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Wang Y, Chen H, Pan Q, Wang J, Jiao X, Zhang Y. Development and evaluation of rapid and accurate one-tube RPA-CRISPR-Cas12b-based detection of mcr-1 and tet(X4). Appl Microbiol Biotechnol 2024; 108:345. [PMID: 38801527 DOI: 10.1007/s00253-024-13191-6] [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: 07/20/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
The emergence and quick spread of the plasmid-mediated tigecycline resistance gene tet(X4) and colistin resistance gene mcr-1 have posed a great threat to public health and raised global concerns. It is imperative to develop rapid and accurate detection systems for the onsite surveillance of mcr-1 and tet(X4). In this study, we developed one-tube recombinase polymerase amplification (RPA) and CRISPR-Cas12b integrated mcr-1 and tet(X4) detection systems. We identified mcr-1- and tet(X4)-conserved and -specific protospacers through a comprehensive BLAST search based on the NCBI nt database and used them for assembling the detection systems. Our developed one-tube RPA-CRISPR-Cas12b-based detection systems enabled the specific detection of mcr-1 and tet(X4) with a sensitivity of 6.25 and 9 copies within a detection time of ~ 55 and ~ 40 min, respectively. The detection results using pork and associated environmental samples collected from retail markets demonstrated that our developed mcr-1 and tet(X4) detection systems could successfully monitor mcr-1 and tet(X4), respectively. Notably, mcr-1- and tet(X4)-positive strains were isolated from the positive samples, as revealed using the developed detection systems. Whole-genome sequencing of representative strains identified an mcr-1-carrying IncI2 plasmid and a tet(X4)-carrying IncFII plasmid, which are known as important vectors for mcr-1 and tet(X4) transmission, respectively. Taken together, our developed one-tube RPA-CRISPR-Cas12b-based mcr-1 and tet(X4) detection systems show promising potential for the onsite detection of mcr-1 and tet(X4). KEY POINTS: • One-tube RPA-CRISPR-Cas12b-based mcr-1 and tet(X4) detection systems were developed based on identified novel protospacers. • Both detection systems exhibited high sensitivity and specification with a sample-to-answer time of less than 1 h. • The detection systems show promising potential for onsite detection of mcr-1 and tet(X4).
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Affiliation(s)
- Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Qingyun Pan
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China
| | - Xin'an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China.
- Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, 225009, China.
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Watson E, Hamilton S, Silva N, Moss S, Watkins C, Baily J, Forster T, Hall AJ, Dagleish MP. Variations in antimicrobial resistance genes present in the rectal faeces of seals in Scottish and Liverpool Bay coastal waters. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123936. [PMID: 38588972 DOI: 10.1016/j.envpol.2024.123936] [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: 12/11/2023] [Revised: 03/04/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Antibiotic resistance genes originating from human activity are considered important environmental pollutants. Wildlife species can act as sentinels for coastal environmental contamination and in this study we used qPCR array technology to investigate the variety and abundance of antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and integrons circulating within seal populations both near to and far from large human populations located around the Scottish and northwest English coast. Rectal swabs were taken from 50 live grey seals and nine live harbour seals. Nucleic acids were stabilised upon collection, enabling extraction of sufficient quality and quantity DNA for downstream analysis. 78 ARG targets, including genes of clinical significance, four MGE targets and three integron targets were used to monitor genes within 22 sample pools. 30 ARGs were detected, as well as the integrons intl1 and intl2 and tnpA transposase. Four β-lactam, nine tetracycline, two phenicol, one trimethoprim, three aminoglycoside and ten multidrug resistance genes were detected as well as mcr-1 which confers resistance to colistin, an important drug of last resort. No sulphonamide, vancomycin, macrolide, lincosamide or streptogramin B (MLSB) resistance genes were detected. Resistance genes were detected in all sites but the highest number of ARGs (n = 29) was detected in samples derived from grey seals on the Isle of May, Scotland during the breeding season, and these genes also had the highest average abundance in relation to the 16S rRNA gene. This pilot study demonstrates the effectiveness of a culture-independent workflow for global analysis of ARGs within the microbiota of live, free-ranging, wild animals from habitats close to and remote from human habitation, and highlights seals as a valuable indicator species for monitoring the presence, abundance and land-sea transference of resistance genes within and between ecosystems.
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Affiliation(s)
- Eleanor Watson
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK.
| | - Scott Hamilton
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK
| | - Nuno Silva
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK
| | - Simon Moss
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, KY16 8LB, Scotland, UK
| | - Craig Watkins
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK
| | - Johanna Baily
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK
| | - Thorsten Forster
- LifeArc, Bioquarter, 9 Little France Road, Edinburgh, EH16 4UX, Scotland, UK
| | - Ailsa J Hall
- Sea Mammal Research Unit, Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, KY16 8LB, Scotland, UK
| | - Mark P Dagleish
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Edinburgh, Scotland, EH26 0PZ, UK
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Wang Q, Han YY, Zhang TJ, Chen X, Lin H, Wang HN, Lei CW. Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes. Int J Food Microbiol 2024; 415:110634. [PMID: 38401379 DOI: 10.1016/j.ijfoodmicro.2024.110634] [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: 12/29/2023] [Revised: 02/08/2024] [Accepted: 02/18/2024] [Indexed: 02/26/2024]
Abstract
Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.
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Affiliation(s)
- Qin Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Ying-Yue Han
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Tie-Jun Zhang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Xuan Chen
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Heng Lin
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Hong-Ning Wang
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
| | - Chang-Wei Lei
- College of Life Sciences, Sichuan University, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China.
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Lencina FA, Bertona M, Stegmayer MA, Olivero CR, Frizzo LS, Zimmermann JA, Signorini ML, Soto LP, Zbrun MV. Prevalence of colistin-resistant Escherichia coli in foods and food-producing animals through the food chain: A worldwide systematic review and meta-analysis. Heliyon 2024; 10:e26579. [PMID: 38434325 PMCID: PMC10904249 DOI: 10.1016/j.heliyon.2024.e26579] [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: 01/05/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024] Open
Abstract
The purpose of this systematic review and meta-analysis was to summarize the available scientific evidence on the prevalence of colistin-resistant Escherichia coli strains isolated from foods and food-producing animals, the mobile colistin-resistant genes involved, and the impact of the associated variables. A systematic review was carried out in databases according to selection criteria and search strategies established a priori. Random-effect meta-analysis models were fitted to estimate the prevalence of colistin-resistant Escherichia coli and to identify the factors associated with the outcome. In general, 4.79% (95% CI: 3.98%-5.76%) of the food and food-producing animal samples harbored colistin-resistant Escherichia coli (total number of colistin-resistant Escherichia coli/total number of samples), while 5.70% (95% confidence interval: 4.97%-6.52%) of the E. coli strains isolated from food and food-producing animal samples harbored colistin resistance (total number of colistin-resistant Escherichia coli/total number of Escherichia coli isolated samples). The prevalence of colistin-resistant Escherichia coli increased over time (P < 0.001). On the other hand, 65.30% (95% confidence interval: 57.77%-72.14%) of colistin resistance was mediated by the mobile colistin resistance-1 gene. The mobile colistin resistance-1 gene prevalence did not show increases over time (P = 0.640). According to the findings, other allelic variants (mobile colistin resistance 2-10 genes) seem to have less impact on prevalence. A higher prevalence of colistin resistance was estimated in developing countries (P < 0.001), especially in samples (feces and intestinal content, meat, and viscera) derived from poultry and pigs (P < 0.001). The mobile colistin resistance-1 gene showed a global distribution with a high prevalence in most of the regions analyzed (>50%). The prevalence of colistin-resistant Escherichia coli and the mobile colistin resistance-1 gene has a strong impact on the entire food chain. The high prevalence estimated in the retail market represents a potential risk for consumers' health. There is an urgent need to implement based-evidence risk management measures under the "One Health" approach to guarantee public health, food safety, and a sustainable future.
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Affiliation(s)
- Florencia Aylen Lencina
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Matías Bertona
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - María Angeles Stegmayer
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Carolina Raquel Olivero
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Laureano Sebastián Frizzo
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - Jorge Alberto Zimmermann
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
| | - Marcelo Lisandro Signorini
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
| | - Lorena Paola Soto
- Laboratory of Food Analysis, Institute of Veterinary Science (ICiVet Litoral), National University of the Litoral, National Council of Scientific and Technical Research (UNL/CONICET), Esperanza, Argentina
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
| | - María Virginia Zbrun
- Department of Public Health, Faculty of Veterinary Science – Litoral National University, Esperanza, Argentina
- Instituto de Investigación de la Cadena Láctea (INTA-CONICET), Estación Experimental Agropecuaria Rafaela, Ruta 34 Km 227, Rafaela, Santa Fe, Argentina
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Biswas U, Das S, Barik M, Mallick A. Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces. Curr Microbiol 2023; 81:12. [PMID: 37989899 DOI: 10.1007/s00284-023-03521-8] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023]
Abstract
In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.
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Affiliation(s)
- Urmy Biswas
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Surojit Das
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Mili Barik
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Abhi Mallick
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
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Zhang X, Peng L, Ke Y, Zhao D, Yu G, Zhou Y, Li X, Weng X. Emergence of a clinical isolate of E. coil ST297 co-carrying bla NDM-13 and mcr-1.1 in China. J Infect Public Health 2023; 16:1813-1820. [PMID: 37741016 DOI: 10.1016/j.jiph.2023.09.007] [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: 03/22/2023] [Revised: 06/20/2023] [Accepted: 09/17/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND The coexistence of carbapenem resistance genes and mcr-1.1 in Enterobacterales has been an urgent and persistent threat to global public health. In this study, we isolated a clinical NB4833, an Escherichia coli isolate that co-carries mcr-1.1 and blaNDM-13. OBJECTIVES This study aimed to isolate a clinical NB4833, an Escherichia coli isolate that co-carries mcr-1.1 and blaNDM-13 and investigated the phenotypic and genotypic characteristics of plasmids harbored by E. coli isolate NB4833. METHODS Antimicrobial susceptibility testing and conjugation assay were performed on E. coli isolate NB4833. Stability of the plasmid and growth rate determination were used to characterize the plasmids harboring mcr-1.1 and blaNDM-13. In addition, the genetic characteristics of the plasmids were analyzed based on whole-genome sequencing of the strain and comparative genetic analysis with related plasmids. RESULTS Whole-genome sequencing showed that the isolate carried multiple resistance genes and possessed phenotypes indicative of all antibiotic resistance except tigecycline. And the mcr-1.1- and blaNDM-13-harbouring plasmids showed relatively high similarity to the related plasmids. The pNB4833-NDM-13 plasmid was capable of trans conjugation with an efficiency of 1.04 × 10-2 in a filter mating experiment and the transconjugant J53/ pNB4833-NDM-13 was able to be stably inherited after 10 days of passage. CONCLUSIONS To our knowledge, this is the first report of the coexistence of the IncI2 plasmid carrying mcr-1.1 and a blaNDM-13-carrying integrated IncFIB/IncFII plasmid in an ST297 clinical E. coli isolate. In addition, we investigated a novel plasmid carrying blaNDM-13. Our study expands the diversity of plasmids carrying blaNDM-13, which exhibits epidemic importance in bacterial resistance. Therefore, there are important measures that should be taken to prevent the spread of these plasmids.
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Affiliation(s)
- Xiaofan Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Lei Peng
- Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yefang Ke
- Department of Clinical Laboratory, Ningbo Women and Children's Hospital, Ningbo, Zhejiang 315012, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Guoqing Yu
- Department of Clinical Laboratory, Conch Hospital of Anhui Medical University, Wuhu, Anhui 241000, China
| | - Ying Zhou
- Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, China; Birth Defects Prevention Laboratory, Ningbo Women and Children's Hospital, Ningbo, Zhejiang 315012, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China.
| | - Xingbei Weng
- The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315010, China.
