogens and part of the top emergent species associated with antimicrobial resistance that has become one of the greatest threat to public health in the twenty-first century. This bacterium is provided with a wide set of virulence factors that contribute to pathogenesis in acute and chronic infections. This review aims to summarize the impact of multidrug resistance on the virulence and fitness of P. aeruginosa. Although it is generally assumed that acquisition of resistant determinants is associated with a fitness cost, several studies support that resistance mutations may not be associated with a decrease in virulence and/or that certain compensatory mutations may allow multidrug resistance strains to recover their initial fitness. We discuss the interplay between resistance profiles and virulence from a microbiological perspective but also the clinical consequences in outcomes and the economic impact.
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Affiliation(s)
- Elena Sendra
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain
| | - Almudena Fernández-Muñoz
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
| | - Laura Zamorano
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Pablo Horcajada
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain.
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Silvia Gómez-Zorrilla
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain.
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
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Kim D, Kang DY, Choi MH, Hong JS, Kim HS, Kim YR, Kim YA, Uh Y, Shin KS, Shin JH, Kim SH, Shin JH, Jeong SH. Fitness costs of Tn1546-type transposons harboring the vanA operon by plasmid type and structural diversity in Enterococcus faecium. Ann Clin Microbiol Antimicrob 2024; 23:62. [PMID: 38978096 PMCID: PMC11229256 DOI: 10.1186/s12941-024-00722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/28/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND This study analyzed the genetic traits and fitness costs of vancomycin-resistant Enterococcus faecium (VREfm) blood isolates carrying Tn1546-type transposons harboring the vanA operon. METHODS All E. faecium blood isolates were collected from eight general hospitals in South Korea during one-year study period. Antimicrobial susceptibility testing and vanA and vanB PCR were performed. Growth rates of E. faecium isolates were determined. The vanA-positive isolates were subjected to whole genome sequencing and conjugation experiments. RESULTS Among 308 E. faecium isolates, 132 (42.9%) were positive for vanA. All Tn1546-type transposons harboring the vanA operon located on the plasmids, but on the chromosome in seven isolates. The plasmids harboring the vanA operon were grouped into four types; two types of circular, nonconjugative plasmids (Type A, n = 50; Type B, n = 46), and two types of putative linear, conjugative plasmids (Type C, n = 16; Type D, n = 5). Growth rates of vanA-positive E. faecium isolates were significantly lower than those of vanA-negative isolates (P < 0.001), and reduction in growth rate under vancomycin pressure was significantly larger in isolates harboring putative linear plasmids than in those harboring circular plasmids (P = 0.020). CONCLUSIONS The possession of vanA operon was costly to bacterial hosts in antimicrobial-free environment, which provide evidence for the importance of reducing vancomycin pressure for prevention of VREfm dissemination. Fitness burden to bacterial hosts was varied by type and size of the vanA operon-harboring plasmid.
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Affiliation(s)
- Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospita, l, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, South Korea
| | - Da Young Kang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospita, l, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, South Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospita, l, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, South Korea
| | - Jun Sung Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospita, l, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, South Korea
- Department of Companion Animal Health and Science, Silla University, Busan, South Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, Hallym University College of Medicine, Hwaseong, South Korea
| | - Young Ree Kim
- Department of Laboratory Medicine, Jeju National University College of Medicine, Jeju, South Korea
| | - Young Ah Kim
- Department of Laboratory Medicine, National Health Insurance Service, Ilsan Hospital, Goyang, South Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Kyeong Seob Shin
- Department of Laboratory Medicine, Chungbuk National University College of Medicine, Cheongju, South Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine and Paik Institute for Clinical Research, Inje University College of Medicine, Busan, South Korea
| | - Soo Hyun Kim
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Gangnam Severance Hospita, l, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 06273, South Korea.
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6
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Liu Y, Chu K, Hua Z, Li Q, Lu Y, Ye F, Dong Y, Li X. Dynamics of antibiotic resistance genes in the sediments of a water-diversion lake and its human exposure risk behaviour. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172563. [PMID: 38641096 DOI: 10.1016/j.scitotenv.2024.172563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
The dynamics and exposure risk behaviours of antibiotic resistance genes (ARGs) in the sediments of water-diversion lakes remain poorly understood. In this study, spatiotemporal investigations of ARG profiles in sediments targeting non-water (NWDP) and water diversion periods (WDP) were conducted in Luoma Lake, a typical water-diversion lake, and an innovative dynamics-based risk assessment framework was constructed to evaluate ARG exposure risks to local residents. ARGs in sediments were significantly more abundant in the WDP than in the NWDP, but there was no significant variation in their spatial distribution in either period. Moreover, the pattern of ARG dissemination in sediments was unchanged between the WDP and NWDP, with horizontal gene transfer (HGT) and vertical gene transfer (VGT) contributing to ARG dissemination in both periods. However, water diversion altered the pattern in lake water, with HGT and VGT in the NWDP but only HGT in the WDP, which were critical pathways for the dissemination of ARGs. The significantly lower ARG sediment-water partition coefficient in the WDP indicated that water diversion could shift the fate of ARGs and facilitate their aqueous partitioning. Risk assessment showed that all age groups faced a higher human exposure risk of ARGs (HERA) in the WDP than in the NWDP, with the 45-59 age group having the highest risk. Furthermore, HERA increased overall with the bacterial carrying capacity in the local environment and peaked when the carrying capacity reached three (NWDP) or four (WDP) orders of magnitude higher than the observed bacterial population. HGT and VGT promoted, whereas ODF covering gene mutation and loss mainly reduced HERA in the lake. As the carrying capacity increased, the relative contribution of ODF to HERA remained relatively stable, whereas the dominant mechanism of HERA development shifted from HGT to VGT.
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Affiliation(s)
- Yuanyuan Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Kejian Chu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China.
| | - Zulin Hua
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Qiming Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Ying Lu
- Institute for Smart City of Chongqing University in Liyang, Liyang 213300, PR China
| | - Fuzhu Ye
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Yueyang Dong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
| | - Xiaoqing Li
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, PR China; Yangtze Institute for Conservation and Development, Hohai University, Nanjing 210098, PR China
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Zhang D, Li H, Yang Q, Xu Y. Microbial-mediated conversion of soil organic carbon co-regulates the evolution of antibiotic resistance. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134404. [PMID: 38688217 DOI: 10.1016/j.jhazmat.2024.134404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/02/2024]
Abstract
The influence of organic carbon on the proliferation of antibiotic resistance genes (ARGs) in the soil has been widely documented. However, it is unclear how soil organic carbon (SOC) interacts with the evolution of antibiotic resistance in bacteria. Here, we examined the variations in ARGs abundance during SOC mineralization and explored the microbiological mechanisms and key metabolic pathways involved in their coevolution. The results showed that the SOC mineralization rate was closely correlated with ARGs abundance (p < 0.05). High organic carbon (OC) mineralization was conducive to the occurrence of multidrug resistance genes. For example, multidrug_transporter and mexB increased 2.26 and 7.83 times from the initial level. The competitor (stress) evolutionary strategy model revealed that higher OC inputs drive environmental microorganisms to evolve from stress tolerant to high resistance and strong adaptation. Meta-genomic and transcriptomic analyses revealed that the conversion process of pyruvate to acetyl-CoA to acetate was the critical metabolic pathway for the co-regulation of antibiotic resistance. Gene deletion validation trials have demonstrated that the key functional genes (ackA and pta) involved in this process can modulate the development of vancomycin and multidrug resistance. This outcome provides a preliminary framework for microbial mechanisms that target the co-regulation of microbial OC conversion and the evolution of antibiotic resistance.
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Affiliation(s)
- Dandan Zhang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China; College of Resources and Environment, Jilin Agricultural University, Changchun 130118, China
| | - Houyu Li
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Qifan Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
| | - Yan Xu
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China.
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8
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Lai HY, Cooper TF. Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition. Proc Biol Sci 2024; 291:20240735. [PMID: 38889784 DOI: 10.1098/rspb.2024.0735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Antibiotic resistance genes (ARGs) benefit host bacteria in environments containing corresponding antibiotics, but it is less clear how they are maintained in environments where antibiotic selection is weak or sporadic. In particular, few studies have measured if the direct effect of ARGs on host fitness is fixed or if it depends on the host strain, perhaps marking some ARG-host combinations as selective refuges that can maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in 11 diverse Escherichia spp. strains. Three ARGs (blaTEM-116, cat and dfrA5, encoding resistance to β-lactams, chloramphenicol, and trimethoprim, respectively) imposed an overall cost, but all ARGs had an effect in at least one host strain, reflecting a significant strain interaction effect. A simulation predicts these interactions can cause the success of ARGs to depend on available host strains, and, to a lesser extent, can cause host strain success to depend on the ARGs present in a community. These results indicate the importance of considering ARG effects across different host strains, and especially the potential of refuge strains to allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.
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Affiliation(s)
- Huei-Yi Lai
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
| | - Tim F Cooper
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1023, New Zealand
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9
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Hinz A, Amado A, Kassen R, Bank C, Wong A. Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli. Mol Biol Evol 2024; 41:msae086. [PMID: 38709811 PMCID: PMC11110942 DOI: 10.1093/molbev/msae086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024] Open
Abstract
The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness effects (i.e. costs) imposed by AMR mutations during growth in the absence of antibiotics. According to this assumption, resistant strains will be outcompeted by susceptible strains that do not pay the cost during the period of restriction. The fitness effects of AMR mutations are generally studied in laboratory reference strains grown in standard growth environments; however, the genetic and environmental context can influence the magnitude and direction of a mutation's fitness effects. In this study, we measure how three sources of variation impact the fitness effects of Escherichia coli AMR mutations: the type of resistance mutation, the genetic background of the host, and the growth environment. We demonstrate that while AMR mutations are generally costly in antibiotic-free environments, their fitness effects vary widely and depend on complex interactions between the mutation, genetic background, and environment. We test the ability of the Rough Mount Fuji fitness landscape model to reproduce the empirical data in simulation. We identify model parameters that reasonably capture the variation in fitness effects due to genetic variation. However, the model fails to accommodate the observed variation when considering multiple growth environments. Overall, this study reveals a wealth of variation in the fitness effects of resistance mutations owing to genetic background and environmental conditions, which will ultimately impact their persistence in natural populations.
