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Xia C, Yan R, Liu C, Zhai J, Zheng J, Chen W, Cao X. Epidemiological and genomic characteristics of global blaNDM-carrying Escherichia coli. Ann Clin Microbiol Antimicrob 2024; 23:58. [PMID: 38907245 PMCID: PMC11193274 DOI: 10.1186/s12941-024-00719-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
BACKGROUND Escherichia. coli is the most frequent host for New Delhi metallo-β-lactamase (NDM) which hydrolyzes almost all β-lactams except aztreonam. The worldwide spread of blaNDM-carrying E. coli heavily threatens public health. OBJECTIVE This study aimed to explore the global genomic epidemiology of blaNDM- carrying E. coli isolates, providing information for preventing the dissemination of such strains. METHODS Global E. coli genomes were downloaded from NCBI database and blaNDM was detected using BLASTP. Per software was used to extract meta information on hosts, resources, collection data, and countries of origin from GenBank. The sequence types (STs) and distribution of antimicrobial resistance gene (ARG) were analyzed by CLC Workbench; Plasmid replicons, serotypes and virulence genes (VFs) were analyzed by submitting the genomes to the websites. Statistical analyses were performed to access the relationships among ARGs and plasmid replicons. RESULTS Until March 2023, 1,774 out of 33,055 isolates collected during 2003-2022 were found to contain blaNDM in total. Among them, 15 blaNDM variants were found with blaNDM-5 (74.1%) being most frequent, followed by blaNDM-1 (16.6%) and blaNDM-9 (4.6%). Among the 213 ARGs identified, 27 blaCTX-M and 39 blaTEM variants were found with blaCTX-M-15 (n = 438, 24.7%) and blaTEM-1B (n = 1092, 61.6%) being the most frequent ones, respectively. In addition, 546 (30.8%) plasmids mediated ampC genes, 508 (28.6%) exogenously acquired 16 S rRNA methyltransferase encoding genes and 262 (14.8%) mcr were also detected. Among the 232 distinct STs, ST167 (17.2%) were the most prevalent. As for plasmids, more than half of isolates contained IncFII, IncFIB and IncX3. The VF terC, gad, traT and iss as well as the serotypes O101:H9 (n = 231, 13.0%), O8:H9 (n = 115, 6.5%) and O9:H30 (n = 99, 5.6%) were frequently observed. CONCLUSIONS The study delves into the intricate relationship between plasmid types, virulence factors, and ARGs, which provides valuable insights for clinical treatment and public health interventions, and serves as a critical resource for guiding future research, surveillance, and implementation of effective strategies to address the challenges posed by blaNDM-carrying E. coli. The findings underscore the urgent need for sustained global collaboration, surveillance efforts, and antimicrobial stewardship to mitigate the impact of these highly resistant strains on public health.
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Affiliation(s)
- Changyu Xia
- Department of Laboratory Medicine, Peking University First Hospital, Beijing, China
| | - Ruyu Yan
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Junbin Zhai
- Department of Laboratory Medicine, Peking University First Hospital, Beijing, China
| | - Jie Zheng
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China
| | - Wei Chen
- Clinical Research Center, the Second Hospital of Nanjing, Affiliated to Nanjing University of Chinese Medicine, Senior technologist Zhongshan Road 321, Nanjing, Jiangsu Province, 210003, China.
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Jiangsu, China.