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Aldali HJ, Khan A, Alshehri AA, Aldali JA, Meo SA, Hindi A, Elsokkary EM. Hospital-Acquired Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Observational Study. Microorganisms 2023; 11:1595. [PMID: 37375097 DOI: 10.3390/microorganisms11061595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Worldwide, hospital-acquired infections (HAIs) are continuously rising within healthcare settings, leading to high mortality and morbidity rates. Many hospitals have reported the spread of carbapenemases globally, specifically within the E. coli and K. pneumoniae species. This study was aimed at analyzing the state of hospital-acquired, carbapenem-resistant E. coli and K. pneumoniae in the United Kingdom between 2009 and 2021. Moreover, the study analyzed the most efficacious approaches to patient management for controlling the carbapenem-resistant Enterobacteriaceae (CRE) spread. Initially, 1094 articles were identified as relevant for screening, and among them, 49 papers were eligible for full-text screening, with a total of 14 articles meeting the inclusion criteria. The information was recorded from published articles through PubMed, the Web of Science, Scopus, Science Direct, and the Cochrane library and was used to search for hospital-acquired carbapenem-resistant E. coli and K pneumoniae in the UK between 2009 and 2021, in order to evaluate the spread of CRE in hospitals. The total number of carbapenem-resistant E. coli was 1083 and this was 2053 for carbapenem-resistant K. pneumoniae in more than 63 UK hospitals. KPC was the dominant carbapenemase produced by K. pneumoniae. The results showed that the treatment options considered depended on the type of carbapenemase produced; K. pneumoniae showed more resistance to a treatment options, i.e., Colistin, than the other carbapenemase. The current state of the UK is at minimal risk for a CRE outbreak; however, appropriate treatment and infection control measures are highly required to prevent this CRE spread at the regional and global levels. The present study findings have an important message for physicians, healthcare workers, and policymakers about hospital-acquired carbapenem-resistant E. coli and K. pneumoniae spread and approaches to patient management.
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Affiliation(s)
- Hamzah J Aldali
- Cellular and Molecular Medicine, College of Biomedical Science, University of Bristol, Bristol BS8 1DT, UK
- School of Life Sciences, Faculty of Health & Life Sciences, Coventry University, Coventry CV2 2DX, UK
| | - Azra Khan
- School of Life Sciences, Faculty of Health & Life Sciences, Coventry University, Coventry CV2 2DX, UK
| | - Abdullah A Alshehri
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Al Huwaya, Taif 26571, Saudi Arabia
| | - Jehad A Aldali
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University, Riyadh 13317, Saudi Arabia
| | - Sultan Ayoub Meo
- Department of Physiology, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
| | - Ali Hindi
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PT, UK
| | - Emadeldin M Elsokkary
- Department of Psychology, Imam Mohammad Ibn Saud Islamic University, Riyadh 13317, Saudi Arabia
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Nordhoff K, Scharlach M, Effelsberg N, Knorr C, Rocker D, Claussen K, Egelkamp R, Mellmann AC, Moss A, Müller I, Roth SA, Werckenthin C, Wöhlke A, Ehlers J, Köck R. Epidemiology and zoonotic transmission of mcr-positive and carbapenemase-producing Enterobacterales on German turkey farms. Front Microbiol 2023; 14:1183984. [PMID: 37346748 PMCID: PMC10280733 DOI: 10.3389/fmicb.2023.1183984] [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: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/23/2023] Open
Abstract
Introduction The emergence of carbapenem-resistant bacteria causing serious infections may lead to more frequent use of previously abandoned antibiotics like colistin. However, mobile colistin resistance genes (mcr) can jeopardise its effectiveness in both human and veterinary medicine. In Germany, turkeys have been identified as the food-producing animal most likely to harbour mcr-positive colistin-resistant Enterobacterales (mcr-Col-E). Therefore, the aim of the present study was to assess the prevalence of both mcr-Col-E and carbapenemase-producing Enterobacterales (CPE) in German turkey herds and humans in contact with these herds. Methods In 2018 and 2019, 175 environmental (boot swabs of turkey faeces) and 46 human stool samples were analysed using a combination of enrichment-based culture, PCR, core genome multilocus sequence typing (cgMLST) and plasmid typing. Results mcr-Col-E were detected in 123 of the 175 turkey farms in this study (70.3%). mcr-Col-E isolates were Escherichia coli (98.4%) and Klebsiella spp. (1.6%). Herds that had been treated with colistin were more likely to harbour mcr-Col-E, with 82.2% compared to 66.2% in untreated herds (p = 0.0298). Prevalence also depended on husbandry, with 7.1% mcr-Col-E in organic farms compared to 74.5% in conventional ones (p < 0.001). In addition, four of the 46 (8.7%) human participants were colonised with mcr-Col-E. mcr-Col-E isolates from stables had minimum inhibitory concentrations (MICs) from 4 to ≥ 32 mg/l, human isolates ranged from 4 to 8 mg/l. cgMLST showed no clonal transmission of isolates. For one farm, plasmid typing revealed great similarities between plasmids from an environmental and a human sample. No CPE were found in turkey herds or humans. Discussion These findings confirm that mcr-Col-E-prevalence is high in turkey farms, but no evidence of direct zoonotic transmission of clonal mcr-Col-E strains was found. However, the results indicate that plasmids may be transmitted between E. coli isolates from animals and humans.
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Affiliation(s)
- Katja Nordhoff
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
- Perioperative Inflammation and Infection, Department of Human Medicine, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | | | | | - Carolin Knorr
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
| | - Dagmar Rocker
- Public Health Agency of Lower Saxony (NLGA), Hanover, Germany
| | - Katja Claussen
- Public Health Agency of Lower Saxony (NLGA), Hanover, Germany
| | | | | | - Andreas Moss
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
| | - Ilona Müller
- Public Health Agency of Lower Saxony (NLGA), Hanover, Germany
| | | | - Christiane Werckenthin
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
| | - Anne Wöhlke
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
| | - Joachim Ehlers
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Oldenburg, Germany
| | - Robin Köck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Hygiene and Environmental Medicine, University Medicine Essen, Essen, Germany
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Talat A, Miranda C, Poeta P, Khan AU. Farm to table: colistin resistance hitchhiking through food. Arch Microbiol 2023; 205:167. [PMID: 37014461 DOI: 10.1007/s00203-023-03476-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 04/05/2023]
Abstract
Colistin is a high priority, last-resort antibiotic recklessly used in livestock and poultry farms. It is used as an antibiotic for treating multi-drug resistant Gram-negative bacterial infections as well as a growth promoter in poultry and animal farms. The sub-therapeutic doses of colistin exert a selection pressure on bacteria leading to the emergence of colistin resistance in the environment. Colistin resistance gene, mcr are mostly plasmid-mediated, amplifying the horizontal gene transfer. Food products such as chicken, meat, pork etc. disseminate colistin resistance to humans through zoonotic transfer. The antimicrobial residues used in livestock and poultry often leaches to soil and water through faeces. This review highlights the recent status of colistin use in food-producing animals, its association with colistin resistance adversely affecting public health. The underlying mechanism of colistin resistance has been explored. The prohibition of over-the-counter colistin sales and as growth promoters for animals and broilers has exhibited effective stewardship of colistin resistance in several countries.
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Affiliation(s)
- Absar Talat
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Carla Miranda
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Department of Sciences, University Institute of Health Sciences (IUCS), CESPU, CRL, Gandra, Portugal
- Toxicology Research Unit (TOXRUN), IUCS, CESPU, CRL, Gandra, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-Os-Montes and Alto Douro (UTAD)UTAD, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Asad U Khan
- Medical and Molecular Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Zelendova M, Papagiannitsis CC, Sismova P, Medvecky M, Pomorska K, Palkovicova J, Nesporova K, Jakubu V, Jamborova I, Zemlickova H, Dolejska M. Plasmid-mediated colistin resistance among human clinical Enterobacterales isolates: national surveillance in the Czech Republic. Front Microbiol 2023; 14:1147846. [PMID: 37180238 PMCID: PMC10174314 DOI: 10.3389/fmicb.2023.1147846] [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: 01/19/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
The occurrence of colistin resistance has increased rapidly among Enterobacterales around the world. We performed a national survey of plasmid-mediated colistin resistance in human clinical isolates through a retrospective analysis of samples from 2009 to 2017 and a prospective sampling in 2018-2020. The aim of this study was to identify and characterize isolates with mcr genes from various regions of the Czech Republic using whole genome sequencing (WGS). Of all 1932 colistin-resistant isolates analyzed, 73 (3.8%) were positive for mcr genes. Most isolates carried mcr-1 (48/73) and were identified as Escherichia coli (n = 44) and Klebsiella pneumoniae (n = 4) of various sequence types (ST). Twenty-five isolates, including Enterobacter spp. (n = 24) and Citrobacter freundii (n = 1) carrying the mcr-9 gene were detected; three of them (Enterobacter kobei ST54) co-harbored the mcr-4 and mcr-9 genes. Multi-drug resistance phenotype was a common feature of mcr isolates and 14% (10/73) isolates also co-harbored clinically important beta-lactamases, including two isolates with carbapenemases KPC-2 and OXA-48. Phylogenetic analysis of E. coli ST744, the dominant genotype in this study, with the global collection showed Czech isolates belonged to two major clades, one containing isolates from Europe, while the second composed of isolates from diverse geographical areas. The mcr-1 gene was carried by IncX4 (34/73, 47%), IncHI2/ST4 (6/73, 8%) and IncI2 (8/73, 11%) plasmid groups. Small plasmids belonging to the ColE10 group were associated with mcr-4 in three isolates, while mcr-9 was carried by IncHI2/ST1 plasmids (4/73, 5%) or the chromosome (18/73, 25%). We showed an overall low level of occurrence of mcr genes in colistin-resistant bacteria from human clinical samples in the Czech Republic.
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Affiliation(s)
- Marketa Zelendova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Petra Sismova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Matej Medvecky
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Chemistry, Faculty of Science, University of Hradec Králové, Hradec Králové, Czechia
| | - Katarina Pomorska
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
| | - Jana Palkovicova
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | | | - Vladislav Jakubu
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Ivana Jamborova
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
| | - Helena Zemlickova
- NRL for ATB, The National Institute of Public Health, Centre for Epidemiology and Microbiology, Prague, Czechia
- Department of Microbiology, 3rd Faculty of Medicine, Kralovske Vinohrady University Hospital and National Institute of Public Health, Charles University, Prague, Czechia
| | - Monika Dolejska
- Department of Biology and Wildlife Diseases, Faculty of Veterinary Hygiene and Ecology, University of Veterinary Sciences Brno, Brno, Czechia
- CEITEC VETUNI, University of Veterinary Sciences Brno, Brno, Czechia
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital Brno, Brno, Czechia
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Pilsen, Czechia
- *Correspondence: Monika Dolejska,
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Ewers C, Göpel L, Prenger-Berninghoff E, Semmler T, Kerner K, Bauerfeind R. Occurrence of mcr-1 and mcr-2 colistin resistance genes in porcine Escherichia coli isolates (2010-2020) and genomic characterization of mcr-2-positive E. coli. Front Microbiol 2022; 13:1076315. [PMID: 36569100 PMCID: PMC9780603 DOI: 10.3389/fmicb.2022.1076315] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction The global emergence of plasmid-mediated colistin resistance is threatening the efficacy of colistin as one of the last treatment options against multi-drug resistant Gram-negative bacteria. To date, ten mcr-genes (mcr-1 to mcr-10) were reported. While mcr-1 has disseminated globally, the occurrence of mcr-2 was reported scarcely. Methods and results We determined the occurrence of mcr-1 and mcr-2 genes among Escherichia coli isolates from swine and performed detailed genomic characterization of mcr-2-positive strains. In the years 2010-2017, 7,614 porcine E. coli isolates were obtained from fecal swine samples in Europe and isolates carrying at least one of the virulence associated genes predicting Shiga toxin producing E. coli (STEC), enterotoxigenic E. coli (ETEC) or enteropathogenic E. coli (EPEC) were stored. 793 (10.4%) of these isolates carried the mcr-1 gene. Of 1,477 additional E. coli isolates obtained from sheep blood agar containing 4 mg/L colistin between 2018 and 2020, 36 (2.4%) isolates were mcr-1-positive. In contrast to mcr-1, the mcr-2 gene occurred at a very low frequency (0.13%) among the overall 9,091 isolates. Most mcr-2-positive isolates originated from Belgium (n = 9), one from Spain and two from Germany. They were obtained from six different farms and revealed multilocus sequence types ST10, ST29, ST93, ST100, ST3057 and ST5786. While the originally described mcr-2.1 was predominant, we also detected a new mcr-2 variant in two isolates from Belgium, which was termed mcr-2.8. MCR-2 isolates were mostly classified as ETEC or ETEC-like, while one isolate from Spain represented an atypical enteropathogenic E. coli (aEPEC; eae+). The ST29-aEPEC isolate carried mcr-2 on the chromosome. Another eight isolates carried their mcr-2 gene on IncX4 plasmids that resembled the pKP37-BE MCR-2 plasmid originally described in Belgium in 2015. Three ST100 E. coli isolates from a single farm in Belgium carried the mcr-2.1 gene on a 47-kb self-transmissible IncP type plasmid of a new IncP-1 clade. Discussion This is the first report of mcr-2 genes in E. coli isolates from Germany. The detection of a new mcr-2 allele and a novel plasmid backbone suggests the presence of so far undetected mcr-2 variants and mobilizable vehicles.