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Affiliation(s)
- Aaron Hinz
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - André Amado
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Claudia Bank
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Division of Theoretical Ecology and Evolution, Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Evolutionary Dynamics Group, Gulbenkian Science Institute, Oeiras, Portugal
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
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10
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Barceló IM, Escobar-Salom M, Cabot G, Perelló-Bauzà P, Jordana-Lluch E, Taltavull B, Torrens G, Rojo-Molinero E, Zamorano L, Pérez A, Oliver A, Juan C. Transferable AmpCs in Klebsiella pneumoniae: interplay with peptidoglycan recycling, mechanisms of hyperproduction, and virulence implications. Antimicrob Agents Chemother 2024; 68:e0131523. [PMID: 38517189 PMCID: PMC11064642 DOI: 10.1128/aac.01315-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/29/2024] [Indexed: 03/23/2024] Open
Abstract
Chromosomal and transferable AmpC β-lactamases represent top resistance mechanisms in different gram-negatives, but knowledge regarding the latter, mostly concerning regulation and virulence-related implications, is far from being complete. To fill this gap, we used Klebsiella pneumoniae (KP) and two different plasmid-encoded AmpCs [DHA-1 (AmpR regulator linked, inducible) and CMY-2 (constitutive)] as models to perform a study in which we show that blockade of peptidoglycan recycling through AmpG permease inactivation abolished DHA-1 inducibility but did not affect CMY-2 production and neither did it alter KP pathogenic behavior. Moreover, whereas regular production of both AmpC-type enzymes did not attenuate KP virulence, when blaDHA-1 was expressed in an ampG-defective mutant, Galleria mellonella killing was significantly (but not drastically) attenuated. Spontaneous DHA-1 hyperproducer mutants were readily obtained in vitro, showing slight or insignificant virulence attenuations together with high-level resistance to β-lactams only mildly affected by basal production (e.g., ceftazidime, ceftolozane/tazobactam). By analyzing diverse DHA-1-harboring clinical KP strains, we demonstrate that the natural selection of these hyperproducers is not exceptional (>10% of the collection), whereas mutational inactivation of the typical AmpC hyperproduction-related gene mpl was the most frequent underlying mechanism. The potential silent dissemination of this kind of strains, for which an important fitness cost-related contention barrier does not seem to exist, is envisaged as a neglected threat for most β-lactams effectiveness, including recently introduced combinations. Analyzing whether this phenomenon is applicable to other transferable β-lactamases and species as well as determining the levels of conferred resistance poses an essential topic to be addressed.IMPORTANCEAlthough there is solid knowledge about the regulation of transferable and especially chromosomal AmpC β-lactamases in Enterobacterales, there are still gaps to fill, mainly related to regulatory mechanisms and virulence interplays of the former. This work addresses them using Klebsiella pneumoniae as model, delving into a barely explored conception: the acquisition of a plasmid-encoded inducible AmpC-type enzyme whose production can be increased through selection of chromosomal mutations, entailing dramatically increased resistance compared to basal expression but minor associated virulence costs. Accordingly, we demonstrate that clinical K. pneumoniae DHA-1 hyperproducer strains are not exceptional. Through this study, we warn for the first time that this phenomenon may be a neglected new threat for β-lactams effectiveness (including some recently introduced ones) silently spreading in the clinical context, not only in K. pneumoniae but potentially also in other pathogens. These facts must be carefully considered in order to design future resistance-preventive strategies.
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Affiliation(s)
- Isabel M. Barceló
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Maria Escobar-Salom
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Gabriel Cabot
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pau Perelló-Bauzà
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
| | - Elena Jordana-Lluch
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Biel Taltavull
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Estrella Rojo-Molinero
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Laura Zamorano
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Astrid Pérez
- National Center for Microbiology, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Antonio Oliver
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carlos Juan
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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11
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Vincent J, Tenore A, Mattei MR, Frunzo L. Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms. Bull Math Biol 2024; 86:63. [PMID: 38664322 DOI: 10.1007/s11538-024-01289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/27/2024] [Indexed: 05/23/2024]
Abstract
In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.
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Affiliation(s)
- Julien Vincent
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
- Microbial Ecology Laboratory, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Alberto Tenore
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
| | - Maria Rosaria Mattei
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy.
| | - Luigi Frunzo
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
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12
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Nguyen ANT, Gorrell R, Kwok T, Connallon T, McDonald MJ. Horizontal gene transfer facilitates the molecular reverse-evolution of antibiotic sensitivity in experimental populations of H. pylori. Nat Ecol Evol 2024; 8:315-324. [PMID: 38177692 DOI: 10.1038/s41559-023-02269-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024]
Abstract
Reversing the evolution of traits harmful to humans, such as antimicrobial resistance, is a key ambition of applied evolutionary biology. A major impediment to reverse evolution is the relatively low spontaneous mutation rates that revert evolved genotypes back to their ancestral state. However, the repeated re-introduction of ancestral alleles by horizontal gene transfer (HGT) could make reverse evolution likely. Here we evolve populations of an antibiotic-resistant strain of Helicobacter pylori in growth conditions without antibiotics while introducing an ancestral antibiotic-sensitive allele by HGT. We evaluate reverse evolution using DNA sequencing and find that HGT facilitates the molecular reverse evolution of the antibiotic resistance allele, and that selection for high rates of HGT drives the evolution of increased HGT rates in low-HGT treatment populations. Finally, we use a theoretical model and carry out simulations to infer how the fitness costs of antibiotic resistance, rates of HGT and effects of genetic drift interact to determine the probability and predictability of reverse evolution.
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Affiliation(s)
- An N T Nguyen
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Rebecca Gorrell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Terry Kwok
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
- Biomedical Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tim Connallon
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia.
- Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
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13
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Siedentop B, Rüegg D, Bonhoeffer S, Chabas H. My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages. Proc Biol Sci 2024; 291:20232449. [PMID: 38262608 PMCID: PMC10805597 DOI: 10.1098/rspb.2023.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteria are infected by mobile genetic elements like plasmids and virulent phages, and those infections significantly impact bacterial ecology and evolution. Recent discoveries reveal that some plasmids carry anti-phage immune systems like CRISPR-Cas, suggesting that plasmids may participate in the coevolutionary arms race between virulent phages and bacteria. Intuitively, this seems reasonable as virulent phages kill the plasmid's obligate host. However, the efficiency of CRISPR-Cas systems carried by plasmids can be expected to be lower than those carried by the chromosome due to continuous segregation loss, creating susceptible cells for phage amplification. To evaluate the anti-phage protection efficiency of CRISPR-Cas on plasmids, we develop a stochastic model describing the dynamics of a virulent phage infection against which a conjugative plasmid defends using CRISPR-Cas. We show that CRISPR-Cas on plasmids provides robust protection, except in limited parameter sets. In these cases, high segregation loss favours phage outbreaks by generating a population of defenceless cells on which the phage can evolve and escape CRISPR-Cas immunity. We show that the phage's ability to exploit segregation loss depends strongly on the evolvability of both CRISPR-Cas and the phage itself.
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Affiliation(s)
- Berit Siedentop
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Dario Rüegg
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
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14
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Risely A, Newbury A, Stalder T, Simmons BI, Top EM, Buckling A, Sanders D. Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes. Nat Commun 2024; 15:555. [PMID: 38228585 PMCID: PMC10791616 DOI: 10.1038/s41467-024-44827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains.
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Affiliation(s)
- Alice Risely
- School of Science, Engineering, and Environment, University of Salford, Salford, M5 4WT, UK
| | - Arthur Newbury
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Thibault Stalder
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Benno I Simmons
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Eva M Top
- Department of Biological Sciences, University of Idaho, Moscow, ID, USA
- Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID, USA
| | - Angus Buckling
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Dirk Sanders
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
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15
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Liu Z, Gao Y, Wang M, Liu Y, Wang F, Shi J, Wang Z, Li R. Adaptive evolution of plasmid and chromosome contributes to the fitness of a blaNDM-bearing cointegrate plasmid in Escherichia coli. THE ISME JOURNAL 2024; 18:wrae037. [PMID: 38438143 PMCID: PMC10976473 DOI: 10.1093/ismejo/wrae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/08/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Large cointegrate plasmids recruit genetic features of their parental plasmids and serve as important vectors in the spread of antibiotic resistance. They are now frequently found in clinical settings, raising the issue of how to limit their further transmission. Here, we conducted evolutionary research of a large blaNDM-positive cointegrate within Escherichia coli C600, and discovered that adaptive evolution of chromosome and plasmid jointly improved bacterial fitness, which was manifested as enhanced survival ability for in vivo and in vitro pairwise competition, biofilm formation, and gut colonization ability. From the plasmid aspect, large-scale DNA fragment loss is observed in an evolved clone. Although the evolved plasmid imposes a negligible fitness cost on host bacteria, its conjugation frequency is greatly reduced, and the deficiency of anti-SOS gene psiB is found responsible for the impaired horizontal transferability rather than the reduced fitness cost. These findings unveil an evolutionary strategy in which the plasmid horizontal transferability and fitness cost are balanced. From the chromosome perspective, all evolved clones exhibit parallel mutations in the transcriptional regulatory stringent starvation Protein A gene sspA. Through a sspA knockout mutant, transcriptome analysis, in vitro transcriptional activity assay, RT-qPCR, motility test, and scanning electron microscopy techniques, we demonstrated that the mutation in sspA reduces its transcriptional inhibitory capacity, thereby improving bacterial fitness, biofilm formation ability, and gut colonization ability by promoting bacterial flagella synthesis. These findings expand our knowledge of how cointegrate plasmids adapt to new bacterial hosts.