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Li Y, Sun X, Dong N, Wang Z, Li R. Global distribution and genomic characteristics of carbapenemase-producing Escherichia coli among humans, 2005-2023. Drug Resist Updat 2024; 72:101031. [PMID: 38071860 DOI: 10.1016/j.drup.2023.101031] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/27/2023] [Accepted: 11/30/2023] [Indexed: 01/08/2024]
Abstract
Carbapenem-resistant Escherichia coli (CREC) has become a major public health problem worldwide. To date, there is a limited understanding of the global distribution of CREC. In this study, we performed a comprehensive genomic analysis of 7, 731 CRECs of human origin collected from different countries worldwide between 2005 and 2023. Our results showed that these CRECs were distributed in 75 countries, mainly from the United States (17.49%), China (14.88%), and the United Kingdom (14.73%). Eight carbapenemases were identified among the CRECs analyzed, including KPC, IMP, NDM, VIM, OXA, FRI, GES, and IMI. NDM was the most predominant carbapenemase (52.15%), followed by OXA (30.09%) and KPC (14.72%). Notably, all CRECs carried multiple antibiotic resistance genes (ARGs), with 178 isolates carrying mcr-1 and 9 isolates carrying tet(X). The CREC isolates were classified into 465 known sequence types (STs), with ST167 being the most common (11.5%). Correlation analysis demonstrated the significant role of mobile genetic elements in facilitating the transfer of carbapenem resistance genes. Furthermore, some CRECs from different countries showed high genetic similarity, suggesting clonal transmission exists. According to the GWAS results, the genetic difference of blaNDM-positive CRECs from China were mainly enriched in bacterial Type IV secretion system pathways compared with those from the United Kingdom and the United States. Therefore, continuous global surveillance of CRECs is imperative in the future.
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Affiliation(s)
- Yan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Xinran Sun
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, PR China
| | - Zhiqiang Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, PR China.
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, PR China.
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Yassin A, Huralska M, Pogue JM, Dixit D, Sawyer RG, Kaye KS. State of the Management of Infections Caused by Multidrug-Resistant Gram-Negative Organisms. Clin Infect Dis 2023; 77:e46-e56. [PMID: 37738671 DOI: 10.1093/cid/ciad499] [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: 02/27/2023] [Indexed: 09/24/2023] Open
Abstract
In the past decade, the prevalence of multidrug-resistant gram-negative (MDR-GN) bacterial infections has increased significantly, leading to higher rates of morbidity and mortality. Treating these infections poses numerous challenges, particularly when selecting appropriate empiric therapy for critically ill patients for whom the margin for error is low. Fortunately, the availability of new therapies has improved the treatment landscape, offering safer and more effective options. However, there remains a need to establish and implement optimal clinical and therapeutic approaches for managing these infections. Here, we review strategies for identifying patients at risk for MDR-GN infections, propose a framework for the choice of empiric and definitive treatment, and explore effective multidisciplinary approaches to managing patients in the hospital while ensuring a safe transition to outpatient settings.
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Affiliation(s)
- Arsheena Yassin
- Department of Pharmacy, Robert Wood Johnson University Hospital, New Brunswick, New Jersey, USA
| | - Mariya Huralska
- Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Jason M Pogue
- Department of Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, Michigan, USA
- Department of Pharmacy, Michigan Medicine, Ann Arbor, Michigan, USA
| | - Deepali Dixit
- Department of Pharmacy, Robert Wood Johnson University Hospital, New Brunswick, New Jersey, USA
- Ernest Mario School of Pharmacy, Rutgers, State University of New Jersey, Piscataway, New Jersey, USA
| | - Robert G Sawyer
- Department of Surgery, Western Michigan University Homer Stryker School of Medicine, Kalamazoo, Michigan, USA
| | - Keith S Kaye
- Division of Allergy, Immunology and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
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Chen R, Wang G, Wang Q, Zhang M, Wang Y, Wan Z, Si Z, Bai Y, Song Z, Lu X, Hao Y. Antimicrobial resistance and molecular epidemiology of carbapenem-resistant Escherichia coli from urinary tract infections in Shandong, China. Int Microbiol 2023; 26:1157-1166. [PMID: 37145384 DOI: 10.1007/s10123-023-00369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/15/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVES Urinary tract infection (UTI) is one of the most common extraintestinal infections, and uropathogenic Escherichia coli (UPEC) is the main cause of UTIs. However, the ability to treat UTI has been compromised by the increase in antimicrobial resistance, especially carbapenem resistance. Here, we aimed to characterize the antimicrobial resistance and molecular epidemiology of carbapenem-resistant UPEC isolated in Shandong, China. METHODS In total, 17 carbapenem-resistant UPEC (CR-UPEC) isolates were collected from July 2017 to May 2020 in the Shandong Provincial Hospital. Whole-genome sequencing and bioinformatics analyses were performed to understand the molecular epidemiology of CR-UPEC. Phylogenetic groups, drug resistance genes, biofilm formation, and virulence-related gene profiles of the isolates were analyzed. Plasmid profiling and conjugation assay were performed to evaluate the ability to transfer carbapenem resistance-related genes to other E. coli isolates. Biofilm formation was also evaluated, as it is important for the persistence of infectious diseases. RESULTS We observed that 15 out of 17 CR-UPEC strains were blaNDM producers, among which 4 isolates could transfer blaNDM to recipient cells. The predominant sequence type was ST167 (6/17), followed by ST410 (3/17). The most prevalent phylogenetic group was phylogenetic group A (10/17), followed by phylogenetic group C (3/17). One isolate was resistant to polymyxin, which was caused by the carriage of a transferable plasmid harboring mcr-1. Statistical analysis did not reveal any significant difference in the carriage rate of fimbriae-coding genes between strong and weak biofilm producers. CONCLUSIONS Our observations may assist in developing new therapeutic methods for drug-resistant organisms.