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Affiliation(s)
- Christa Ewers
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany,*Correspondence: Christa Ewers,
| | - Lisa Göpel
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Ellen Prenger-Berninghoff
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Torsten Semmler
- NG1 Microbial Genomics, Robert Koch Institute, Berlin, Germany
| | - Katharina Kerner
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
| | - Rolf Bauerfeind
- Faculty of Veterinary Medicine, Institute of Hygiene and Infectious Diseases of Animals, Justus Liebig University Giessen, Giessen, Germany
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Emergence of coexistence of a novel bla NDM-5-harbouring IncI1-I plasmid and an mcr-1.1-harbouring IncHI2 plasmid in a clinical Escherichia coli isolate in China. J Infect Public Health 2022; 15:1363-1369. [PMID: 36334462 DOI: 10.1016/j.jiph.2022.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Co-harbouring of carbapenem and colistin resistance genes in multidrug-resistant Enterobacterales strains poses a serious public health problem. In this study, an MCR-1.1 and NDM-5 coproducing Escherichia coli strain named EC6563 was isolated and characterized. OBJECTIVES This study aimed to characterize a clinical carbapenem-resistant E. coli isolate which co-harbours mcr-1.1 and blaNDM-5 on separate plasmids, and explored the phenotypic and genotypic characteristics of the mcr-1.1- and blaNDM-5-harbouring plasmids. METHODS E. coli isolate EC6563 was subjected to antimicrobial susceptibility testing, conjugation assay, stability of the plasmid and growth rate determination. In addition, the whole genome sequence of this strain was obtained and the genetic characteristics of the mcr-1.1- and blaNDM-5-harbouring plasmids were analyzed. RESULTS Carbapenem-resistant E. coli isolate EC6563 was resistant to all the tested antibiotics except tigecycline. Bioinformatic analysis confirmed that the IncHI2 plasmid carrying mcr-1.1 was highly similar to the previously reported mcr-1.1-harbouring plasmid pGDP37-4, and carried multiple drug resistance genes and the IncI1-I plasmid carrying blaNDM-5 had low similarity to the published blaNDM-5-carrying IncI1-I plasmid pEC-16-10-NDM-5. The pEC6563-NDM5 plasmid was capable of conjugation with an efficiency of 1.34 × 10-2 in a filter mating experiment. The transconjugant J53/pEC6563-NDM5 was able to be stably inherited after 12 days of passage. CONCLUSIONS To the best of our knowledge, this is the first time that an IncHI2 plasmid carrying mcr-1.1 and an IncI1-I plasmid carrying blaNDM-5 is found to coexist in an E. coli isolate. Our research expands the known diversity of plasmids in NDM-5-producing Enterobacterales strains. Meanwhile, effective measures should be taken to prevent the spread of these plasmids.
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Antimicrobial Susceptibility of Salmonella Isolated from Chickens and Humans in Wau, South Sudan. Int J Microbiol 2022. [DOI: 10.1155/2022/8570081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background. Salmonella infections are a public health problem across the globe. In South Sudan, there is little information regarding the prevalence and antibiotic resistance patterns of Salmonella. Therefore, this study assessed the prevalence and antimicrobial susceptibility of Salmonella isolates from chickens and humans in South Sudan. Fecal samples were collected and cultured on Xylose Lysine Deoxycholate Agar for the isolation of Salmonella and confirmed using biochemical tests and PCR through the amplification of the invA gene. A total of 417 fecal samples were examined, of which 270 (64.7%) were chicken cloacal swabs while 147 (35.3%) were humans’ stool specimens. Results. Eleven (11) Salmonella isolates were isolated from humans while nine were from chickens. All 11 isolates from humans were susceptible to sulfamethoxazole-trimethoprim, chloramphenicol, streptomycin, cefotaxime, nalidixic acid, and gentamicin. However, 4 (36.7%) isolates showed resistance to ciprofloxacin, 2 (18.9%) to ampicillin, and 1 (9.1%) to tetracycline. All chicken isolates were susceptible to chloramphenicol, streptomycin, sulfamethoxazole-trimethoprim, ciprofloxacin, cefotaxime, nalidixic acid, and gentamicin but showed resistance to tetracycline 2 (22.2%) and ampicillin 1 (11.1%). Conclusion. Antimicrobial resistant isolates were isolated in both chickens and humans. Further, MDR isolates were found in both chicken and human samples, and this is a public health concern. This, therefore, calls for concerted efforts to educate producers and consumers on public health, food safety, food hygiene in food production, and enhancement of surveillance programmes on zoonotic bacteria and antimicrobial susceptibility.
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Plasmidome in mcr-1 harboring carbapenem-resistant enterobacterales isolates from human in Thailand. Sci Rep 2022; 12:19051. [PMID: 36351969 PMCID: PMC9646850 DOI: 10.1038/s41598-022-21836-7] [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: 06/13/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
The emergence of the mobile colistin-resistance genes mcr-1 has attracted significant attention worldwide. This study aimed to investigate the genetic features of mcr-1-carrying plasmid among carbapenem-resistant Enterobacterales (CRE) isolates and the potential genetic basis governing transmission. Seventeen mcr-harboring isolates were analyzed based on whole genome sequencing using short-read and long-read platforms. All the mcr-1-carrying isolates could be conjugatively transferred into a recipient Escherichia coli UB1637. Among these 17 isolates, mcr-1 was located on diverse plasmid Inc types, consisting of IncX4 (11/17; 64.7%), IncI2 (4/17; 23.53%), and IncHI/IncN (2/17; 11.76%). Each of these exhibited remarkable similarity in the backbone set that is responsible for plasmid replication, maintenance, and transfer, with differences being in the upstream and downstream regions containing mcr-1. The IncHI/IncN type also carried other resistance genes (blaTEM-1B or blaTEM-135). The mcr-1-harboring IncX4 plasmids were carried in E. coli ST410 (7/11; 63.6%) and ST10 (1/11; 9.1%) and Klebsiella pneumoniae ST15 (1/11; 9.1%), ST336 (1/11; 9.1%), and ST340 (1/11; 9.1%). The IncI2-type plasmid was harbored in E. coli ST3052 (1/4; 25%) and ST1287 (1/4; 25%) and in K. pneumoniae ST336 (2/4; 50%), whereas IncHI/IncN were carried in E. coli ST6721 (1/2; 50%) and new ST (1/2; 50%). The diverse promiscuous plasmids may facilitate the spread of mcr-1 among commensal E. coli or K. pneumoniae strains in patients. These results can provide information for a surveillance system and infection control for dynamic tracing.
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Yang C, Chen K, Ye L, Heng H, Chan EWC, Chen S. Genetic and drug susceptibility profiles of mcr-1-bearing foodborne Salmonella strains collected in Shenzhen, China during the period 2014-2017. Microbiol Res 2022; 265:127211. [PMID: 36191468 DOI: 10.1016/j.micres.2022.127211] [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: 07/16/2022] [Revised: 09/24/2022] [Accepted: 09/25/2022] [Indexed: 10/14/2022]
Abstract
Colistin resistance mediated by mcr-1-bearing plasmids poses a new challenge to treatment of Salmonella infections. To probe the scale of the problem that colistin resistance mediated by mcr-1 plasmids among Salmonella, the prevalence of mcr-1 in foodborne Salmonella recovered from 2014 to 2017 in Shenzhen, China and genetic profile of mcr-1 positive isolates were investigated. All mcr-1 positives Salmonella strains were collected from food products, characterized by PCR and MALDI-TOF, and subjected to antimicrobial susceptibility testing, whole-genome sequencing, bioinformatics analysis, and conjugation. Twenty-eight mcr-1-positive Salmonella strains were recovered from pork. The rate of recovery displayed an increasing trend and was often accompanied by multidrug resistance. Salmonella Typhimurium was the most prevalent serotypes. Comparative genomic analysis indicated that the mcr-1 gene was located on the transferable IncX4 plasmids, as well as the IncHI2 plasmids, in which the gene was associated with ISApl1. All two types of plasmids were often detected in zoonotic pathogen. Transferable 251K mcr-1-bearing IncHI2 type plasmids were frequently reported in human and food-producing animals, but this is first time to detect a certain number in food. These findings show that dissemination of these two types of plasmids is responsible for the increase in the prevalence of colistin resistance in Salmonella strains in recent years, leading to rapid emergence of MDR Salmonella upon acquisition of these two mcr-1-bearing plasmids. Transmission of IncX4 and IncHI2 plasmids in Salmonella would cause huge public health concerns in controlling foodborne infections caused by Salmonella.
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Affiliation(s)
- Chen Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Heng Heng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Edward Wai Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China; State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.
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Mmatli M, Mbelle NM, Osei Sekyere J. Global epidemiology, genetic environment, risk factors and therapeutic prospects of mcr genes: A current and emerging update. Front Cell Infect Microbiol 2022; 12:941358. [PMID: 36093193 PMCID: PMC9462459 DOI: 10.3389/fcimb.2022.941358] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 08/01/2022] [Indexed: 12/28/2022] Open
Abstract
Background Mobile colistin resistance (mcr) genes modify Lipid A molecules of the lipopolysaccharide, changing the overall charge of the outer membrane. Results and discussion Ten mcr genes have been described to date within eleven Enterobacteriaceae species, with Escherichia coli, Klebsiella pneumoniae, and Salmonella species being the most predominant. They are present worldwide in 72 countries, with animal specimens currently having the highest incidence, due to the use of colistin in poultry for promoting growth and treating intestinal infections. The wide dissemination of mcr from food animals to meat, manure, the environment, and wastewater samples has increased the risk of transmission to humans via foodborne and vector-borne routes. The stability and spread of mcr genes were mediated by mobile genetic elements such as the IncHI2 conjugative plasmid, which is associated with multiple mcr genes and other antibiotic resistance genes. The cost of acquiring mcr is reduced by compensatory adaptation mechanisms. MCR proteins are well conserved structurally and via enzymatic action. Thus, therapeutics found effective against MCR-1 should be tested against the remaining MCR proteins. Conclusion The dissemination of mcr genes into the clinical setting, is threatening public health by limiting therapeutics options available. Combination therapies are a promising option for managing and treating colistin-resistant Enterobacteriaceae infections whilst reducing the toxic effects of colistin.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, United States
- Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
- *Correspondence: John Osei Sekyere, ;
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Jangir PK, Yang Q, Shaw LP, Caballero JD, Ogunlana L, Wheatley R, Walsh T, MacLean RC. Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of resistance to a last-resort antibiotic. eLife 2022; 11:78834. [PMID: 35943060 PMCID: PMC9363117 DOI: 10.7554/elife.78834] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Bacterial pathogens show high levels of chromosomal genetic diversity, but the influence of this diversity on the evolution of antibiotic resistance by plasmid acquisition remains unclear. Here, we address this problem in the context of colistin, a 'last line of defence' antibiotic. Using experimental evolution, we show that a plasmid carrying the MCR-1 colistin resistance gene dramatically increases the ability of Escherichia coli to evolve high-level colistin resistance by acquiring mutations in lpxC, an essential chromosomal gene involved in lipopolysaccharide biosynthesis. Crucially, lpxC mutations increase colistin resistance in the presence of the MCR-1 gene, but decrease the resistance of wild-type cells, revealing positive sign epistasis for antibiotic resistance between the chromosomal mutations and a mobile resistance gene. Analysis of public genomic datasets shows that lpxC polymorphisms are common in pathogenic E. coli, including those carrying MCR-1, highlighting the clinical relevance of this interaction. Importantly, lpxC diversity is high in pathogenic E. coli from regions with no history of MCR-1 acquisition, suggesting that pre-existing lpxC polymorphisms potentiated the evolution of high-level colistin resistance by MCR-1 acquisition. More broadly, these findings highlight the importance of standing genetic variation and plasmid/chromosomal interactions in the evolutionary dynamics of antibiotic resistance.