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Affiliation(s)
- Ziyi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- College of Animal Science and Technology & College of Veterinary medicine, Zhejiang Agriculture and Forestry University, Hangzhou, 311300 Zhejiang Province, People's Republic of China
| | - Yanyun Gao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Mianzhi Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Yuan Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023 Jiangsu Province, People's Republic of China
| | - Zhiqiang Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Agricultural Science and Technology Development, Yangzhou, 225009 Jiangsu Province, People's Republic of China
| | - Ruichao Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Jiangsu Key Lab of Zoonosis, Yangzhou, 225009 Jiangsu Province, People's Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, 225009 Jiangsu Province, People's Republic of China
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16
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Barceló IM, Escobar-Salom M, Jordana-Lluch E, Torrens G, Oliver A, Juan C. Filling knowledge gaps related to AmpC-dependent β-lactam resistance in Enterobacter cloacae. Sci Rep 2024; 14:189. [PMID: 38167986 PMCID: PMC10762043 DOI: 10.1038/s41598-023-50685-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Enterobacter cloacae starred different pioneer studies that enabled the development of a widely accepted model for the peptidoglycan metabolism-linked regulation of intrinsic class C cephalosporinases, highly conserved in different Gram-negatives. However, some mechanistic and fitness/virulence-related aspects of E. cloacae choromosomal AmpC-dependent resistance are not completely understood. The present study including knockout mutants, β-lactamase cloning, gene expression analysis, characterization of resistance phenotypes, and the Galleria mellonella infection model fills these gaps demonstrating that: (i) AmpC enzyme does not show any collateral activity impacting fitness/virulence; (ii) AmpC hyperproduction mediated by ampD inactivation does not entail any biological cost; (iii) alteration of peptidoglycan recycling alone or combined with AmpC hyperproduction causes no attenuation of E. cloacae virulence in contrast to other species; (iv) derepression of E. cloacae AmpC does not follow a stepwise dynamics linked to the sequential inactivation of AmpD amidase homologues as happens in Pseudomonas aeruginosa; (v) the enigmatic additional putative AmpC-type β-lactamase generally present in E. cloacae does not contribute to the classical cephalosporinase hyperproduction-based resistance, having a negligible impact on phenotypes even when hyperproduced from multicopy vector. This study reveals interesting particularities in the chromosomal AmpC-related behavior of E. cloacae that complete the knowledge on this top resistance mechanism.
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Affiliation(s)
- Isabel M Barceló
- Health Research Institute of the Balearic Islands (IdISBa), 07010, Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), 07010, Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - María Escobar-Salom
- Health Research Institute of the Balearic Islands (IdISBa), 07010, Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), 07010, Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Elena Jordana-Lluch
- Health Research Institute of the Balearic Islands (IdISBa), 07010, Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), 07010, Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87, Umeå, Sweden
| | - Antonio Oliver
- Health Research Institute of the Balearic Islands (IdISBa), 07010, Palma, Spain
- Microbiology Department, University Hospital Son Espases (HUSE), 07010, Palma, Spain
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Carlos Juan
- Health Research Institute of the Balearic Islands (IdISBa), 07010, Palma, Spain.
- Microbiology Department, University Hospital Son Espases (HUSE), 07010, Palma, Spain.
- Centro de Investigación Biomédica en Red, Área Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029, Madrid, Spain.
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17
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Eccleston RC, Manko E, Campino S, Clark TG, Furnham N. A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife 2023; 12:e84756. [PMID: 38132182 PMCID: PMC10807863 DOI: 10.7554/elife.84756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/21/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogen evolution of drug resistance often occurs in a stepwise manner via the accumulation of multiple mutations that in combination have a non-additive impact on fitness, a phenomenon known as epistasis. The evolution of resistance via the accumulation of point mutations in the DHFR genes of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) has been studied extensively and multiple studies have shown epistatic interactions between these mutations determine the accessible evolutionary trajectories to highly resistant multiple mutations. Here, we simulated these evolutionary trajectories using a model of molecular evolution, parameterised using Rosetta Flex ddG predictions, where selection acts to reduce the target-drug binding affinity. We observe strong agreement with pathways determined using experimentally measured IC50 values of pyrimethamine binding, which suggests binding affinity is strongly predictive of resistance and epistasis in binding affinity strongly influences the order of fixation of resistance mutations. We also infer pathways directly from the frequency of mutations found in isolate data, and observe remarkable agreement with the most likely pathways predicted by our mechanistic model, as well as those determined experimentally. This suggests mutation frequency data can be used to intuitively infer evolutionary pathways, provided sufficient sampling of the population.
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Affiliation(s)
- Ruth Charlotte Eccleston
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Emilia Manko
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Taane G Clark
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Nicholas Furnham
- Department of Infection Biology, London School of Hygiene and Tropical MedicineLondonUnited Kingdom
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18
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Tadesse BT, Keddy KH, Rickett NY, Zhusupbekova A, Poudyal N, Lawley T, Osman M, Dougan G, Kim JH, Lee JS, Jeon HJ, Marks F. Vaccination to Reduce Antimicrobial Resistance Burden-Data Gaps and Future Research. Clin Infect Dis 2023; 77:S597-S607. [PMID: 38118013 PMCID: PMC10732565 DOI: 10.1093/cid/ciad562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
Abstract
Antimicrobial resistance (AMR) poses an immediate danger to global health. If unaddressed, the current upsurge in AMR threatens to reverse the achievements in reducing the infectious disease-associated mortality and morbidity associated with antimicrobial treatment. Consequently, there is an urgent need for strategies to prevent or slow the progress of AMR. Vaccines potentially contribute both directly and indirectly to combating AMR. Modeling studies have indicated significant gains from vaccination in reducing AMR burdens for specific pathogens, reducing mortality/morbidity, and economic loss. However, quantifying the real impact of vaccines in these reductions is challenging because many of the study designs used to evaluate the contribution of vaccination programs are affected by significant background confounding, and potential selection and information bias. Here, we discuss challenges in assessing vaccine impact to reduce AMR burdens and suggest potential approaches for vaccine impact evaluation nested in vaccine trials.
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Affiliation(s)
- Birkneh Tilahun Tadesse
- International Vaccine Institute, Seoul, Republic of Korea
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | | | - Nimesh Poudyal
- International Vaccine Institute, Seoul, Republic of Korea
| | - Trevor Lawley
- Wellcome Sanger Institute and Microbiotica, Cambridge, United Kingdom
| | - Majdi Osman
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Jerome H Kim
- International Vaccine Institute, Seoul, Republic of Korea
- Seoul National University, College of Natural Sciences, Seoul, Republic of Korea
| | - Jung-Seok Lee
- International Vaccine Institute, Seoul, Republic of Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
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19
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Gordon J, Gheorghe M, Goldenberg S, Miller R, Dennis J, Al-Taie A. Capturing Value Attributes in the Economic Evaluation of Ceftazidime with Avibactam for Treating Severe Aerobic Gram-Negative Bacterial Infections in the United Kingdom. PHARMACOECONOMICS 2023; 41:1657-1673. [PMID: 37587392 PMCID: PMC10635959 DOI: 10.1007/s40273-023-01310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
INTRODUCTION Antimicrobial resistance remains a serious and growing threat to public health, both globally and in the UK, leading to diminishing effectiveness of antimicrobials. Despite a clear need for new antimicrobials, the clinical pipeline is insufficient, driven by high research and development costs and limited expected returns on investment. To counteract this, National Institute for Health and Care Excellence (NICE) and National Health Service (NHS) England have launched a reimbursement mechanism, de-linked from volume of sales, that aims to reduce economic risk by recognising the broader population-level value of antimicrobials. The objective of this study was to quantify the value of ceftazidime-avibactam for treating gram-negative infections in the UK considering some of these broader value elements unique to antimicrobials. METHODS A previously developed dynamic disease transmission and cost-effectiveness model was applied to assess the value of introducing ceftazidime-avibactam to UK treatment practice in the management of gram-negative hospital-acquired infections in line with the licenced indications for ceftazidime-avibactam. Model inputs were parameterised using sources aligned to the UK perspective. RESULTS The introduction of ceftazidime-avibactam into a two-line treatment sequence saved over 2300 lives, leading to a gain of 27,600 life years and 22,000 quality-adjusted life years (QALY) at an additional cost of £17 million, over a ten-year transmission period. Ceftazidime-avibactam was associated with a net monetary benefit of £642 million at willingness to pay threshold of £30,000 per QALY; even at a lower threshold of £20,000 per QALY, the net monetary benefit is £422 million. DISCUSSION Increasing the diversity of antimicrobial treatments through the introduction of an additional antimicrobial, in this instance ceftazidime-avibactam, was associated with substantial clinical and economic benefits, when considering broader population-level value. Despite revealing considerable benefits, the value of ceftazidime-avibactam is only partially reflected in this analysis. Further efforts are required to fully operationalise the spectrum, transmission, enablement, diversity and insurance (STEDI) value framework and accurately reflect the population-level value of antimicrobials.
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Affiliation(s)
- Jason Gordon
- Health Economics and Outcomes Research Ltd., Unit A, Cardiff Gate Business Park, Copse Walk, Pontprennau, Cardiff, CF23 8RB, UK.
| | | | - Simon Goldenberg
- Centre for Clinical Infection and Diagnostics Research, King's College London and Guy's & St. Thomas' NHS Foundation Trust, London, UK
| | - Ryan Miller
- Health Economics and Outcomes Research Ltd., Unit A, Cardiff Gate Business Park, Copse Walk, Pontprennau, Cardiff, CF23 8RB, UK
| | - James Dennis
- Health Economics and Outcomes Research Ltd., Unit A, Cardiff Gate Business Park, Copse Walk, Pontprennau, Cardiff, CF23 8RB, UK
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20
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Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023; 24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Control interventions steer the evolution of molecules, viruses, microorganisms or other cells towards a desired outcome. Applications range from engineering biomolecules and synthetic organisms to drug, therapy and vaccine design against pathogens and cancer. In all these instances, a control system alters the eco-evolutionary trajectory of a target system, inducing new functions or suppressing escape evolution. Here, we synthesize the objectives, mechanisms and dynamics of eco-evolutionary control in different biological systems. We discuss how the control system learns and processes information about the target system by sensing or measuring, through adaptive evolution or computational prediction of future trajectories. This information flow distinguishes pre-emptive control strategies by humans from feedback control in biotic systems. We establish a cost-benefit calculus to gauge and optimize control protocols, highlighting the fundamental link between predictability of evolution and efficacy of pre-emptive control.
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Affiliation(s)
- Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, Seattle, WA, USA.
- Department of Applied Mathematics, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA, USA.
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21
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Thani AB. DNA supercoiling and regulation of intrinsic β-lactamase in pathogenic Escherichia coli. Arch Microbiol 2023; 205:385. [PMID: 37980630 DOI: 10.1007/s00203-023-03716-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/21/2023]
Abstract
This review addresses the involvement of DNA supercoiling in the development of virulence and antibiotic profiles for uropathogenic Escherichia coli and the emergence of new pathotypes such as strain ST131 (serotype O25:H4). The mechanism suggests a role for topoisomerase enzymes and associated mutations in altering the chromosomal supercoiling state and introducing the required DNA twists for expression of intrinsic β-lactamase by ampC and certain virulence factors. In Escherichia coli, constitutive hyperexpression of intrinsic ampC is associated with specific mutations in the promoter and attenuator regions. However, many reports have documented the involvement of slow growth interventions in the expression of intrinsic resistance determinants. There is evidence that a stationary phase transcriptional switch protein, "BolA," is involved in the expression of the intrinsic ampC gene under starvation conditions. The process involves changes in the activity of the enzyme "gyrase," which leads to a change in the chromosomal DNA topology. Consequently, the DNA is relaxed, and the expression of the bolA gene is upregulated. The evolution of the extraintestinal pathogenic E. coli strain ST131 has demonstrated successful adaptability to various stress conditions and conferred compensatory mutations that endowed the microbe with resistance to fluoroquinolones and β-lactams. The results of this study provided new insights into the evidence for the influence of DNA topology in the expression of virulence genes and various determinants of antibiotic resistance (e.g., the intrinsic ampC gene) in Escherichia coli pathotypes.