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Affiliation(s)
- Ran Chen
- Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Guili Wang
- Department of Clinical Laboratory, Beijing Xiao Tang Shan Hospital, Beijing, 102200, China
| | - Qian Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Meng Zhang
- Department of Clinical Laboratory, Liaocheng Second People's Hospital, Liaocheng, 252600, Shandong, China
| | - Yueling Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Zhongkun Wan
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Zaifeng Si
- Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China
| | - Yuanyuan Bai
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Zhen Song
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Xinglun Lu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China
| | - Yingying Hao
- Department of Clinical Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 9677# Jing-Shi Road, Jinan, 250014, People's Republic of China.
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Ramkisson T, Rip D. Carbapenem resistance in Enterobacterales from agricultural, environmental and clinical origins: South Africa in a global context. AIMS Microbiol 2023; 9:668-691. [PMID: 38173973 PMCID: PMC10758576 DOI: 10.3934/microbiol.2023034] [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: 07/20/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024] Open
Abstract
Carbapenem agents are regarded as last-resort antibiotics, however, bacterial resistance towards carbapenems has been reported in both clinical and agricultural settings worldwide. Carbapenem resistance, defined as the resistance of a bacteria towards one or more carbapenem drugs, can be mediated in either of, or a combination of, three mechanisms-although, the mechanism mediated through the production of carbapenemases (β-lactamases that are able to enzymatically degrade carbapenems) is of most significance. Of particular concern is the occurrence of carbapenemase producing Enterobacterales (CPE), with literature describing a dramatic increase in resistance globally. In South Africa, increases of carbapenemase activity occurring in Enterobacter species, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa have recently been reported. CPE can also be found in agricultural environments, as global studies have documented numerous instances of CPE presence in various animals such as pigs, cattle, seafood, horses and dogs. However, most reports of CPE occurrence in agricultural settings come from Northern America, Europe and some parts of Asia, where more extensive research has been conducted to understand the CPE phenomenon. In comparison to clinical data, there are limited studies investigating the spread of CPE in agricultural settings in Africa, highlighting the importance of monitoring CPE in livestock environments and the food chain. Further research is necessary to uncover the true extent of CPE dissemination in South Africa. This review will discuss the phenomenon of bacterial antibiotic resistance (ABR), the applications of the carbapenem drug and the occurrence of carbapenem resistance globally.
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Affiliation(s)
- Taish Ramkisson
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Diane Rip
- Department of Food Science, Stellenbosch University, Stellenbosch, 7600, South Africa
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Xu Y, Luo J, Lai W, Da J, Yang B, Luo X, Zhan L, Fei Y, Liu L, Zha Y. Multiplex lateral flow test strip for detection of carbapenemase genes using barcoded tetrahedral DNA capture probe-based biosensing interface. Mikrochim Acta 2023; 190:360. [PMID: 37606732 DOI: 10.1007/s00604-023-05903-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/04/2023] [Indexed: 08/23/2023]
Abstract
Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice.