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Affiliation(s)
- Pramod K Jangir
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Liam P Shaw
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Lois Ogunlana
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Rachel Wheatley
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Timothy Walsh
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - R Craig MacLean
- Department of Zoology, University of OxfordOxfordUnited Kingdom
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18
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Turton JF, Pike R, Perry C, Jenkins C, Turton JA, Meunier D, Hopkins KL. Wide distribution of Escherichia coli carrying IncF plasmids containing bla NDM-5 and rmtB resistance genes from hospitalized patients in England. J Med Microbiol 2022; 71. [PMID: 35925786 DOI: 10.1099/jmm.0.001569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The New Delhi metallo-β-lactamase (NDM) variant NDM-5 was first described in 2011 in an isolate of Escherichia coli. We noted that a high proportion of isolates of E. coli positive for bla NDM carbapenemase genes submitted to the UK Health Security Agency (formerly Public Health England) between 2019 and mid-2021 carried the bla NDM-5 allele, with many co-harbouring rmtB, rendering them highly resistant to aminoglycosides as well as to most β-lactams.Hypothesis/Gap Statement. This observation suggested that a common plasmid may be circulating.Aim. To compare these isolates and describe the plasmids carrying these resistance elements.Methodology. All isolates were sequenced on an Illumina platform, with five also subjected to long-read nanopore sequencing to provide complete assemblies. The locations of bla NDM-5, rmtB and other associated genetic elements were identified. Susceptibility testing to a wide range of antibiotics was carried out on representative isolates.Results. The 34 isolates co-harbouring bla NDM-5 and rmtB were from 14 hospital groups and six different regions across England and consisted of 11 distinct sequence types. All carried IncF plasmids. Assembly of the NDM plasmids in five isolates revealed that they carried rmtB and bla NDM-5 in an IncF conjugative plasmid ranging in size from 85.5 to 161 kb. All carried a highly conserved region, previously described in E. coli plasmid pHC105-NDM, that included bla TEM-1B and rmtB followed by sequence bounded by two IS26 elements containing ΔISAba125, bla NDM-5, ble, trpF and tat followed by ISCR1 and an integron with sul1, aadA2 and dfrA12 cassettes. This arrangement has been described in isolates from other countries and continents, suggesting that such plasmids are widely distributed, at least in E. coli, with similar plasmids also found in Klebsiella pneumoniae. Tested isolates were resistant to most antibiotics except colistin, fosfomycin and tigecycline.Conclusion. These observations suggest that conjugative plasmids carrying a highly conserved resistance gene segment have become widespread in England and elsewhere. This study highlights the value of routine whole-genome sequencing in identifying genetic elements responsible for resistance dissemination.
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Affiliation(s)
- Jane F Turton
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Rachel Pike
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | - Claire Jenkins
- Reference Services Division, UK Health Security Agency, 61 Colindale Avenue, London NW9 5HT, UK
| | | | - Danièle Meunier
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
| | - Katie L Hopkins
- Healthcare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Usage and Sepsis Division, UK Health Security Agency, London, UK
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19
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Anyanwu MU, Jaja IF, Nwobi OC, Mgbeahuruike AC, Ikpendu CN, Okafor NA, Oguttu JW. Epidemiology and Traits of Mobile Colistin Resistance ( mcr) Gene-Bearing Organisms from Horses. Microorganisms 2022; 10:microorganisms10081499. [PMID: 35893557 PMCID: PMC9394310 DOI: 10.3390/microorganisms10081499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) threaten the efficacy of colistin (COL), a polymyxin antibiotic that is used as a last-line agent for the treatment of deadly infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. COL has been used for more than 60 years for the prophylactic control and treatment of infections in livestock husbandry but not in horses. Polymyxin B is used for the prophylactic control and empirical treatment of infections in horses without conducting sensitivity tests. The lack of sensitivity testing exerts selection pressure for the acquisition of the mcr gene. By horizontal transfer, mcr-1, mcr-5, and mcr-9 have disseminated among horse populations globally and are harbored by Escherichia coli, Klebsiella, Enterobacter, Citrobacter, and Salmonella species. Conjugative plasmids, insertion sequences, and transposons are the backbone of mcr genes in the isolates, which co-express genes conferring multi- to extensive-drug resistance, including genes encoding extended-spectrum β-lactamase, ampicillinase C, fosfomycin, and fluoroquinolone resistance, and virulence genes. The transmission of mcr genes to/among bacterial strains of equine origin is non-clonal. Contact with horses, horse manure, feed/drinking water, farmers, farmers’ clothing/farm equipment, the consumption of contaminated horse meat and its associated products, and the trading of horses, horse meat, and their associated products are routes for the transmission of mcr-gene-bearing bacteria in, to, and from the equine industry.
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Affiliation(s)
- Madubuike Umunna Anyanwu
- Microbiology Unit, Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 400001, Nigeria;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Ishmael Festus Jaja
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Obichukwu Chisom Nwobi
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka 400001, Nigeria;
| | | | - Chinaza Nnenna Ikpendu
- Department of Veterinary Microbiology, Michael Okpara University of Agriculture, Umudike 440101, Nigeria;
| | | | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
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20
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Yang X, Shu R, Hou L, Ren P, Lu X, Huang Z, Zhong Z, Wang H. mcr-1-Mediated In Vitro Inhibition of Plasmid Transfer Is Reversed by the Intestinal Environment. Antibiotics (Basel) 2022; 11:antibiotics11070875. [PMID: 35884129 PMCID: PMC9311533 DOI: 10.3390/antibiotics11070875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 06/25/2022] [Indexed: 12/03/2022] Open
Abstract
Colistin is regarded as an antibiotic of last resort against multidrug-resistant Gram-negative bacteria, including Klebsiella pneumoniae and Escherichia coli. Colistin resistance is acquired by microorganisms via chromosome-mediated mutations or plasmid-mediated mobile colistin resistance (mcr) gene, in which the transfer of mcr is the predominant factor underlying the spread of colistin resistance. However, the factors that are responsible for the spread of the mcr gene are still unclear. In this study, we observed that mcr-1 inhibited the transfer of the pHNSHP45 backbone in liquid mating. Similar inhibitory effect of mcr-1.6 and chromosomal mutant ΔmgrB suggested that colistin resistance, acquired from either plasmid or chromosomal mutation, hindered the transfer of colistin resistance-related plasmid in vitro. Dual plasmid system further proved that co-existing plasmid transfer was reduced too. However, this inhibitory effect was reversed in vivo. Some factors in the gut, including bile salt and anaerobic conditions, could increase the transfer frequency of the mcr-1-containing plasmid. Our results demonstrated the potential risk for the spread of colistin resistance in the intestine, provide a scientific basis against the transmission of colistin resistance threat.
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Affiliation(s)
- Xiaoman Yang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, China
| | - Rundong Shu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
| | - Leqi Hou
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
| | - Panpan Ren
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
| | - Xin Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206 Beijing, China;
| | - Zhi Huang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
| | - Hui Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, 210095 Nanjing, China; (X.Y.); (R.S.); (L.H.); (P.R.); (Z.H.); (Z.Z.)
- Correspondence: ; Tel.: +86-25-84396645
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21
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Khuntayaporn P, Thirapanmethee K, Chomnawang MT. An Update of Mobile Colistin Resistance in Non-Fermentative Gram-Negative Bacilli. Front Cell Infect Microbiol 2022; 12:882236. [PMID: 35782127 PMCID: PMC9248837 DOI: 10.3389/fcimb.2022.882236] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Colistin, the last resort for multidrug and extensively drug-resistant bacterial infection treatment, was reintroduced after being avoided in clinical settings from the 1970s to the 1990s because of its high toxicity. Colistin is considered a crucial treatment option for Acinetobacter baumannii and Pseudomonas aeruginosa, which are listed as critical priority pathogens for new antibiotics by the World Health Organization. The resistance mechanisms of colistin are considered to be chromosomally encoded, and no horizontal transfer has been reported. Nevertheless, in November 2015, a transmissible resistance mechanism of colistin, called mobile colistin resistance (MCR), was discovered. Up to ten families with MCR and more than 100 variants of Gram-negative bacteria have been reported worldwide. Even though few have been reported from Acinetobacter spp. and Pseudomonas spp., it is important to closely monitor the epidemiology of mcr genes in these pathogens. Therefore, this review focuses on the most recent update on colistin resistance and the epidemiology of mcr genes among non-fermentative Gram-negative bacilli, especially Acinetobacter spp. and P. aeruginosa.
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Affiliation(s)
- Piyatip Khuntayaporn
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- *Correspondence: Piyatip Khuntayaporn,
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
- Antimicrobial Resistance Interdisciplinary Group (AmRIG), Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
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22
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Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11060659. [PMID: 35745513 PMCID: PMC9230117 DOI: 10.3390/pathogens11060659] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.
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23
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Chen H, Mai H, Lopes B, Wen F, Patil S. Novel Pseudomonas aeruginosa Strains Co-Harbouring blaNDM-1 Metallo β-Lactamase and mcr-1 Isolated from Immunocompromised Paediatric Patients. Infect Drug Resist 2022; 15:2929-2936. [PMID: 35706928 PMCID: PMC9189156 DOI: 10.2147/idr.s368566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/27/2022] [Indexed: 12/13/2022] Open
Abstract
Background The rising resistance to carbapenems in Gram-negative bacteria worldwide poses a major clinical and public health risk. This study aimed to characterise carbapenem- and colistin-resistance genes, blaNDM-1 and mcr-1 located on IncX4 plasmid in MDR Pseudomonas aeruginosa, isolated from paediatric patients undergoing chemotherapy as a result of leukaemia. Methods In this study, six carbapenem-resistant strains of P. aeruginosa were isolated from two paediatric patients under chemotherapy treatment (1.8 years old female and 2.1 years male) from the Shenzhen Hospital, China, in the year 2019. Isolates were screened for conventional antibiotics such as tobramycin, cefepime, imipenem, and ciprofloxacin in additional colistin by using the broth dilution method. Furthermore, resistance determinants: mcr-1, blaNDM-1,blaKPC-1, and blaGES were screened using PCR and sequencing followed by multi-locus sequence typing. The horizontal gene transfer and location of mcr-1 and blaNDM-1 were determined by a liquid mating assay. In addition, Incompatibility type (Inc), PCR-based replicon type, and subgroup (MOB) of plasmid were studied. Results The screening for conventional antibiotics isolates showed 100% resistance to all the tested antibiotics except tobramycin. All isolates harboured carbapenemase encoding blaNDM-1, of which three also had mcr-1 located on a single IncX4 transferable plasmid. MLST typing revealed that four strains had a novel (new) STs type, while two belonged to ST1966. Conclusion This study identified for the first time colistin- and carbapenem-resistant MDR P. aeruginosa in paediatric patients with leukaemia in Shenzhen, China. It highlights the need for continuous surveillance in high-risk clones of MDR P. aeruginosa. Prudent use of antibiotics based on local antimicrobial susceptibility and clinical characteristics can help in reducing mortality in immunocompromised patients. ![]()
Point your SmartPhone at the code above. If you have a QR code reader the video abstract will appear. Or use: https://youtu.be/YzFjqeJsNSs
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Affiliation(s)
- Hongyu Chen
- Department of Laboratory Medicine, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China
| | - Huirong Mai
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China
| | - Bruno Lopes
- Department of Microbiology, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Feiqiu Wen
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China
- Feiqiu Wen, Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China, Tel +86-18938690333, Fax +86-755-83009888, Email
| | - Sandip Patil
- Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China
- Paediatric Research Institute, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China
- Correspondence: Sandip Patil, Department of Haematology and Oncology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, 518038, People’s Republic of China, Tel +86-18813934471, Fax +86-755-83008283, Email
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24
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Gorecki A, Musialowski M, Wolacewicz M, Decewicz P, Ferreira C, Vejmelkova D, Grzesiuk M, Manaia CM, Bartacek J, Dziewit L. Development and validation of novel PCR primers for identification of plasmid-mediated colistin resistance (mcr) genes in various environmental settings. JOURNAL OF HAZARDOUS MATERIALS 2022; 425:127936. [PMID: 34883371 DOI: 10.1016/j.jhazmat.2021.127936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/31/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Antibiotic resistance is considered one of the biggest threats to public health and has become a major concern for governments and international organizations. Combating this problem starts with improving global surveillance of antibiotic resistance genes (ARGs) and applying standardized protocols, both in a clinical and environmental context, in agreement with the One Health approach. Exceptional efforts should be directed to controlling ARGs conferring resistance to Critically Important Antimicrobials (CIA). In this study, a systematic literature review to synthesize data on the identification of mcr genes using a PCR technique was performed. Additionally, a novel set of PCR primers for mcr-1 - mcr-9 genes detection was proposed. The developed primers were in silico and experimentally validated by comparison with mcr-specific PCR primers reported in the literature. This validation, besides being a proof-of-concept for primers' usefulness, provided insight into the distribution of mcr genes in municipal wastewater, clay and river sediments, glacier moraine, manure, seagulls and auks feces and daphnids from four countries. This analysis proved that commonly used primers may deliver false results, and some mcr genes may be overlooked in tested samples. Newly-developed PCR primers turned out to be relevant for the screening of mcr genes in various environments.