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Affiliation(s)
- Ali Bin Thani
- Department of Biology, College of Science, University of Bahrain, Zallaq, Kingdom of Bahrain.
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22
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Wang B, Finazzo M, Artsimovitch I. Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range. Genes (Basel) 2023; 14:2044. [PMID: 38002987 PMCID: PMC10670969 DOI: 10.3390/genes14112044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.
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Affiliation(s)
- Bing Wang
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
| | | | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA;
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23
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Alvarez-Molina A, Cobo-Díaz JF, Alexa EA, Crispie F, Prieto M, López M, Cotter PD, Alvarez-Ordóñez A. Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes. Food Res Int 2023; 173:113442. [PMID: 37803768 DOI: 10.1016/j.foodres.2023.113442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/11/2023] [Accepted: 09/09/2023] [Indexed: 10/08/2023]
Abstract
In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.
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Affiliation(s)
| | - José F Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Elena A Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain; Institute of Food Science and Technology, Universidad de León, León, Spain.
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24
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Ogunlana L, Kaur D, Shaw LP, Jangir P, Walsh T, Uphoff S, MacLean RC. Regulatory fine-tuning of mcr-1 increases bacterial fitness and stabilises antibiotic resistance in agricultural settings. THE ISME JOURNAL 2023; 17:2058-2069. [PMID: 37723338 PMCID: PMC10579358 DOI: 10.1038/s41396-023-01509-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/20/2023]
Abstract
Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be maintained in the absence of continual antibiotic exposure. Here we investigate this problem in the context of mcr-1, a globally disseminated gene that confers resistance to colistin, an agricultural antibiotic that is used as a last resort for the treatment of multi-drug resistant infections. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the fitness cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low-cost/high-resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilising mcr-1 at the species level. Regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how regulatory evolution and plasmid transfer can combine to stabilise resistance and limit the impact of reducing antibiotic consumption.
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Affiliation(s)
- Lois Ogunlana
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Divjot Kaur
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Liam P Shaw
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Department of Biosciences, Durham University, Stockton Road, Durham, DH1 3LE, UK
| | - Pramod Jangir
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Timothy Walsh
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
- Ineos Oxford Institute for Antimicrobial Research, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - R C MacLean
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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25
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Dankittipong N, Alderliesten JB, Van den Broek J, Dame-Korevaar MA, Brouwer MSM, Velkers FC, Bossers A, de Vos CJ, Wagenaar JA, Stegeman JA, Fischer EAJ. Comparing the transmission of carbapenemase-producing and extended-spectrum beta-lactamase-producing Escherichia coli between broiler chickens. Prev Vet Med 2023; 219:105998. [PMID: 37647719 DOI: 10.1016/j.prevetmed.2023.105998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
The emergence of carbapenemase-producing Enterobacteriaceae (CPE) is a threat to public health, because of their resistance to clinically important carbapenem antibiotics. The emergence of CPE in meat-producing animals is particularly worrying because consumption of meat contaminated with resistant bacteria comparable to CPE, such as extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, contributed to colonization in humans worldwide. Currently, no data on the transmission of CPE in livestock is available. We performed a transmission experiment to quantify the transmission of CPE between broilers to fill this knowledge gap and to compare the transmission rates of CPE and other antibiotic-resistant E. coli. A total of 180 Ross 308 broiler chickens were distributed over 12 pens on the day of hatch (day 0). On day 5, half of the 10 remaining chickens in each pen were orally inoculated with 5·102 colony-forming units of CPE, ESBL, or chloramphenicol-resistant E. coli (catA1). To evaluate the effect of antibiotic treatment, amoxicillin was given twice daily in drinking water in 6 of the 12 pens from days 2-6. Cloacal swabs of all animals were taken to determine the number of infectious broilers. We used a Bayesian hierarchical model to quantify the transmission of the E. coli strains. E. coli can survive in the environment and serve as a reservoir. Therefore, the susceptible-infectious transmission model was adapted to account for the transmission of resistant bacteria from the environment. In addition, the caecal microbiome was analyzed on day 5 and at the end of the experiment on day 14 to assess the relationship between the caecal microbiome and the transmission rates. The transmission rates of CPE were 52 - 68 per cent lower compared to ESBL and catA1, but it is not clear if these differences were caused by differences between the resistance genes or by other differences between the E. coli strains. Differences between the groups in transmission rates and microbiome diversity did not correspond to each other, indicating that differences in transmission rates were probably not caused by major differences in the community structure in the caecal microbiome. Amoxicillin treatment from day 2-6 increased the transmission rate more than three-fold in all inoculums. It also increased alpha-diversity compared to untreated animals on day 5, but not on day 14, suggesting only a temporary effect. Future research could incorporate more complex transmission models with different species of resistant bacteria into the Bayesian hierarchical model.
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Affiliation(s)
- Natcha Dankittipong
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jesse B Alderliesten
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Jan Van den Broek
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - M Anita Dame-Korevaar
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Michael S M Brouwer
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Francisca C Velkers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Alex Bossers
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Clazien J de Vos
- Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - Jaap A Wagenaar
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands; Wageningen Bioveterinary Research, Wageningen University & Research, Houtribweg 39, Lelystad, the Netherlands
| | - J Arjan Stegeman
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands
| | - Egil A J Fischer
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 7, Utrecht, the Netherlands.
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26
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Zhang Y, Xu D, He Z, Han J, Qu D. Characterization and fitness cost analysis of two plasmids carrying different subtypes of bla NDM in aquaculture farming. Food Microbiol 2023; 115:104327. [PMID: 37567620 DOI: 10.1016/j.fm.2023.104327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 08/13/2023]
Abstract
In recent years, the blaNDM gene, which mediate resistance to carbapenems, has disseminated all over the world, and has also been detected in animals. Understanding the dissemination and accumulation of antibiotic resistance genes (ARGs) in a human-impacted environment is essential to solve the food safety problems caused by antibiotics. In this study, two strains of carbapenem bacteria carrying blaNDM were screened from 244 strains isolated from two T. sinensis farms in Zhejiang province, China. After their plasmids were isolated and sequenced, their structure and gene environment were analyzed and the mechanism of blaNDM gene transfer was explored. The study measured the fitness cost of plasmids carrying different blaNDM subtypes by four biological characteristics experiments. The results showed that the fitness cost of IncC plasmid carrying blaNDM-1 was higher than that of IncX3 plasmid carrying blaNDM-5. Furthermore, the real-time PCR showed that the decrease of transcription level of fitness-related genes lead to the different fitness cost of plasmids carrying different blaNDM subtypes. Fitness of many blaNDM-harboring plasmids enhanced the further dissemination of this gene and increase the risk of blaNDM gene spreading in aquatic environment, and thus further investigation of carbapenem-resistant bacterias among food animals are in urgent need.
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Affiliation(s)
- Yaru Zhang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Dingting Xu
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 311100, Zhejiang, China
| | - Ze He
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jianzhong Han
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Daofeng Qu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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27
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Hong Y, Wu Y, Xie Y, Ben L, Bu X, Pan X, Shao J, Dong Q, Qin X, Wang X. Effects of antibiotic-induced resistance on the growth, survival ability and virulence of Salmonella enterica. Food Microbiol 2023; 115:104331. [PMID: 37567636 DOI: 10.1016/j.fm.2023.104331] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 08/13/2023]
Abstract
Salmonella enterica is an important foodborne pathogen that constitutes a major health hazard. The emergence and aggravation of antibiotic-resistant Salmonella has drawn attention widely around the world. Conducting a risk assessment of antibiotic-resistant foodborne pathogens throughout the food chain is a pressing requirement for ensuring food safety. The growth, survival capability, and virulence of antibiotic-resistant Salmonella represent crucial biological characteristics that play an important role in microbial risk assessment. In this study, eight antibiotic-sensitive S. enterica strains were induced by Ampicillin (Amp) and Ciprofloxacin (CIP), respectively, and AMP-resistant and CIP-resistant mutants were obtained. The growth characteristics under different temperatures (25, 30, 35 °C), viability after exposure to heat (55, 57.5, 60 °C) and acid (HCl, pH = 3.0), the virulence potential (adhesion and invasion to Caco-2 cells, biofilm formation and motility) and the lethality in a model species (Galleria mellonella) were evaluated and compared for S. enterica strains before and after antibiotic exposure. The induction by AMP and CIP are likely to promote cross-antibiotic resistance to their antibiotic classes, β-lactams and quinolones, as well as some compound antibiotics. It was observed that generally the antibiotic-induction-resistant strains showed decreased growth ability and lower heat resistance, although the differences were not significant at all the conditions tested. The AMP-resistant strains were significantly less acid resistance than the sensitive and the CIP-resistant ones, while exhibiting increased biofilm formation ability. In general, the antibiotic-induced resistance did not significantly affect the motility, adherence, or invasion ability of Caco-2 cells. However, CIP-resistant strains displayed lower lethality in G. mellonella infection, whereas AMP-resistant strains did not, and even two strains improved lethality. The study of the biological characteristics of antibiotic-resistant S. enterica is essential in better understanding the microbial risks to both the food chain and human health, thereby facilitating a more accurate risk assessment.
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Affiliation(s)
- Yi Hong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yufan Wu
- Centre of Analysis and Test, School of Chemistry & Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Yani Xie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Leijie Ben
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiangfeng Bu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xinye Pan
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jingdong Shao
- Technology Center of Zhangjiagang Customs, Suzhou, China
| | - Qingli Dong
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiaojie Qin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xiang Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China.
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28
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Jordana-Lluch E, Barceló IM, Escobar-Salom M, Estévez MA, Zamorano L, Gómez-Zorrilla S, Sendra E, Oliver A, Juan C. The balance between antibiotic resistance and fitness/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research. Front Microbiol 2023; 14:1270999. [PMID: 37840717 PMCID: PMC10569695 DOI: 10.3389/fmicb.2023.1270999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
The interplay between antibiotic resistance and bacterial fitness/virulence has attracted the interest of researchers for decades because of its therapeutic implications, since it is classically assumed that resistance usually entails certain biological costs. Reviews on this topic revise the published data from a general point of view, including studies based on clinical strains or in vitro-evolved mutants in which the resistance phenotype is seen as a final outcome, i.e., a combination of mechanisms. However, a review analyzing the resistance/fitness balance from the basic research perspective, compiling studies in which the different resistance pathways and respective biological costs are individually approached, was missing. Here we cover this gap, specifically focusing on Pseudomonas aeruginosa, a pathogen that stands out because of its extraordinary capacity for resistance development and for which a considerable number of recent and particular data on the interplay with fitness/virulence have been released. The revised information, split into horizontally-acquired vs. mutation-driven resistance, suggests a great complexity and even controversy in the resistance-fitness/virulence balance in the acute infection context, with results ranging from high costs linked to certain pathways to others that are seemingly cost-free or even cases of resistance mechanisms contributing to increased pathogenic capacities. The elusive mechanistic basis for some enigmatic data, knowledge gaps, and possibilities for therapeutic exploitation are discussed. The information gathered suggests that resistance-fitness/virulence interplay may be a source of potential antipseudomonal targets and thus, this review poses the elementary first step for the future development of these strategies harnessing certain resistance-associated biological burdens.
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Affiliation(s)
- Elena Jordana-Lluch
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Isabel Mª Barceló
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - María Escobar-Salom
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Miguel A. Estévez
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
| | - Laura Zamorano
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Silvia Gómez-Zorrilla
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Elena Sendra
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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29
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Goh SG, Haller L, Ng C, Charles FR, Jitxin L, Chen H, He Y, Gin KYH. Assessing the additional health burden of antibiotic resistant Enterobacteriaceae in surface waters through an integrated QMRA and DALY approach. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:132058. [PMID: 37459761 DOI: 10.1016/j.jhazmat.2023.132058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/15/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
Antibiotic resistant Enterobacteriaceae pose a significant threat to public health. However, limited studies have evaluated the health risks associated with exposure to antibiotic-resistant bacteria (ARB), especially in natural environments. While quantitative microbial risk assessment (QMRA) assesses microbial risks in terms of the probability of infection, it does not account for the severity of health outcomes. In this study, a QMRA-DALY model was developed to integrate QMRA with health burden (disability-adjusted life years (DALY)) from infections caused by ARB. The model considers uncertainties in probability of infection and health burden assessment using Monte Carlo simulations. The study collected antimicrobial resistance (AMR) surveillance data from surface waters with different land uses. Results revealed water bodies with agricultural land use to be the main AMR hotspots, with the highest additional health burden observed in infections caused by meropenem-resistant E. coli (∆DALY = 0.0105 DALY/event) compared to antibiotic-susceptible E. coli. The estimated ∆DALY for antibiotic-resistant K. pneumoniae was lower than for antibiotic-resistant E. coli (highest ∆DALY = 0.00048 DALY/event). The study highlights the need for better evaluation of AMR associated health burden, and effective measures to mitigate the risks associated with antibiotic-resistant bacteria in natural environments.
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Affiliation(s)
- Shin Giek Goh
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Laurence Haller
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Charmaine Ng
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Francis Rathinam Charles
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Lim Jitxin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Hongjie Chen
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yiliang He
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Karina Yew-Hoong Gin
- NUS Environmental Research Institute, National University of Singapore, Singapore 117411, Singapore; Department of Civil & Environmental Engineering, National University of Singapore, Singapore 117576, Singapore.
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30
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Jiang M, Li X, Xie CL, Chen P, Luo W, Lin CX, Wang Q, Shu DM, Luo CL, Qu H, Ji J. Fructose-enabled killing of antibiotic-resistant Salmonella enteritidis by gentamicin: Insight from reprogramming metabolomics. Int J Antimicrob Agents 2023; 62:106907. [PMID: 37385564 DOI: 10.1016/j.ijantimicag.2023.106907] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023]
Abstract
Salmonella enterica is a food-borne pathogen that poses a severe threat to both poultry production and human health. Antibiotics are critical for the initial treatment of bacterial infections. However, the overuse and misuse of antibiotics results in the rapid evolution of antibiotic-resistant bacteria, and the discovery and development of new antibiotics are declining. Therefore, understanding antibiotic resistance mechanisms and developing novel control measures are essential. In the present study, GC-MS-based metabolomics analysis was performed to determine the metabolic profile of gentamicin sensitive (SE-S) and resistant (SE-R) S. enterica. Fructose was identified as a crucial biomarker. Further analysis demonstrated a global depressed central carbon metabolism and energy metabolism in SE-R. The decrease in the pyruvate cycle reduces the production of NADH and ATP, causing a decrease in membrane potential, which contributes to gentamicin resistance. Exogenous fructose potentiated the effectiveness of gentamicin in killing SE-R by promoting the pyruvate cycle, NADH, ATP and membrane potential, thereby increasing gentamicin intake. Further, fructose plus gentamicin improved the survival rate of chicken infected with gentamicin-resistant Salmonella in vivo. Given that metabolite structures are conserved across species, fructose identified from bacteria could be used as a biomarker for breeding disease-resistant phenotypes in chicken. Therefore, a novel strategy is proposed for fighting against antibiotic-resistant S. enterica, including exploring molecules suppressed by antibiotics and providing a new approach to find pathogen targets for disease resistance in chicken breeding.
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Affiliation(s)
- Ming Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China; The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xia Li
- The Third Affiliated Hospital, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chun-Lin Xie
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Peng Chen
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chu-Xiao Lin
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qiao Wang
- Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ding-Ming Shu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng-Long Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Qu
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
| | - Jian Ji
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
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31
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Brülisauer L, León-Sampedro R, Hall AR. Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro. Plasmid 2023; 128:102706. [PMID: 37652194 DOI: 10.1016/j.plasmid.2023.102706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain-dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.
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Affiliation(s)
- Laura Brülisauer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland.
| | - Ricardo León-Sampedro
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland; Centro de Investigación Biológica en Red, Epidemiología y Salud Pública- CIBERESP, Instituto de Salud Carlos III, Madrid, Spain
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
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32
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Ashrafi R, Bruneaux M, Sundberg LR, Hoikkala V, Karvonen A. Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium. Mol Ecol 2023; 32:4447-4460. [PMID: 37303030 DOI: 10.1111/mec.17040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023]
Abstract
Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, coinfections between bacterial strains and metazoan parasites (fluke Diplostomum pseudospathaceum) and antibiotic exposure. We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to spread and long-term persistence of resistance.
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Affiliation(s)
- Roghaieh Ashrafi
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Matthieu Bruneaux
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Lotta-Riina Sundberg
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Ville Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Anssi Karvonen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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33
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Diaz Caballero J, Wheatley RM, Kapel N, López-Causapé C, Van der Schalk T, Quinn A, Shaw LP, Ogunlana L, Recanatini C, Xavier BB, Timbermont L, Kluytmans J, Ruzin A, Esser M, Malhotra-Kumar S, Oliver A, MacLean RC. Mixed strain pathogen populations accelerate the evolution of antibiotic resistance in patients. Nat Commun 2023; 14:4083. [PMID: 37438338 DOI: 10.1038/s41467-023-39416-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023] Open
Abstract
Antibiotic resistance poses a global health threat, but the within-host drivers of resistance remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and resistance is thought to emerge due to selection for de novo variants. Here we show that mixed strain populations are common in the opportunistic pathogen P. aeruginosa. Crucially, resistance evolves rapidly in patients colonized by multiple strains through selection for pre-existing resistant strains. In contrast, resistance evolves sporadically in patients colonized by single strains due to selection for novel resistance mutations. However, strong trade-offs between resistance and growth rate occur in mixed strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment. In summary, we show that the within-host diversity of pathogen populations plays a key role in shaping the emergence of resistance in response to treatment.
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Affiliation(s)
| | - Rachel M Wheatley
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Natalia Kapel
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Carla López-Causapé
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - Thomas Van der Schalk
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Angus Quinn
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Liam P Shaw
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Lois Ogunlana
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK
| | - Claudia Recanatini
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Leen Timbermont
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Jan Kluytmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Alexey Ruzin
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Mark Esser
- Microbial Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Wilrijk, Belgium
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitari Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdISBa), Palma de Mallorca, Spain
| | - R Craig MacLean
- University of Oxford, Department of Biology, 11a Mansfield Rd, Oxford, UK.
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34
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Fernández-Calvet A, Toribio-Celestino L, Alonso-del Valle A, Sastre-Dominguez J, Valdes-Chiara P, San Millan A, DelaFuente J. The distribution of fitness effects of plasmid pOXA-48 in clinical enterobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001369. [PMID: 37505800 PMCID: PMC10433420 DOI: 10.1099/mic.0.001369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
Antimicrobial resistance (AMR) in bacteria is a major public health problem. The main route for AMR acquisition in clinically important bacteria is the horizontal transfer of plasmids carrying resistance genes. AMR plasmids allow bacteria to survive antibiotics, but they also entail physiological alterations in the host cell. Multiple studies over the last few years have indicated that these alterations can translate into a fitness cost when antibiotics are absent. However, due to technical limitations, most of these studies are based on analysing new associations between plasmids and bacteria generated in vitro, and we know very little about the effects of plasmids in their native bacterial hosts. In this study, we used a CRISPR-Cas9-tool to selectively cure plasmids from clinical enterobacteria to overcome this limitation. Using this approach, we were able to study the fitness effects of the carbapenem resistance plasmid pOXA-48 in 35 pOXA-48-carrying isolates recovered from hospitalized patients. Our results revealed that pOXA-48 produces variable effects across the collection of wild-type enterobacterial strains naturally carrying the plasmid, ranging from fitness costs to fitness benefits. Importantly, the plasmid was only associated with a significant fitness reduction in four out of 35 clones, and produced no significant changes in fitness in the great majority of isolates. Our results suggest that plasmids produce neutral fitness effects in most native bacterial hosts, helping to explain the great prevalence of plasmids in natural microbial communities.