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Affiliation(s)
- Adrian Gorecki
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Marcin Musialowski
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Mikolaj Wolacewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Przemyslaw Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Catarina Ferreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Dana Vejmelkova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Malgorzata Grzesiuk
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, Poland
| | - Celia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, Porto 4169-005, Portugal
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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25
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PixR, a Novel Activator of Conjugative Transfer of IncX4 Resistance Plasmids, Mitigates the Fitness Cost of mcr-1 Carriage in Escherichia coli. mBio 2022; 13:e0320921. [PMID: 35089067 PMCID: PMC8725589 DOI: 10.1128/mbio.03209-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of the plasmid-borne colistin resistance gene mcr-1 threatens public health. IncX4-type plasmids are one of the most epidemiologically successful vehicles for spreading mcr-1 worldwide. Since MCR-1 is known for imposing a fitness cost to its host bacterium, the successful spread of mcr-1-bearing plasmids might be linked to high conjugation frequency, which would enhance the maintenance of the plasmid in the host without antibiotic selection. However, the mechanism of IncX4 plasmid conjugation remains unclear. In this study, we used high-density transposon mutagenesis to identify factors required for IncX4 plasmid transfer. Eighteen essential transfer genes were identified, including five with annotations unrelated to conjugation. Cappable-seq, transcriptome sequencing (RNA-seq), electrophoretic mobility shift assay, and β-galactosidase assay confirmed that a novel transcriptional regulator gene, pixR, directly regulates the transfer of IncX4 plasmids by binding the promoter of 13 essential transfer genes to increase their transcription. PixR is not active under nonmating conditions, while the expression of the pixR, pilX3-4, and pilX11 genes increased 3- to 6-fold upon contact with recipient Escherichia coli C600. Plasmid invasion and coculture competition assays revealed the essentiality of pixR for spreading and persistence of mcr-1-bearing IncX4 plasmids in bacterial populations. Effective conjugation is crucial for alleviating the fitness cost exerted by mcr-1 carriage. The existence of the IncX4-specific pixR gene increases plasmid transmissibility while promoting the invasion and persistence of mcr-1-bearing plasmids in bacterial populations, which helps explain their global prevalence. IMPORTANCE The spread of clinically relevant antibiotic resistance genes is often linked to the dissemination of epidemic plasmids. However, the underlying molecular mechanisms contributing to the successful spread of epidemic plasmids remain unclear. In this report, we shine a light on the transfer activation of IncX4 plasmids. We show how conjugation promotes the invasion and persistence of IncX4 plasmids within a bacterial population. The dissection of the regulatory network of conjugation helps explain the rapid spread of epidemic plasmids in nature. It also reveals potential targets for the development of conjugation inhibitors.
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26
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Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med 2022; 14:15. [PMID: 35172877 PMCID: PMC8849018 DOI: 10.1186/s13073-022-01020-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
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Affiliation(s)
- Claire Waddington
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
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27
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Identification of mcr-1-positive multidrug-resistant Escherichia coli isolates from clinical samples in Shanghai, China. J Glob Antimicrob Resist 2022; 29:88-96. [PMID: 35182776 DOI: 10.1016/j.jgar.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/24/2022] [Accepted: 02/09/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Since the gene encoding mobilized colistin resistance (mcr-1) was first reported in China in 2015, it has been reported in various Enterobacteriaceae worldwide. Escherichia coli, one of the main pathogens causing diarrhea, is the most prevalent, clinically identified species carrying mcr-1. This study aimed to investigate the epidemiologic and genomic characteristics of mcr-1 in E. coli from patients in Shanghai. METHODS Fecal samples were collected from hospitals in Shanghai between 2012 and 2015. Polymerase chain reaction was performed to detect mcr-1, and molecular characteristics of the mcr-1-positive E. coli was determined by antimicrobial susceptibility testing and whole-genome sequencing. RESULTS We detected 40 (3.9%) mcr-1-positive E. coli strains from fecal samples in clinical settings between 2012 and 2015 in Shanghai. mcr-1 was detected in 4 types of E. coli, including aEPEC, EPEC, ETEC, and EAEC. Most strains harboring mcr-1 were isolated from children aged <7 years. Whole-genome sequencing revealed that nearly half of the strains that carried quinolone resistance- or β-lactam resistance-related genes were multidrug-resistant. IncX4 was the predominant type in mcr-1-positive E. coli in Shanghai but the other types of mcr-1-harboring plasmids are highly diverse in genetic context. CONCLUSION These data suggest that mcr-1 is prevalent in E. coli strains, especially those identified in diarrheal patients in Shanghai, and strengthening the surveillance of mcr-1 transmission, especially in children, is essential.
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Characterization of Genetic Elements Carrying mcr-1 Gene in Escherichia coli from the Community and Hospital Settings in Vietnam. Microbiol Spectr 2022; 10:e0135621. [PMID: 35138158 PMCID: PMC8826730 DOI: 10.1128/spectrum.01356-21] [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] [Indexed: 02/06/2023] Open
Abstract
Colistin is widely used in agriculture and aquaculture as prophylaxis, particularly in Asia. Recently, mcr-1 and other mobilizable genes conferring colistin resistance have spread globally in community and hospital populations. Characterizing mcr-1 mobile genetic elements and host genetic background is important to understand the transmission of this resistance mechanism. We conducted whole-genome sequencing of 94 mcr-1-positive Escherichia coli isolates (Mcr1-Ec isolates) from human and animal feces, food, and water in a community cohort (N = 87) and from clinical specimens from a referral hospital (N = 7) in northern Vietnam. mcr-1 was plasmid-borne in 71 and chromosomally carried in 25 (2 isolates contain one copy on chromosome and one copy on a plasmid) of 94 E. coli isolates from the community and hospital settings. All seven clinical isolates carried mcr-1 on plasmids. Replicon types of mcr-1-carrying plasmids included IncI2, IncP, IncX4, and IncFIA single replicons and combinations of IncHI2, IncN, and IncX1 multireplicons. Alignment of a long-read sequence of an IncI2 plasmid from animal feces with short-read sequences of IncI2 plasmids from a healthy human, water, and hospitalized patients showed highly similar structures (query cover from 90% to 98%, overall identity of >81%). We detected the potential existence of multireplicon plasmids harboring mcr-1 regardless of sample setting, confirming 10/71 with long-read sequencing. An intact/conserved Tn6330 transposon sequence or its genetic context variants were found in 6/25 Mcr1-Ec isolates with chromosomally carried mcr-1. The dissemination of mcr-1 is facilitated by a high diversity of plasmid replicon types and a high prevalence of the chromosomal Tn6330 transposon. IMPORTANCE The article presented advances our understanding of genetic elements carrying mcr-1 in Escherichia coli in both community and hospital settings. We provide evidence to suggest that diverse plasmid types, including multireplicon plasmids, have facilitated the successful transmission of mcr-1 in different reservoirs. The widespread use of colistin in agriculture, where a high diversity of bacteria are exposed, has allowed the selection and evolution of various transmission mechanisms that will make it a challenge to get rid of. Colocalization of mcr-1 and other antibiotic resistance genes (ARGs) on multireplicon plasmids adds another layer of complexity to the rapid dissemination of mcr-1 genes among community and hospital bacterial populations and to the slow pandemic of antimicrobial resistance (AMR) in general.
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Li P, Zhan LI, Wang H, Gao W, Gao L, Lv S, Zhang X, Zhu G, Yan Y. First Identification and Limited Dissemination of mcr-1 Colistin Resistance in Salmonella Isolates from Jiaxing. J Food Prot 2022; 85:213-219. [PMID: 34648627 DOI: 10.4315/jfp-21-069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 10/09/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Salmonella, a major foodborne pathogen, causes severe gastrointestinal disease in people and animals worldwide. Plasmid-borne mcr-1, which confers colistin resistance in Salmonella, has significant epidemiological interest for public health safety. Here, we report the first evidence of mcr-1-mediated colistin resistance in one multidrug-resistant strain, 16062, from 355 Salmonella isolates collected for Jiaxing foodborne pathogen monitoring in Zhejiang Province from 2015 to 2019. In addition to colistin, 16062 displayed multidrug resistance to various antimicrobials (β-lactams, quinolone, sulfonamide, florfenicol, ampicillin, streptomycin, nalidixic acid, aminoglycoside, and trimethoprim-sulfamethoxazole). The mcr-1-carrying IncX4 plasmid (p16062-MCR) in this study shares a conserved structure with other mcr-IncX4 plasmids. We found that other antimicrobial-resistance genes (aac(6')-Ib-cr, aadA1, aadA2, aph(3')-Ia, oqxA, oqxB, sul1, and cmlA1) are located on p16062-cmlA, an atypical IncHI2 plasmid, in isolate 16062. This is the first identification of transferable colistin resistance in a foodborne Salmonella isolate collected in Jiaxing City, the 5-year monitoring of which revealed limited dissemination. By determining the genetic features of the plasmid vehicle, the characteristics of transferable mcr genes circulating in isolates from Jiaxing are now clearer. HIGHLIGHTS
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Affiliation(s)
- Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - L I Zhan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310051, China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Wenjie Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Lei Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Shencong Lv
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Guoying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing 314050, China; and
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Prevalence of polymyxin resistance through the food chain, the global crisis. J Antibiot (Tokyo) 2022; 75:185-198. [PMID: 35079146 DOI: 10.1038/s41429-022-00502-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 09/30/2021] [Accepted: 10/10/2021] [Indexed: 12/24/2022]
Abstract
Antimicrobial resistance is one of the vital challenges facing global health today. Multi-drug resistant (MDR) infections are often treated with the narrow-spectrum drugs, colistin (polymyxin E) or polymyxin B, which are last-resort antibiotics for human therapeutics that are effective against Gram-negative bacteria. Unfortunately, resistance to these polymyxins has occurred because of selective pressure caused by the inappropriate use of those antibiotics, especially in farming. The mechanisms of resistance to polymyxins are mediated through intrinsic, mutational, or genetic alteration in chromosomal genes. The mechanism includes the regulatory network controlling chemical modifications of lipid A moiety of lipopolysaccharide, reducing the negative charge of lipid A and its affinity for polymyxins. Additionally, the unique mobile colistin/polymyxin B resistance (mcr) gene reported in Enterobacteriales is responsible for the horizontal dissemination of resistance to polymyxins via the food chain. There is now an urgent need to increase surveillance for detecting resistance to polymyxins. Therefore, this review presents an overview of presently available scientific literature on the mechanism of resistance to polymyxins, with their associated gene variants, evaluation methods, resistance transmission through the food chain via food bacteria, and related risk factors. We further focus on the significant implications of polymyxins usage in India and future views for food safety to preserve polymyxin activity.