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Affiliation(s)
| | | | | | | | | | - Alvaro San Millan
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
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35
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Vanacker M, Lenuzza N, Rasigade JP. The fitness cost of horizontally transferred and mutational antimicrobial resistance in Escherichia coli. Front Microbiol 2023; 14:1186920. [PMID: 37455716 PMCID: PMC10348881 DOI: 10.3389/fmicb.2023.1186920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacteria implies a tradeoff between the benefit of resistance under antimicrobial selection pressure and the incurred fitness cost in the absence of antimicrobials. The fitness cost of a resistance determinant is expected to depend on its genetic support, such as a chromosomal mutation or a plasmid acquisition, and on its impact on cell metabolism, such as an alteration in an essential metabolic pathway or the production of a new enzyme. To provide a global picture of the factors that influence AMR fitness cost, we conducted a systematic review and meta-analysis focused on a single species, Escherichia coli. By combining results from 46 high-quality studies in a multilevel meta-analysis framework, we find that the fitness cost of AMR is smaller when provided by horizontally transferable genes such as those encoding beta-lactamases, compared to mutations in core genes such as those involved in fluoroquinolone and rifampicin resistance. We observe that the accumulation of acquired AMR genes imposes a much smaller burden on the host cell than the accumulation of AMR mutations, and we provide quantitative estimates of the additional cost of a new gene or mutation. These findings highlight that gene acquisition is more efficient than the accumulation of mutations to evolve multidrug resistance, which can contribute to the observed dominance of horizontally transferred genes in the current AMR epidemic.
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Affiliation(s)
- Marie Vanacker
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Natacha Lenuzza
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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36
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Gibson C, Kraemer SA, Klimova N, Guo B, Frigon D. Antibiotic resistance gene sequencing is necessary to reveal the complex dynamics of immigration from sewers to activated sludge. Front Microbiol 2023; 14:1155956. [PMID: 37228381 PMCID: PMC10204801 DOI: 10.3389/fmicb.2023.1155956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023] Open
Abstract
Microbial community composition has increasingly emerged as a key determinant of antibiotic resistance gene (ARG) content. However, in activated sludge wastewater treatment plants (AS-WWTPs), a comprehensive understanding of the microbial community assembly process and its impact on the persistence of antimicrobial resistance (AMR) remains elusive. An important part of this process is the immigration dynamics (or community coalescence) between the influent and activated sludge. While the influent wastewater contains a plethora of ARGs, the persistence of a given ARG depends initially on the immigration success of the carrying population, and the possible horizontal transfer to indigenously resident populations of the WWTP. The current study utilized controlled manipulative experiments that decoupled the influent wastewater composition from the influent microbial populations to reveal the fundamental mechanisms involved in ARG immigration between sewers and AS-WWTP. A novel multiplexed amplicon sequencing approach was used to track different ARG sequence variants across the immigration interface, and droplet digital PCR was used to quantify the impact of immigration on the abundance of the targeted ARGs. Immigration caused an increase in the abundance of over 70 % of the quantified ARGs. However, monitoring of ARG amplicon sequence variants (ARG-ASVs) at the immigration interface revealed various immigration patterns such as (i) suppression of the indigenous mixed liquor ARG-ASV by the immigrant, or conversely (ii) complete immigration failure of the influent ARG-ASV. These immigration profiles are reported for the first time here and highlight the crucial information that can be gained using our novel multiplex amplicon sequencing techniques. Future studies aiming to reduce AMR in WWTPs should consider the impact of influent immigration in process optimisation and design.
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Affiliation(s)
- Claire Gibson
- Department of Civil Engineering and Applied Mechanics, McGill University, Montreal, QC, Canada
| | - Susanne A. Kraemer
- Department of Civil Engineering and Applied Mechanics, McGill University, Montreal, QC, Canada
- Aquatic Contaminants Research Division, Environment and Climate Change Canada, Montreal, QC, Canada
| | - Natalia Klimova
- Department of Civil Engineering and Applied Mechanics, McGill University, Montreal, QC, Canada
| | - Bing Guo
- Department of Civil and Environmental Engineering, Centre for Environmental Health and Engineering, University of Surrey, Surrey, United Kingdom
| | - Dominic Frigon
- Department of Civil Engineering and Applied Mechanics, McGill University, Montreal, QC, Canada
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37
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Jiang H, Jiao X, Yu T, Wang W, Cheng H, Huang G, Fang J. Contribution of different class 2 integron elements to fitness costs in multi-drug resistant Escherichia coli and evaluation of their adaptability in “farm-to-table” environments. Food Microbiol 2023; 113:104279. [PMID: 37098435 DOI: 10.1016/j.fm.2023.104279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
Integrons play a pivotal role in the dissemination of antimicrobial resistance, because they can capture and express exogenous antimicrobial resistance genes. This study aimed to elucidate the structure and contribution of different elements of class 2 integrons to fitness costs in their host bacteria and evaluate their adaptability to the "farm-to-table" process. We mapped 27 typical class 2 integrons of Escherichia coli isolated from aquatic foods and pork products, each harboring an inactive truncated class 2 integrase gene and the gene cassette (GC) array dfrA1-sat2-aadA1 with strong Pc2A/Pc2B promoters. Notably, the fitness costs associated with class 2 integrons depended on the Pc promoter strength and quantity and content of GCs in the array. Additionally, the costs of integrases were activity-dependent, and a balance was identified between GC capture ability and integron stability, which could explain the inactive truncated integrase identified. Although typical class 2 integrons exhibited low-cost structures in E. coli, the bacteria incurred biological costs, including decreasing growth rates and biofilm formation, in farm-to-table environments, especially under low-nutrient conditions. Nevertheless, sub-inhibitory antibiotic concentrations led to the selection of class 2 integron-carrying bacteria. This study provides important insights into how integrons may travel from preharvest to consumer goods.
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38
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Khine NO, Wongsurawat T, Jenjaroenpun P, Hampson DJ, Prapasarakul N. Comparative genomic analysis of Colistin resistant Escherichia coli isolated from pigs, a human and wastewater on colistin withdrawn pig farm. Sci Rep 2023; 13:5124. [PMID: 36991093 PMCID: PMC10060365 DOI: 10.1038/s41598-023-32406-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
In this study, genomic and plasmid characteristics of Escherichia coli were determined with the aim of deducing how mcr genes may have spread on a colistin withdrawn pig farm. Whole genome hybrid sequencing was applied to six mcr-positive E. coli (MCRPE) strains isolated from pigs, a farmworker and wastewater collected between 2017 and 2019. Among these, mcr-1.1 genes were identified on IncI2 plasmids from a pig and wastewater, and on IncX4 from the human isolate, whereas mcr-3 genes were found on plasmids IncFII and IncHI2 in two porcine strains. The MCRPE isolates exhibited genotypic and phenotypic multidrug resistance (MDR) traits as well as heavy metal and antiseptic resistance genes. The mcr-1.1-IncI2 and IncX4 plasmids carried only colistin resistance genes. Whereas, the mcr-3.5-IncHI2 plasmid presented MDR region, with several mobile genetic elements. Despite the MCRPE strains belonged to different E. coli lineages, mcr-carrying plasmids with high similarities were found in isolates from pigs and wastewater recovered in different years. This study highlighted that several factors, including the resistomic profile of the host bacteria, co-selection via adjunct antibiotic resistance genes, antiseptics, and/or disinfectants, and plasmid-host fitness adaptation may encourage the maintenance of plasmids carrying mcr genes in E. coli.
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Affiliation(s)
- Nwai Oo Khine
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David J Hampson
- School of Veterinary Medicine, Murdoch University, Perth, WA, Australia
| | - Nuvee Prapasarakul
- Center of Excellence in Diagnosis and Monitoring of Animal Pathogens (DMAP), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
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Wang J, Raza W, Jiang G, Yi Z, Fields B, Greenrod S, Friman VP, Jousset A, Shen Q, Wei Z. Bacterial volatile organic compounds attenuate pathogen virulence via evolutionary trade-offs. THE ISME JOURNAL 2023; 17:443-452. [PMID: 36635489 PMCID: PMC9938241 DOI: 10.1038/s41396-023-01356-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.
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Affiliation(s)
- Jianing Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Waseem Raza
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
- Institute for Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Gaofei Jiang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Zhang Yi
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Bryden Fields
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Samuel Greenrod
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ville-Petri Friman
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK.
- Department of Microbiology, University of Helsinki, Helsinki, 00014, Finland.
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, PR China.
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40
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Pulami D, Kämpfer P, Glaeser SP. High diversity of the emerging pathogen Acinetobacter baumannii and other Acinetobacter spp. in raw manure, biogas plants digestates, and rural and urban wastewater treatment plants with system specific antimicrobial resistance profiles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160182. [PMID: 36395844 DOI: 10.1016/j.scitotenv.2022.160182] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Carbapenem-resistant Acinetobacter baumannii causing immense treatment problems in hospitals. There is still a knowledge gap on the abundance and stability of acquired resistances and the diversity of resistant Acinetobacter in the environment. The aim of the study was to investigate the diversity and antimicrobial resistances of Acinetobacter spp. released from livestock and human wastewater into the environment. Raw and digested manure of small scale on farm biogas plants as well as untreated and treated wastewater and sewage sludge of rural and urban wastewater treatment plants (WWTPs) were studied comparatively. A total of 132 Acinetobacter isolates were phylogenetically identified (16S rRNA gene and rpoB sequence analyses) and 14 different phylotypes were detected. Fiftytwo isolates represented A. baumannii which were cultured from raw and digested manure of different biogas plants, and most stages of the rural WWTP (no hospital wastewater receiving) and the two studied urban WWTPs receiving veterinarian and human hospital wastewater. Multi-locus sequence typing (Pasteur_MLST) identified 23 novel and 12 known STs of A. baumannii. Most novel STs (18/23) were cultured from livestock samples and the rural WWTP. A. baumannii isolates from livestock and the rural WWTP were susceptible to carbapenems, colistin, ciprofloxacin, ceftazidime, and piperacillin. In contrast, A. baumannii isolates from the two urban WWTPs showed clinical linkage with respect to MLST and were multi-drug resistant (MDR). The presence of viable A. baumannii in digested manure and sewage sludge confirmed the survival of the strict aerobic bacteria during anoxic conditions. The study indicated the spread of diverse Acinetobacter from anthropogenic sources into the environment with a strong linkage of clinial associated MDR A. baumannii strains to the inflow of hospital wastewater to WWTPs. A more frequent detection of Acinetobacter in sewage sludge than effluent waters indicated that particle-attachment of Acinetobacter must be considered by the risk assessment of these bacteria.