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Fortini D, Owczarek S, Dionisi AM, Lucarelli C, Arena S, Carattoli A, Villa L, García-Fernández A. Colistin Resistance Mechanisms in Human Salmonella enterica Strains Isolated by the National Surveillance Enter-Net Italia (2016–2018). Antibiotics (Basel) 2022; 11:antibiotics11010102. [PMID: 35052978 PMCID: PMC8772777 DOI: 10.3390/antibiotics11010102] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 12/11/2022] Open
Abstract
Background: A collection of human-epidemiologically unrelated S. enterica strains collected over a 3-year period (2016 to 2018) in Italy by the national surveillance Enter-Net Italia was analysed. Methods: Antimicrobial susceptibility tests, including the determination of minimal inhibitory concentrations (MICs) for colistin, were performed. Colistin resistant strains were analysed by PCR to detect mobile colistin resistance (mcr) genes. In mcr-negative S. enterica serovar Enteritidis strains, chromosomal mutations potentially involved in colistin resistance were identified by a genomic approach. Results: The prevalence of colistin-resistant S. enterica strains was 7.7%, the majority (87.5%) were S. Enteritidis. mcr genes were identified only in one strain, a S. Typhimurium monophasic variant, positive for both mcr-1.1 and mcr-5.1 genes in an IncHI2 ST4 plasmid. Several chromosomal mutations were identified in the colistin-resistant mcr-negative S. Enteritidis strains in proteins involved in lipopolysaccharide and outer membrane synthesis and modification (RfbN, LolB, ZraR) and in a component of a multidrug efflux pump (MdsC). These mutated proteins were defined as possible candidates for colistin resistance in mcr-negative S. Enteritidis of our collection. Conclusions: The colistin national surveillance in Salmonella spp. in humans, implemented with genomic-based surveillance, permitted to monitor colistin resistance, determining the prevalence of mcr determinants and the study of new candidate mechanisms for colistin resistance.
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Affiliation(s)
- Daniela Fortini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Slawomir Owczarek
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Anna Maria Dionisi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Claudia Lucarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Alessandra Carattoli
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy;
| | | | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
| | - Aurora García-Fernández
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (D.F.); (S.O.); (A.M.D.); (C.L.); (S.A.); (L.V.)
- Correspondence:
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Lopez-Diaz M, Ellaby N, Turton J, Woodford N, Tomas M, Ellington MJ. NDM-1 carbapenemase resistance gene vehicles emergent on distinct plasmid backbones from the IncL/M family. J Antimicrob Chemother 2022; 77:620-624. [PMID: 34993543 DOI: 10.1093/jac/dkab466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/11/2021] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVES To assess the genetic contexts surrounding blaNDM-1 genes carried on IncM plasmids harboured by six carbapenemase-producing Enterobacterales (CPE) isolates referred to the UK Health Security Agency's Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit. METHODS Between 2014 and 2018, the AMRHAI Reference Unit undertook WGS of CPE isolates using Illumina NGS. Nanopore sequencing was used for selected isolates and publicly available plasmid references were downloaded. Analysis of incRNA, which encodes the antisense RNA regulating plasmidic repA gene expression, was performed and bioinformatics tools were used to analyse whole plasmid sequences. RESULTS Of 894 NDM-positive isolates of Enterobacterales, 44 NDM-1-positive isolates of five different species (Citrobacter spp., Enterobacter cloacae, Escherichia coli, Klebsiella pneumoniae and Klebsiella oxytoca) encoded the IncRNA locus of IncM2 plasmids. Long-read sequencing of six diverse isolates revealed related IncM2, NDM-1-encoding plasmids. Plasmid 'backbone' areas were conserved and contrasted with highly variable resistance regions. Sub-groupings of IncM2 plasmids encoding blaNDM-1 were detected; one sub-group occurred in five different health regions of England in every year. The diversity of NDM-1-encoding resistance gene integrons and transposons and their insertions sites in the plasmids indicated that NDM-1 has been acquired repeatedly by IncM2 variants. CONCLUSIONS The use of sequencing helped inform: (i) a wide geographical distribution of isolates encoding NDM-1 on emergent IncM2 plasmids; (ii) variant plasmids have acquired NDM-1 separately; and (iii) dynamic arrangements and evolution of the resistance elements in this plasmid group. The geographical and temporal distribution of IncM2 plasmids that encode NDM-1 highlights them as a public health threat that requires ongoing monitoring.
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Affiliation(s)
- Maria Lopez-Diaz
- UK Health Security Agency, 61 Colindale Avenue, London, UK.,Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
| | | | - Jane Turton
- UK Health Security Agency, 61 Colindale Avenue, London, UK
| | - Neil Woodford
- UK Health Security Agency, 61 Colindale Avenue, London, UK
| | - Maria Tomas
- Microbiology Department-Biomedical Research Institute A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
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Majewski P, Gutowska A, Smith DGE, Hauschild T, Majewska P, Hryszko T, Gizycka D, Kedra B, Kochanowicz J, Glowiński J, Drewnowska J, Swiecicka I, Sacha PT, Wieczorek P, Iwaniuk D, Sulewska A, Charkiewicz R, Makarewicz K, Zebrowska A, Czaban S, Radziwon P, Niklinski J, Tryniszewska EA. Plasmid Mediated mcr-1.1 Colistin-Resistance in Clinical Extraintestinal Escherichia coli Strains Isolated in Poland. Front Microbiol 2021; 12:547020. [PMID: 34956105 PMCID: PMC8703133 DOI: 10.3389/fmicb.2021.547020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2021] [Indexed: 01/27/2023] Open
Abstract
Objectives: The growing incidence of multidrug-resistant (MDR) bacteria is an inexorable and fatal challenge in modern medicine. Colistin is a cationic polypeptide considered a “last-resort” antimicrobial for treating infections caused by MDR Gram-negative bacterial pathogens. Plasmid-borne mcr colistin resistance emerged recently, and could potentially lead to essentially untreatable infections, particularly in hospital and veterinary (livestock farming) settings. In this study, we sought to establish the molecular basis of colistin-resistance in six extraintestinal Escherichia coli strains. Methods: Molecular investigation of colistin-resistance was performed in six extraintestinal E. coli strains isolated from patients hospitalized in Medical University Hospital, Bialystok, Poland. Complete structures of bacterial chromosomes and plasmids were recovered with use of both short- and long-read sequencing technologies and Unicycler hybrid assembly. Moreover, an electrotransformation assay was performed in order to confirm IncX4 plasmid influence on colistin-resistance phenotype in clinical E. coli strains. Results: Here we report on the emergence of six mcr-1.1-producing extraintestinal E. coli isolates with a number of virulence factors. Mobile pEtN transferase-encoding gene, mcr-1.1, has been proved to be encoded within a type IV secretion system (T4SS)-containing 33.3 kbp IncX4 plasmid pMUB-MCR, next to the PAP2-like membrane-associated lipid phosphatase gene. Conclusion: IncX4 mcr-containing plasmids are reported as increasingly disseminated among E. coli isolates, making it an “epidemic” plasmid, responsible for (i) dissemination of colistin-resistance determinants between different E. coli clones, and (ii) circulation between environmental, industrial, and clinical settings. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.
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Affiliation(s)
- Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anna Gutowska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | | | - Tomasz Hryszko
- Second Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Białystok, Białystok, Poland
| | - Dominika Gizycka
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Boguslaw Kedra
- Second Department of General and Gastroenterological Surgery, Medical University of Białystok, Białystok, Poland
| | - Jan Kochanowicz
- Department of Neurology, Medical University of Białystok, Białystok, Poland
| | - Jerzy Glowiński
- Department of Vascular Surgery and Transplantation, Medical University of Białystok, Białystok, Poland
| | - Justyna Drewnowska
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Pawel T Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Dominika Iwaniuk
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | | | | | - Slawomir Czaban
- Department of Anesthesiology and Intensive Care, Medical University of Białystok, Białystok, Poland
| | - Piotr Radziwon
- Regional Centre for Transfusion Medicine, Białystok, Poland.,Department of Hematology, Medical University of Białystok, Białystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Elzbieta A Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
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Prevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms. One Health 2021; 13:100354. [PMID: 34934795 PMCID: PMC8654966 DOI: 10.1016/j.onehlt.2021.100354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022] Open
Abstract
The treatment of infections due to colistin-resistant (Col-E) and carbapenemase-producing (CPE) Enterobacterales challenges clinicians both in human and veterinary medicine. Preventing zoonotic transmission of these multidrug-resistant bacteria is a Public Health priority. This study investigates the prevalence of Col-E and CPE on 81 pig farms in North-West Germany as well as among 138 directly exposed humans working on these farms. Between March 2018 and September 2020, 318 samples of porcine feces were taken using boot swabs. Farm workers provided a stool sample. Both a selective culture-based approach and a molecular detection of colistin (mcr-1 to mcr-5) and carbapenem resistance determinants (bla OXA-48/bla VIM/bla KPC/bla NDM) was used to screen all samples. Isolates from farm workers and farms were compared using core genome multilocus-sequence typing (cgMLST) and plasmid-typing. CPE were cultured neither from porcine feces nor from human stool samples. In one stool sample, bla OXA-48 was detected, but no respective CPE isolate was found. Col-E were found in 18/318 porcine (5.7%) samples from 10/81 (12.3%) farms and 2/138 (1.4%) farmers, respectively. All Col-E isolates were Escherichia coli harboring mcr-1. Both farm workers colonized with Col-E worked on farms where no Col-E were detected in porcine samples. In conclusion, CPE were absent on German pig farms. This supports findings of culture-based national monitoring systems and provides evidence that even when improving the diagnostic sensitivity by using molecular detection techniques in addition to culture, CPE are not prevalent. Col-E were prevalent in porcine feces despite a recent decrease in colistin usage among German livestock and absence of colistin treatments on the sampled farms. Farmers carried Col-E, but zoonotic transmission was not confirmed.
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Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia. Microorganisms 2021; 9:microorganisms9122515. [PMID: 34946117 PMCID: PMC8705591 DOI: 10.3390/microorganisms9122515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently poses a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carrying mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n = 586). mcr-1 genes were detected using a previously developed qPCR assay, and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates, including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans, carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene-carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological backgrounds.
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Freire CMADS, Taunay-Rodrigues A, Gonzatti MB, Fonseca FMP, Freire JEDC. New insights about the EptA protein and its correlation with the pmrC gene in polymyxin resistance in Pseudomonas aeruginosa. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100042. [PMID: 34841333 PMCID: PMC8610356 DOI: 10.1016/j.crmicr.2021.100042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/30/2021] [Accepted: 06/06/2021] [Indexed: 11/19/2022] Open
Abstract
Computational biology. Bacterial resistance. Pseudomonas aeruginosa. Gram-negative bacteria. Polymyxin.
Nowadays, clinical and scientific interest in antibiotics, as polymyxin, has increased due to the large number of reports of multiresistant Gram-negative bacteria, as Pseudomonas aeruginosa. The aim of this study was to investigate a related group of proteins for resistance to polymyxins, encoded by P. aeruginosa genome, through in silico analysis. The mobilized colistin resistance 1 (MCR1) protein from Escherichia coli was used for comparison. Similar sequences to the protein MCR1 in P. aeruginosa were analysed for physicochemical properties. 31 protein isoforms in P. aeruginosa (EptA) were found able to confer resistance to polymyxin showing protein lengths between 551 and 572 amino acids, with molecular mass values between 61.36 - 62. 80 kDa, isoelectric point between 6.10 to 7.17, instability index between 33.76 to 41.87, aliphatic index between 98.67 to 102.63 and the hydropathyindex between - 0.008 to 0.094. These proteins belong to the DUF1705 superfamily with bit-score values between 559.81 and 629.78. A high degree of similarity between EpTAs in P. aeruginosa was observed in relation to other proteins that confer resistance to polymyxins, present in Gram-negative bacteria species of clinical interest. Although, further studies are needed to identify the actual contribution of EptAs in P. aeruginosa species.
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Dadashi M, Sameni F, Bostanshirin N, Yaslianifard S, Khosravi-Dehaghi N, Nasiri MJ, Goudarzi M, Hashemi A, Hajikhani B. Global Prevalence and Molecular Epidemiology of mcr-Mediated Colistin Resistance in Escherichia coli Clinical Isolates: A Systematic Review. J Glob Antimicrob Resist 2021; 29:444-461. [PMID: 34788692 DOI: 10.1016/j.jgar.2021.10.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/10/2021] [Accepted: 10/25/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND AND AIM The continuing rise in infections caused by multi-drug resistant (MDR) bacteria is one of the most serious public health issues in today's societies. Colistin is a last-resort antimicrobial medication used to treat infections caused by MDR gram-negative bacteria; therefore resistance to this antibiotic is extremely hazardous. The current study aimed to evaluate the global prevalence and distribution of colistin resistance genes among human clinical isolates of Escherichia coli (E. coli) as a systematic review. METHODS PubMed, Embase, and Web of Science databases were systematically searched. For further evaluation, all original English-language articles that demonstrated colistin resistance in E. coli clinical isolates published between 2000 and 2020 were examined. RESULTS Out of 4857 initial articles, after various stages of review and evaluation, 190 related articles were selected. More than 79 % of the publications selected in this research were published from 2014 to 2020. In Asia, Europe, America, Africa, and Oceania, the prevalence of mobilized colistin resistance (mcr) producing colistin-resistant E. coli was 66.72%, 25.48%, 5.19%, 2.27%, and 0.32 %, respectively. CONCLUSION The recent widespread spreading of E. coli strains harboring mcr conferring colistin resistance, especially in Asia and Europe, is concerning and needs more attention.
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Affiliation(s)
- Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Fatemeh Sameni
- Department of Microbiology, School of Medicine, Shahed University, Tehran, Iran
| | - Nazila Bostanshirin
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Somayeh Yaslianifard
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Nafiseh Khosravi-Dehaghi
- Department of Pharmacognosy, School of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran; Evidence-Based Phytotherapy and Complementary Medicine Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Hashemi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Dallman TJ, Charles H, Prochazka M, Sinka K, Hughes G, Godbole G, Jenkins C. Emergence of novel strains of Shigella flexneri associated with sexual transmission in adult men in England, 2019-2020. J Med Microbiol 2021; 70. [PMID: 34665107 PMCID: PMC8604172 DOI: 10.1099/jmm.0.001437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
National surveillance of shigellosis in England revealed an increase in sexually transmitted Shigella flexneri in adult males in 2019 that persisted throughout 2020. We observed a resurgence of azithromycin-resistant S. flexneri serotype 3a, and the emergence of two novel multidrug-resistant clades of S. flexneri 2a and S. flexneri 1b.
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Affiliation(s)
- Timothy J Dallman
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Hannah Charles
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Mateo Prochazka
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Katy Sinka
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Gwenda Hughes
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Gauri Godbole
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
| | - Claire Jenkins
- National Infection Service, Public Health England, 61 Colindale Avenue, London, UK
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Anyanwu MU, Jaja IF, Okpala COR, Jaja CJI, Oguttu JW, Chah KF, Shoyinka VS. Potential sources and characteristic occurrence of mobile colistin resistance ( mcr) gene-harbouring bacteria recovered from the poultry sector: a literature synthesis specific to high-income countries. PeerJ 2021; 9:e11606. [PMID: 34707919 PMCID: PMC8500085 DOI: 10.7717/peerj.11606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/23/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding the sources, prevalence, phenotypic and genotypic characteristics of mcr gene-harbouring bacteria (MGHB) in the poultry sector is crucial to supplement existing information. Through this, the plasmid-mediated colistin resistance (PMCR) could be tackled to improve food safety and reduce public health risks. Therefore, we conducted a literature synthesis of potential sources and characteristic occurrence of MGHB recovered from the poultry sector specific to the high-income countries (HICs). Colistin (COL) is a last-resort antibiotic used for treating deadly infections. For more than 60 years, COL has been used in the poultry sector globally, including the HICs. The emergence and rapid spread of mobile COL resistance (mcr) genes threaten the clinical use of COL. Currently, ten mcr genes (mcr-1 to mcr-10) have been described. By horizontal and vertical transfer, the mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, and mcr-9 genes have disseminated in the poultry sector in HICs, thus posing a grave danger to animal and human health, as harboured by Escherichia coli, Klebsiella pneumoniae, Salmonella species, and Aeromonas isolates. Conjugative and non-conjugative plasmids are the major backbones for mcr in poultry isolates from HICs. The mcr-1, mcr-3 and mcr-9 have been integrated into the chromosome, making them persist among the clones. Transposons, insertion sequences (IS), especially ISApl1 located downstream and upstream of mcr, and integrons also drive the COL resistance in isolates recovered from the poultry sector in HICs. Genes coding multi-and extensive-drug resistance and virulence factors are often co-carried with mcr on chromosome and plasmids in poultry isolates. Transmission of mcr to/among poultry strains in HICs is clonally unrestricted. Additionally, the contact with poultry birds, manure, meat/egg, farmer's wears/farm equipment, consumption of contaminated poultry meat/egg and associated products, and trade of poultry-related products continue to serve as transmission routes of MGHB in HICs. Indeed, the policymakers, especially those involved in antimicrobial resistance and agricultural and poultry sector stakeholders-clinical microbiologists, farmers, veterinarians, occupational health clinicians and related specialists, consumers, and the general public will find this current literature synthesis very useful.
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Affiliation(s)
- Madubuike Umunna Anyanwu
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nsukka, Enugu, Nigeria
| | - Ishmael Festus Jaja
- Livestock and Pasture Science, University of Fort Hare, Alice, Eastern Cape, South Africa
| | - Charles Odilichukwu R. Okpala
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Chinwe-Juliana Iwu Jaja
- Department of Nursing and Midwifery, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, Western Cape, South Africa
| | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, University of South Africa, Johannesburg, Gauteng, South Africa
| | - Kennedy Foinkfu Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nsukka, Enugu, Nigeria
| | - Vincent Shodeinde Shoyinka
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nsukka, Enugu, Nigeria
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Liu G, Qian H, Lv J, Tian B, Bao C, Yan H, Gu B. Emergence of mcr-1-Harboring Salmonella enterica Serovar Sinstorf Type ST155 Isolated From Patients With Diarrhea in Jiangsu, China. Front Microbiol 2021; 12:723697. [PMID: 34603249 PMCID: PMC8483771 DOI: 10.3389/fmicb.2021.723697] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: This study analyzed the antimicrobial resistance phenotypes and mechanisms of quinolone, cephalosporins, and colistin resistance in nontyphoidal Salmonella from patients with diarrhea in Jiangsu, China. Methods: A total of 741 nontyphoidal Salmonella isolates were collected from hospitals in major cities of Jiangsu Province, China between 2016 and 2017. Their susceptibility to commonly used antibiotics was evaluated by broth micro-dilution and sequencing analysis of resistance genes screened by a PCR method. For mcr-1 positive isolates, genetic relationship study was carried out by pulsed-field gel electrophoresis and multiloci sequence typing analysis. The transferability of these plasmids was measured with conjugation experiments and the genetic locations of mcr-1 were analyzed by pulsed-field gel electrophoresis profiles of S1-digested genomic DNA and subsequent Southern blot hybridization. Results: Among 741 nontyphoidal Salmonella isolates, the most common serotypes identified were S. Typhimurium (n=257, 34.7%) and S. Enteritidis (n=127, 17.1%), and the isolates showed 21.7, 20.6, and 5.0% resistance to cephalosporins, ciprofloxacin, and colistin, respectively. Among the 335 nalidixic acid-resistant Salmonella, 213 (63.6%) and 45 (13.4%) had at least one mutation in gyrA and parC. Among the plasmid-borne resistance, qnrS1 (85; 41.9%) and aac(6')-Ib-cr4 (75; 36.9%) were the most common quinolone resistance (PMQR) genes, while bla CTX-M-14 (n=35) and bla CTX-M-55 (n=46) were found to be dominant extended-spectrum beta-lactamase (ESBL) genes in nontyphoidal Salmonella. In addition, eight mcr-1-harboring strains were detected since 2016 and they were predominate in children under the age of 7years. Conjugation assays showed the donor Salmonella strain has functional and transferable colistin resistance and Southern blot hybridization revealed that mcr-1 was located in a high molecular weight plasmid. Conclusion: In nontyphoidal Salmonella, there is a rapidly increasing trend of colistin resistance and this is the first report of patients harboring mcr-1-positive Salmonella with a new ST type ST155 and new serotype S. Sinstorf. These findings demonstrate the necessity for cautious use and the continuous monitoring of colistin in clinical applications.
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Affiliation(s)
- Guoye Liu
- Department of Clinical Laboratory, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Huimin Qian
- Department of Acute Infectious Disease Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Jingwen Lv
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Benshun Tian
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Changjun Bao
- Department of Acute Infectious Disease Prevention and Control, Jiangsu Provincial Center for Disease Prevention and Control, Nanjing, China
| | - Hong Yan
- Laboratory Medicine Center, The Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Abstract
Antimicrobial resistance is one of the most serious threats to medical science. Food supply is recognized as a potential source of resistant bacteria, leading to the development of surveillance programs targeting primarily poultry, pork, and beef. These programs are limited in scope, not only in the commodities tested, but also in the organisms targeted (Escherichia coli, Salmonella, and Campylobacter); consequently, neither the breadth of food products available nor the organisms that may harbour clinically relevant and (or) mobile resistance genes are identified. Furthermore, there is an inadequate understanding of how international trade in food products contributes to the global dissemination of resistance. This is despite the recognized role of international travel in disseminating antimicrobial-resistant organisms, notably New Delhi metallo-beta-lactamase. An increasing number of studies describing antimicrobial-resistant organisms in a variety of imported foods are summarized in this review.
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Affiliation(s)
- Dongyun Jung
- Department of Food Science and Agricultural Chemistry, McGill University, Montreal, Quebec, Canada
| | - Beverly J Morrison
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Joseph E Rubin
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Gogry FA, Siddiqui MT, Sultan I, Haq QMR. Current Update on Intrinsic and Acquired Colistin Resistance Mechanisms in Bacteria. Front Med (Lausanne) 2021; 8:677720. [PMID: 34476235 PMCID: PMC8406936 DOI: 10.3389/fmed.2021.677720] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023] Open
Abstract
Colistin regained global interest as a consequence of the rising prevalence of multidrug-resistant Gram-negative Enterobacteriaceae. In parallel, colistin-resistant bacteria emerged in response to the unregulated use of this antibiotic. However, some Gram-negative species are intrinsically resistant to colistin activity, such as Neisseria meningitides, Burkholderia species, and Proteus mirabilis. Most identified colistin resistance usually involves modulation of lipid A that decreases or removes early charge-based interaction with colistin through up-regulation of multistep capsular polysaccharide expression. The membrane modifications occur by the addition of cationic phosphoethanolamine (pEtN) or 4-amino-l-arabinose on lipid A that results in decrease in the negative charge on the bacterial surface. Therefore, electrostatic interaction between polycationic colistin and lipopolysaccharide (LPS) is halted. It has been reported that these modifications on the bacterial surface occur due to overexpression of chromosomally mediated two-component system genes (PmrAB and PhoPQ) and mutation in lipid A biosynthesis genes that result in loss of the ability to produce lipid A and consequently LPS chain, thereafter recently identified variants of plasmid-borne genes (mcr-1 to mcr-10). It was hypothesized that mcr genes derived from intrinsically resistant environmental bacteria that carried chromosomal pmrC gene, a part of the pmrCAB operon, code three proteins viz. pEtN response regulator PmrA, sensor kinase protein PmrAB, and phosphotransferase PmrC. These plasmid-borne mcr genes become a serious concern as they assist in the dissemination of colistin resistance to other pathogenic bacteria. This review presents the progress of multiple strategies of colistin resistance mechanisms in bacteria, mainly focusing on surface changes of the outer membrane LPS structure and other resistance genetic determinants. New handier and versatile methods have been discussed for rapid detection of colistin resistance determinants and the latest approaches to revert colistin resistance that include the use of new drugs, drug combinations and inhibitors. Indeed, more investigations are required to identify the exact role of different colistin resistance determinants that will aid in developing new less toxic and potent drugs to treat bacterial infections. Therefore, colistin resistance should be considered a severe medical issue requiring multisectoral research with proper surveillance and suitable monitoring systems to report the dissemination rate of these resistant genes.
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Affiliation(s)
| | | | - Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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Portes AB, Rodrigues G, Leitão MP, Ferrari R, Conte Junior CA, Panzenhagen P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J Appl Microbiol 2021; 132:872-889. [PMID: 34480840 DOI: 10.1111/jam.15282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.