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Affiliation(s)
- Dipen Pulami
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany
| | - Peter Kämpfer
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany
| | - Stefanie P Glaeser
- Institut for Applied Microbiology, Justus-Liebig-University Giessen, Germany.
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41
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Emara Y, Jolliet O, Finkbeiner M, Heß S, Kosnik M, Siegert MW, Fantke P. Comparative selective pressure potential of antibiotics in the environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120873. [PMID: 36529346 DOI: 10.1016/j.envpol.2022.120873] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
To guide both environmental and public health policy, it is important to assess the degree of antibiotic resistance selection pressure under measured environmental concentrations (MECs), and to compare the efficacy of different mitigation strategies to minimize the spread of resistance. To this end, the resistance selection and enrichment potential due to antibiotic emissions into the environment must be analysed from a life cycle perspective, for a wide range of antibiotics, and considering variations in the underlying fitness costs between different resistance mutations and genes. The aim of this study is to consistently derive fitness cost-dependent minimum selective concentrations (MSCs) from readily available bacterial inhibition data and to build MSC-based species sensitivity distributions (SSDs). These are then used to determine antibiotic-specific resistance selection concentrations predicted to promote resistance in 5% of exposed bacterial species (RSC5). Using a previously developed competition model, we provide estimated MSC10 endpoints for 2,984 antibiotic and bacterial species combinations; the largest set of modelled MSCs available to date. Based on constructed SSDs, we derive RSC5 for 128 antibiotics with four orders of magnitude difference in their 'selective pressure potential' in the environment. By comparing our RSC5 to MECs, we highlight specific environmental compartments (e.g. hospital and wastewater effluents, lakes and rivers), as well as several antibiotics (e.g. ciprofloxacin, norfloxacin, enrofloxacin, and tetracycline), to be scrutinized for their potential role in resistance selection and dissemination. In addition to enabling comparative risk screening of the selective pressure potential of multiple antibiotics, our SSD-derived RSC5 provide the point of departure for calculating new life cycle-based characterization factors for antibiotics to compare mitigation strategies, thereby contributing towards a 'One-Health' approach to tackling the global antibiotic resistance crisis.
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Affiliation(s)
- Yasmine Emara
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark
| | - Olivier Jolliet
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Department of Environmental Health Sciences, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
| | - Matthias Finkbeiner
- Department of Environmental Technology, Technical University Berlin, 10623, Berlin, Germany.
| | - Stefanie Heß
- Institute of Microbiology, Technische Universität Dresden, 01847, Dresden, Germany.
| | - Marissa Kosnik
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
| | - Marc-William Siegert
- Department of Environmental Technology, Technical University Berlin, 10623, Berlin, Germany
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.
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42
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Berbers B, Vanneste K, Roosens NHCJ, Marchal K, Ceyssens PJ, De Keersmaecker SCJ. Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium. Microb Genom 2023; 9:mgen000925. [PMID: 36748573 PMCID: PMC9973847 DOI: 10.1099/mgen.0.000925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/03/2022] [Indexed: 01/25/2023] Open
Abstract
For antimicrobial resistance (AMR) surveillance, it is important not only to detect AMR genes, but also to determine their plasmidic or chromosomal location, as this will impact their spread differently. Whole-genome sequencing (WGS) is increasingly used for AMR surveillance. However, determining the genetic context of AMR genes using only short-read sequencing is complicated. The combination with long-read sequencing offers a potential solution, as it allows hybrid assemblies. Nevertheless, its use in surveillance has so far been limited. This study aimed to demonstrate its added value for AMR surveillance based on a case study of extended-spectrum beta-lactamases (ESBLs). ESBL genes have been reported to occur also on plasmids. To gain insight into the diversity and genetic context of ESBL genes detected in clinical isolates received by the Belgian National Reference Center between 2013 and 2018, 100 ESBL-producing Shigella and 31 ESBL-producing Salmonella were sequenced with MiSeq and a representative selection of 20 Shigella and six Salmonella isolates additionally with MinION technology, allowing hybrid assembly. The bla CTX-M-15 gene was found to be responsible for a rapid rise in the ESBL Shigella phenotype from 2017. This gene was mostly detected on multi-resistance-carrying IncFII plasmids. Based on clustering, these plasmids were determined to be distinct from the circulating plasmids before 2017. They were spread to different Shigella species and within Shigella sonnei between multiple genotypes. Another similar IncFII plasmid was detected after 2017 containing bla CTX-M-27 for which only clonal expansion occurred. Matches of up to 99 % to plasmids of various bacterial hosts from all over the world were found, but global alignments indicated that direct or recent ESBL-plasmid transfers did not occur. It is most likely that travellers introduced these in Belgium and subsequently spread them domestically. However, a clear link to a specific country could not be made. Moreover, integration of bla CTX-M in the chromosome of two Shigella isolates was determined for the first time, and shown to be related to ISEcp1. In contrast, in Salmonella, ESBL genes were only found on plasmids, of which bla CTX-M-55 and IncHI2 were the most prevalent, respectively. No matching ESBL plasmids or cassettes were detected between clinical Shigella and Salmonella isolates. The hybrid assembly data allowed us to check the accuracy of plasmid prediction tools. MOB-suite showed the highest accuracy. However, these tools cannot replace the accuracy of long-read and hybrid assemblies. This study illustrates the added value of hybrid assemblies for AMR surveillance and shows that a strategy where even just representative isolates of a collection used for hybrid assemblies could improve international AMR surveillance as it allows plasmid tracking.
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Affiliation(s)
- Bas Berbers
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, 1050 Brussels, Belgium
| | | | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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43
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Bethke JH, Ma HR, Tsoi R, Cheng L, Xiao M, You L. Vertical and horizontal gene transfer tradeoffs direct plasmid fitness. Mol Syst Biol 2022; 19:e11300. [PMID: 36573357 PMCID: PMC9912019 DOI: 10.15252/msb.202211300] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/28/2022] Open
Abstract
Plasmid fitness is directed by two orthogonal processes-vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here, we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical Escherichia coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
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Affiliation(s)
- Jonathan H Bethke
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA
| | - Helena R Ma
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA
| | - Ryan Tsoi
- Department of Biomedical EngineeringDuke UniversityNCDurhamUSA
| | - Li Cheng
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
| | - Minfeng Xiao
- BGI‐ShenzhenShenzhenChina,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI‐ShenzhenShenzhenChina
| | - Lingchong You
- Department of Molecular Genetics and MicrobiologyDuke UniversityNCDurhamUSA,Department of Biomedical EngineeringDuke UniversityNCDurhamUSA,Center for Quantitative BiodesignDuke UniversityNCDurhamUSA,School of Biology and Biological EngineeringSouth China University of TechnologyGuangzhouChina
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44
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Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids. mSphere 2022; 7:e0018422. [PMID: 36416553 PMCID: PMC9769657 DOI: 10.1128/msphere.00184-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is one of the major threats to public health worldwide. The mechanisms involved in the plasmid/host coadaptation are still poorly characterized, and their understanding is crucial to comprehend the genesis and evolution of multidrug-resistant bacteria. With this purpose, we designed an experimental evolution using Haemophilus influenzae RdKW20 as the model strain carrying the ColE1-like plasmid pB1000. Five H. influenzae populations adapted previously to the culture conditions were transformed with pB1000 and subsequently evolved to compensate for the plasmid-associated fitness cost. Afterward, we performed an integrative multiomic analysis combining genomics, transcriptomics, and metabolomics to explore the molecular mechanisms involved in the compensatory evolution of the plasmid. Our results demonstrate that minimal modifications in the host are responsible for plasmid adaptation. Among all of them, the most enriched process was amino acid metabolism, especially those pathways related to serine, tryptophan, and arginine, eventually related to the genesis and resolution of plasmid dimers. Additional rearrangements occurred during the plasmid adaptation, such as an overexpression of the ribonucleotide reductases and metabolic modifications within specific membrane phospholipids. All these findings demonstrate that the plasmid compensation occurs through the combination of diverse host-mediated mechanisms, of which some are beyond genomic and transcriptomic modifications. IMPORTANCE The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis. It is generally accepted that the acquisition and maintenance of mobile genetic elements entail a fitness cost to its host, which is susceptible to be alleviated through a coadaptation process or compensatory evolution. Notwithstanding, despite recent major efforts, the underlying mechanisms involved in this adaptation remain poorly characterized. Analyzing the plasmid/host coadaptation from a multiomic perspective sheds light on the physiological processes involved in the compensation, providing a new understanding on the genesis and evolution of plasmid-mediated antimicrobial-resistant bacteria.
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45
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Mahazu S, Prah I, Ota Y, Hayashi T, Nukui Y, Suzuki M, Hoshino Y, Akeda Y, Suzuki T, Ishino T, Ablordey A, Saito R. Klebsiella Species and Enterobacter cloacae Isolates Harboring blaOXA-181 and blaOXA-48: Resistome, Fitness Cost, and Plasmid Stability. Microbiol Spectr 2022; 10:e0332022. [PMID: 36453894 PMCID: PMC9769605 DOI: 10.1128/spectrum.03320-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
IncX3 and IncL plasmids have been named as catalysts advancing dissemination of blaOXA-181 and blaOXA-48 genes. However, their impact on the performance of host cells is vastly understudied. Genetic characteristics of blaOXA-48- and blaOXA-181-containing Klebsiella pneumoniae (EFN299), Klebsiella quasipneumoniae (EFN262), and Enterobacter cloacae (EFN743) isolated from clinical samples in a Ghanaian hospital were investigated by whole-genome sequencing. Transfer of plasmids by conjugation and electroporation, plasmid stability, fitness cost, and genetic context of blaOXA-48, blaOXA-181, and blaDHA-1 were assessed. blaOXA-181 was carried on two IncX3 plasmids, an intact 51.5-kb IncX3 plasmid (p262-OXA-181) and a 45.3-kb IncX3 plasmid (p743-OXA-181) without replication protein sequence. The fluoroquinolone-resistant gene qnrS1 region was also excised, and unlike in p262-OXA-181, the blaOXA-181 drug-resistant region was not found on a composite transposon. blaOXA-48 was carried on a 74.6-kb conjugative IncL plasmid with unknown ~10.9-kb sequence insertion. This IncL plasmid proved to be highly transferable, with a conjugation efficiency of 1.8 × 10-2. blaDHA-1 was present on an untypeable 22.2 kb genetic structure. Plasmid stability test revealed plasmid loss rate between 4.3% and 12.4%. The results also demonstrated that carriage of IncX3-blaOXA-181 or IncL-blaOXA-48 plasmids was not associated with any fitness defect, but rather an enhanced competitive ability of host cells. This study underscores the significant contribution of IncX3 and IncL plasmids in the dissemination of resistance genes and their efficient transfer calls for regular monitoring to control the expansion of resistant strains. IMPORTANCE The growing rate of antibiotic resistance is an important global health threat. This threat is exacerbated by the lack of safe and potent alternatives to carbapenems in addition to the slow developmental process of newer and effective antibiotics. Infections by carbapenem-resistant Gram-negative bacteria are becoming almost untreatable, leading to poor clinical outcomes and high mortality rates. OXA-48-like carbapenemases are one of the most widespread carbapenemases accounting for resistance among Enterobacteriaecae. We characterized OXA-48- and OXA-181-producing Enterobacteriaecae to gain insights into the genetic basis and mechanism of resistance to carbapenems. Findings from the study showed that the genes encoding these enzymes were carried on highly transmissible plasmids, one of which had sequences absent in other similar plasmids. This implies that mobile genetic elements are important players in the dissemination of resistance genes. Further characterization of this plasmid is warranted to determine the role of this sequence in the spread of resistance genes.
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Affiliation(s)
- Samiratu Mahazu
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Ota
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoko Ishino
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
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46
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Nishimoto AT, Dao TH, Jia Q, Ortiz-Marquez JC, Echlin H, Vogel P, van Opijnen T, Rosch JW. Interspecies recombination, not de novo mutation, maintains virulence after β-lactam resistance acquisition in Streptococcus pneumoniae. Cell Rep 2022; 41:111835. [PMID: 36516783 PMCID: PMC9850807 DOI: 10.1016/j.celrep.2022.111835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 07/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
As opposed to de novo mutation, β-lactam resistance in S. pneumoniae is often conferred via homologous recombination during horizontal gene transfer. We hypothesize that β-lactam resistance in pathogenic streptococci is restricted to naturally competent species via intra-/interspecies recombination due to in vivo fitness trade-offs of de novo penicillin-binding protein (PBP) mutations. We show that de novo mutant populations have abrogated invasive disease capacity and are difficult to evolve in vivo. Conversely, serially transformed recombinant strains efficiently integrate resistant oral streptococcal DNA, gain penicillin resistance and tolerance, and retain virulence in mice. Large-scale changes in pbp2X, pbp2B, and non-PBP-related genes occur in recombinant isolates. Our results indicate that horizontal transfer of β-lactam resistance engenders initially favorable or minimal cost changes in vivo compared with de novo mutation(s), underscoring the importance of recombination in the emergence of β-lactam resistance and suggesting why some pathogenic streptococci lacking innate competence remain universally susceptible.
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Affiliation(s)
- Andrew T. Nishimoto
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Tina H. Dao
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,These authors contributed equally
| | - Qidong Jia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | | | - Haley Echlin
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Peter Vogel
- Department of Pathology and Veterinary Pathology Core, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tim van Opijnen
- Department of Biology, Boston College, Boston, MA 02467, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Lead contact,Correspondence:
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47
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DelaFuente J, Toribio-Celestino L, Santos-Lopez A, León-Sampedro R, Alonso-Del Valle A, Costas C, Hernández-García M, Cui L, Rodríguez-Beltrán J, Bikard D, Cantón R, San Millan A. Within-patient evolution of plasmid-mediated antimicrobial resistance. Nat Ecol Evol 2022; 6:1980-1991. [PMID: 36303001 PMCID: PMC7613874 DOI: 10.1038/s41559-022-01908-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/12/2022] [Indexed: 12/15/2022]
Abstract
Antimicrobial resistance (AMR) in bacteria is a major threat to public health; one of the key elements in the spread and evolution of AMR in clinical pathogens is the transfer of conjugative plasmids. The drivers of AMR evolution have been studied extensively in vitro but the evolution of plasmid-mediated AMR in vivo remains poorly explored. Here, we tracked the evolution of the clinically relevant plasmid pOXA-48, which confers resistance to the last-resort antibiotics carbapenems, in a large collection of enterobacterial clones isolated from the gut of hospitalized patients. Combining genomic and experimental approaches, we first characterized plasmid diversity and the genotypic and phenotypic effects of multiple plasmid mutations on a common genetic background. Second, using cutting-edge genomic editing in wild-type multidrug-resistant enterobacteria, we dissected three cases of within-patient plasmid-mediated AMR evolution. Our results revealed compensatory evolution of plasmid-associated fitness cost and the evolution of enhanced plasmid-mediated AMR in bacteria evolving in the gut of hospitalized patients. Crucially, we observed that the evolution of pOXA-48-mediated AMR in vivo involves a pivotal trade-off between resistance levels and bacterial fitness. This study highlights the need to develop new evolution-informed approaches to tackle plasmid-mediated AMR dissemination.
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Affiliation(s)
- Javier DelaFuente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Alfonso Santos-Lopez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | - Ricardo León-Sampedro
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Institute of Integrative Biology, Department of Environmental Systems Science, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Aida Alonso-Del Valle
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Coloma Costas
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Marta Hernández-García
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Lun Cui
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Jerónimo Rodríguez-Beltrán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - David Bikard
- Institut Pasteur, Universite de Paris Cité, Centre National de la Recherche Scientifique Unité Mixte de Recherche 6047, Synthetic Biology, Paris, France
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal-Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Centro de Investigación Biológica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alvaro San Millan
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain.
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain.
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48
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Hernandez‐Beltran JCR, Miró Pina V, Siri‐Jégousse A, Palau S, Peña‐Miller R, González Casanova A. Segregational instability of multicopy plasmids: A population genetics approach. Ecol Evol 2022; 12:e9469. [PMID: 36479025 PMCID: PMC9720003 DOI: 10.1002/ece3.9469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 12/11/2022] Open
Abstract
Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, nontransmissible plasmids tend to be carried in multiple copies per cell, with the added benefit of exhibiting increased gene dosage and resistance levels. But carrying multiple copies also results in a high metabolic burden to the bacterial host, therefore reducing the overall fitness of the population. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? In this manuscript, we address this question by postulating and analyzing a population genetics model to evaluate the interaction between selective pressure, the number of plasmid copies carried by each cell, and the metabolic burden associated with plasmid bearing in the absence of selection for plasmid-encoded traits. Parameter values of the model were estimated experimentally using Escherichia coli K12 carrying a multicopy plasmid encoding for a fluorescent protein and bla TEM-1, a gene conferring resistance to β-lactam antibiotics. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we show that plasmid copy number is a highly optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.
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Affiliation(s)
- J. Carlos R. Hernandez‐Beltran
- Systems Biology Program, Center for Genomic SciencesUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
| | - Verónica Miró Pina
- Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
- Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Arno Siri‐Jégousse
- Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Sandra Palau
- Departamento de Probabilidad y Estadística, Instituto de Investigación en Matemáticas Aplicadas y en SistemasUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
| | - Rafael Peña‐Miller
- Systems Biology Program, Center for Genomic SciencesUniversidad Nacional Autónoma de MéxicoCuernavacaMexico
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49
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Zhou Z, Shuai X, Lin Z, Meng L, Ba X, Holmes MA, Chen H. Short-term inhalation exposure evaluations of airborne antibiotic resistance genes in environments. J Environ Sci (China) 2022; 122:62-71. [PMID: 35717091 DOI: 10.1016/j.jes.2021.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/06/2021] [Accepted: 10/06/2021] [Indexed: 06/15/2023]
Abstract
Antibiotic resistance is a sword of Damocles that hangs over humans. In regards to airborne antibiotic resistance genes (AARGs), critical knowledge gaps still exist in the identification of hotspots and quantification of exposure levels in different environments. Here, we have studied the profiles of AARGs, mobile genetic elements (MGEs) and bacterial communities in various atmospheric environments by high throughput qPCR and 16S rRNA gene sequencing. We propose a new AARGs exposure dose calculation that uses short-term inhalation (STI). Swine farms and hospitals were high-risk areas where AARGs standardised abundance was more abundant than suburbs and urban areas. Additionally, resistance gene abundance in swine farm worker sputum was higher than that in healthy individuals in other environments. The correlation between AARGs with MGEs and bacteria was strong in suburbs but weak in livestock farms and hospitals. STI exposure analysis revealed that occupational intake of AARGs (via PM10) in swine farms and hospitals were 110 and 29 times higher than in suburbs, were 1.5 × 104, 5.6 × 104 and 5.1 × 102 copies, i.e., 61.9%, 75.1% and 10.7% of the overall daily inhalation intake, respectively. Our study comprehensively compares environmental differences in AARGs to identify high-risk areas, and forwardly proposes the STI exposure dose of AARGs to guide risk assessment.
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Affiliation(s)
- Zhenchao Zhou
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Xinyi Shuai
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zejun Lin
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingxuan Meng
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoliang Ba
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 9DA , UK
| | - Hong Chen
- Institute of Environmental Technology, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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50
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Impact of Freeze Storage on the Estimation of Phenotypic Antimicrobial Resistance Prevalence in Escherichia coli Collected from Faecal Samples from Healthy Humans and Chickens. Antibiotics (Basel) 2022; 11:antibiotics11111643. [DOI: 10.3390/antibiotics11111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Many studies on phenotypic antimicrobial resistance (AMR) of bacteria from healthy populations are conducted on freeze-stored samples. However, the impact of this practice on phenotypic AMR is not known. We investigated the prevalence of phenotypic AMR in Escherichia coli from chicken (n = 10) and human (n = 11) faecal samples collected from healthy subjects, subject to freeze storage (−20 °C and −80 °C) for 1, 2, 3, and 6 months. We compared counts of E. coli and prevalence of phenotypic resistance against five antimicrobials commonly used in chicken farming (ciprofloxacin, enrofloxacin, doxycycline, gentamicin, and florfenicol) with samples processed within 24 h of collection. Prevalence of phenotypic AMR was estimated by performing differential counts on agar media with and without antimicrobials. At −20 °C, there was a considerable reduction in E. coli counts over time, and this reduction was greater for human samples (−0.630 log10 units per 100 days) compared with chicken samples (−0.178 log10 units per 100 days). For most antimicrobials, AMR prevalence estimates decreased in freeze-stored samples both in humans and chickens over time. Based on these results, we conclude that results on the prevalence of phenotypic AMR on samples from freeze-stored samples are unreliable, and only fresh samples should be used in such studies.
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