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Affiliation(s)
- Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Grazielle Rodrigues
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Mylenna Palma Leitão
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rafaela Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
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Anyanwu MU, Jaja IF, Oguttu JW, Jaja CJ, Chah KF, Shodeinde Shoyinka V. Is Africa ready for mobile colistin resistance threat? Infect Ecol Epidemiol 2021; 11:1962781. [PMID: 34377360 PMCID: PMC8344256 DOI: 10.1080/20008686.2021.1962781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 07/27/2021] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance is a growing public health problem and a threat to effective treatment and prevention of an array of infections caused by bacteria. Africa is already faced with many socio-economic and health crises. Many countries in Africa can seldom boast of a standardized health care facility comparable to those in developed countries. Yet, the non-therapeutic use of COL has been banned in developed countries. However, in Africa, except for South Africa, COL is an over-the-counter (OTC) medication sold and dispensed by non-professionals/without a veterinarian's supervision. The ban of non-therapeutic COL in developed countries has proven to reduce the development of mobile colistin resistance (MCR) in humans and animals. The unregulated use of COL has been proven to select pathogenic and commensal bacteria resistance. A transmissible plasmid-mediated colistin determinant, mobile COL resistance (mcr) gene, which is rapidly transferred/acquired horizontally or laterally intra/inter-species/genera, has been reported. A highly promiscuous mobile genetic element like plasmids containing transposons, insertion sequences, and integrons aid the carriage/rapid transfer and acquisition of these mcr genes. Hence, we highlight the danger posed by escalating colistin (COL) resistance in the continent and the impetus to halt the indiscriminate and non-therapeutic use of COL to protect public health.
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Affiliation(s)
| | - Ishmael Festus Jaja
- Department of Livestock and Pasture Science, University of Fort Hare, Alice, South Africa
- Risk and Vulnerability Science Centre, University of Fort Hare, Alice, South Africa
| | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, University of South Africa, Roodepoort Johannesburg, South Africa
| | - Chinwe Juliana Jaja
- Risk and Vulnerability Science Centre, University of Fort Hare, Alice, South Africa
| | - Kennedy Foinkfu Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Nigeria
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Arai N, Sekizuka T, Tamamura-Andoh Y, Barco L, Hinenoya A, Yamasaki S, Iwata T, Watanabe-Yanai A, Kuroda M, Akiba M, Kusumoto M. Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan. Front Microbiol 2021; 12:690947. [PMID: 34276624 PMCID: PMC8281233 DOI: 10.3389/fmicb.2021.690947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.
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Affiliation(s)
- Nobuo Arai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukino Tamamura-Andoh
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Lisa Barco
- Reference Laboratory for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Padua, Italy
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Taketoshi Iwata
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Ayako Watanabe-Yanai
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masato Akiba
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan.,Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan
| | - Masahiro Kusumoto
- National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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Snyman Y, Whitelaw AC, Barnes JM, Maloba MRB, Newton-Foot M. Characterisation of mobile colistin resistance genes (mcr-3 and mcr-5) in river and storm water in regions of the Western Cape of South Africa. Antimicrob Resist Infect Control 2021; 10:96. [PMID: 34187559 PMCID: PMC8244157 DOI: 10.1186/s13756-021-00963-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/26/2021] [Indexed: 11/21/2022] Open
Abstract
Background Colistin is regarded as a last-resort antimicrobial against multi-drug resistant Gram-negative bacteria (GNB), therefore the dissemination of colistin resistance in the environment is of great concern. Horizontal transfer of mobile colistin resistance (mcr) genes to potential pathogens poses a serious problem. This study aimed to describe the presence of colistin resistant GNB and mcr genes in river and storm water in regions of the Western Cape. Methods Water samples were collected from three rivers during May 2019 and January 2020 and two storm water samples were collected in November 2019. Colistin resistant GNB were cultured on MacConkey agar containing colistin and identified by MALDI-TOF. Colistin resistance was confirmed using broth microdilution (BMD). mcr-1-5 genes were detected by PCR performed directly on the water samples and on the colistin resistant isolates. mcr functionality was assessed by BMD after cloning the mcr genes into pET-48b(+) and expression in SHuffle T7 E. coli. Results mcr-5.1 and various mcr-3 gene variants were detected in the Plankenburg-, Eerste- and Berg rivers and in storm water from Muizenberg, and only mcr-5.1 was detected in storm water from Fish Hoek. Colistin resistant GNB were isolated from all of the water sources. Aeromonas spp. were the most common colistin resistant organisms detected in the water sources; 25% (6/24) of colistin resistant Aeromonas spp. isolated from the Berg river contained novel mcr-3 variants; mcr-3.33 (n = 1), mcr-3.34 (n = 1) mcr-3.35 (n = 1) mcr-3.36 (n = 2) and mcr-3.37 (n = 1), which were confirmed to confer colistin resistance. Conclusions The mcr-5.1 and mcr-3 colistin resistance gene variants were present in widely dispersed water sources in regions of the Western Cape. The mcr genes were only detected in water sampled downstream of and alongside communities, suggesting that their presence is driven by human influence/contamination. This is the first documentation of mcr-3 and mcr-5 gene variants in any setting in South Africa. Spill-over of these genes to communities could result in horizontal gene transfer to pathogenic bacteria, exacerbating the challenge of controlling multidrug resistant GNB infections. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00963-2.
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Affiliation(s)
- Yolandi Snyman
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.
| | - Andrew C Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Jo M Barnes
- Division of Community Health, Department Epidemiology, Stellenbosch University, Cape Town, South Africa
| | - Motlatji R B Maloba
- Department of Medical Microbiology, University of the Free State, Bloemfontein, South Africa.,National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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Alghoribi MF, Desin TS, Alswaji AA, Al Alwan BH, Alzayer M, Okdah L, Al Johani S, Balkhy HH, Doumith M. OXA-48 carbapenemase-producing Salmonella enterica serovar Kentucky ST198 isolated from Saudi Arabia. J Antimicrob Chemother 2021; 75:2006-2008. [PMID: 32154842 DOI: 10.1093/jac/dkaa077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Majed F Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Taseen S Desin
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman A Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Bassam H Al Alwan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Maha Alzayer
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Genomic Research Department, King Fahd Medical City, Riyadh, Saudi Arabia
| | - Sameera Al Johani
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Michel Doumith
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Patchanee P, Chokesajjawatee N, Santiyanont P, Chuammitri P, Deeudom M, Monteith W, Sheppard SK, Pascoe B, Prasertsee T. Characterisation of Salmonella enterica clones carrying mcr-1 plasmids in meat products and patients in Northern Thailand using long read sequencing. Int J Food Microbiol 2021; 358:109314. [PMID: 34176647 DOI: 10.1016/j.ijfoodmicro.2021.109314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022]
Abstract
Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially food of livestock origin. Antimicrobial resistance (AMR) in Salmonella has been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatedness among Salmonella enterica isolates, which displayed identical DNA fingerprint profiles. Ten S. enterica isolates were selected from meat and human cases with an identical rep-PCR profile of serovars Rissen (n = 4), Weltevreden (n = 4), and Stanley (n = 2). We used long-read whole genome sequencing (WGS) on the MinION sequencing platform to type isolates and investigate in silico the presence of specific AMR genes. Antimicrobial susceptibility testing was tested by disk diffusion and gradient diffusion method to corroborate the AMR phenotype. Multidrug resistance and resistance to more than one antimicrobial agent were observed in eight and nine isolates, respectively. Resistance to colistin with an accompanying mcr-1 gene was observed among the Salmonella isolates. The analysis of core genome and whole genome MLST revealed that the Salmonella from meat and human salmonellosis were genetically related. Hence, it could be concluded that meat is one of the important sources for Salmonella infection in human.
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Affiliation(s)
- Prapas Patchanee
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Nipa Chokesajjawatee
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pannita Santiyanont
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Phongsakorn Chuammitri
- Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Manu Deeudom
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - William Monteith
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom
| | - Samuel K Sheppard
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ben Pascoe
- Integrative Research Center for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand; The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, BA2 7BA, United Kingdom; Division of Clinical Microbiology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai 50200, Thailand.
| | - Teerarat Prasertsee
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand.
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A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nat Commun 2021; 12:2879. [PMID: 34001879 PMCID: PMC8128892 DOI: 10.1038/s41467-021-23091-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022] Open
Abstract
As whole-genome sequencing capacity becomes increasingly decentralized, there is a growing opportunity for collaboration and the sharing of surveillance data within and between countries to inform typhoid control policies. This vision requires free, community-driven tools that facilitate access to genomic data for public health on a global scale. Here we present the Pathogenwatch scheme for Salmonella enterica serovar Typhi (S. Typhi), a web application enabling the rapid identification of genomic markers of antimicrobial resistance (AMR) and contextualization with public genomic data. We show that the clustering of S. Typhi genomes in Pathogenwatch is comparable to established bioinformatics methods, and that genomic predictions of AMR are highly concordant with phenotypic susceptibility data. We demonstrate the public health utility of Pathogenwatch with examples selected from >4,300 public genomes available in the application. Pathogenwatch provides an intuitive entry point to monitor of the emergence and spread of S. Typhi high risk clones. Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.
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Bilal H, Rehman TU, Khan MA, Hameed F, Jian ZG, Han J, Yang X. Molecular Epidemiology of mcr-1, bla KPC-2, and bla NDM-1 Harboring Clinically Isolated Escherichia coli from Pakistan. Infect Drug Resist 2021; 14:1467-1479. [PMID: 33888998 PMCID: PMC8057800 DOI: 10.2147/idr.s302687] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/11/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The multiple-drug resistant Escherichia coli are among the deadliest pathogens causing life-threatening infections. This study was planned to determine the molecular epidemiology of mcr-1, bla KPC-2, and bla NDM-1 harboring clinically isolated E. coli from Pakistan. Methods In total, 545 strains of E. coli from clinical samples were collected from June 2018 to September 2019. All the isolates were screened for colistin-resistance, extended-spectrum-β-lactamases (ESBL), and carbapenemases through the micro-dilution method, Double-Disk-Synergy-Test (DDST), and Modified-Hodge-Test (MHT). The detection, sequence-typing, conjugal transfer, S1-PFGE, plasmid-replicon-typing, and southern-blotting for mcr, ESBL, and carbapenemase-encoding genes were performed. Findings A total of four (0.73%) colistin-resistant strains carrying alongside mcr-1 and bla CTX-M-15 genes, three of these strains also had the bla TEM-1 gene. The presence of ESBL genes was detected in 139 (25.5%) isolates harboring bla CTXM-15 (74.82%), bla TEM (34.53%), bla SHV (28.06%) and bla OXA-1 (28.78%). In 129 carbapenemase-producers, 35.83% possessed bla NDM-1, 26.67% bla KPC-2, 8.3% bla OXA-48, 25% bla VIM-1, and 20.83% bla IMP-1 genes. The sequence typing revealed that mcr-1 harboring isolates belonged to ST405, ST117, and ST156. Fifty percent of bla KPC-2 and 48.83% of bla NDM-1 were found on ST131 and ST1196, respectively. Two rare types of STs, ST7584, and ST8671 were also identified in this study. The mcr-1 gene was located on Incl2 (60-kb) plasmid. The bla KPC-2 was present on (140-kb) IncH12, (100-kb) IncN, (90-kb) Incl1, while bla NDM-1 was located on (70-kb) IncFIIK, (140-kb) IncH12, (100-kb) IncN, (60-kb) IncA/C, and (45-kb) IncFII plasmids, which were successfully trans-conjugated. Among the plasmid types, the Incl1 carrying bla KPC-2, IncH12 harboring bla KPC-2 and bla NDM-1, and IncFIIK carrying bla NDM-1 were for the first time detected in Pakistan. Conclusion The mcr-1, bla KPC-2, and bla NDM-1 genes finding in various clonal and plasmids types indicate that a substantial selection of the resistance genes had occurred in our clinical strains.
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Affiliation(s)
- Hazrat Bilal
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Tayyab Ur Rehman
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Muhammad Asif Khan
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Fareeha Hameed
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Zhang Gao Jian
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Jianxiong Han
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
| | - Xingyuan Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, Hefei, People's Republic of China
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