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Affiliation(s)
- Yongjie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Jie Luo
- Department of Laboratory Medicine, Guizhou Provincial Second People's Hospital, Guiyang, 550002, Guizhou, China
| | - Wei Lai
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jingjing Da
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Bin Yang
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Xiangrong Luo
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Lin Zhan
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Ying Fei
- School of Medical Laboratory, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Lin Liu
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
| | - Yan Zha
- NHC Key Laboratory of Pulmonary Immunological Diseases, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
- Renal Division, Department of Medicine, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
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Carramaschi IN, de C Queiroz MM, da Mota FF, Zahner V. First Identification of bla NDM-1 Producing Escherichia coli ST 9499 Isolated from Musca domestica in the Urban Center of Rio de Janeiro, Brazil. Curr Microbiol 2023; 80:278. [PMID: 37436443 DOI: 10.1007/s00284-023-03393-y] [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: 02/02/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
The present study presents phenotypic and molecular characterization of a multidrug-resistant strain of Escherichia coli (Lemef26), belonging to sequence type ST9499 carrying a blaNDM-1 carbapenem resistance gene. The bacterium was isolated from a specimen of Musca domestica, collected in proximity to a hospital in Rio de Janeiro City, Brazil. The strain was identified as E. coli by matrix-assisted laser desorption-ionization time of flight mass spectrometry (Maldi-TOF-MS) and via genotypic analysis (Whole-Genome Sequencing-WGS), followed by phylogenetic analysis, antibiotic resistance profiling (using phenotypic and genotypic methods) and virulence genotyping. Interestingly, the blaNDM-1 was the only resistance determinant detected using a panel of common resistance genes, as evaluated by PCR. In contrast, WGS detected genes conferring resistance to aminoglycosides, fluoroquinolones, quinolones, trimethoprim, beta-lactams, chloramphenicol, macrolides, sulfonamide, tetracycline, lincosamide and streptogramin B. Conjugation experiments demonstrated the transfer of carbapenem resistance, via acquisition of the blaNDM-1 sequence, to a sensitive receptor strain of E. coli, indicating that blaNDM-1 is located on a conjugative plasmid (most likely of the IncA/C incompatibility group, in association with the transposon Tn3000). Phylogenetic analyses placed Lemef26 within a clade of strains exhibiting allelic and environment diversity, with the greatest level of relatedness recorded with a strain isolated from a human source suggesting a possible anthropogenic origin. Analysis of the virulome revealed the presence of fimbrial and pilus genes, including a CFA/I fimbriae (cfaABCDE), common pilus (ecpABCDER), laminin-bind fimbrae (elfADG), hemorrhagic pilus (hcpABC) and fimbrial adherence determinants (stjC) indicates the ability of strain Lemef26 to colonize animal hosts. To the best of our knowledge, this study represents the first report of blaNDM-1 carbapenemase gene in an E. coli strain isolated from M. domestica. In concordance with the findings of previous studies on the carriage of MDR bacteria by flies, the data presented herein provide support to the idea that flies may represent a convenient means (as sentinel animals) for the monitoring of environmental contamination with multidrug-resistant bacteria.
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Affiliation(s)
- Isabel N Carramaschi
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
| | - Margareth M de C Queiroz
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
| | - Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, RJ, Brazil
| | - Viviane Zahner
- Laboratório de Entomologia Médica e Forense, Instituto Oswaldo Cruz, Fiocruz, Avenida Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, Cep 21040-360, Brazil.
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Ma W, Zhu B, Wang W, Wang Q, Cui X, Wang Y, Dong X, Li X, Ma J, Cheng F, Shi X, Chen L, Niu S, Hao M. Genetic and enzymatic characterization of two novel bla NDM-36, -37 variants in Escherichia coli strains. Eur J Clin Microbiol Infect Dis 2023; 42:471-480. [PMID: 36810726 PMCID: PMC9998317 DOI: 10.1007/s10096-023-04576-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023]
Abstract
The widespread of different NDM variants in clinical Enterobacterales isolates poses a serious public health concern, which requires continuous monitoring. In this study, three E. coli strains carrying two novel blaNDM variants of blaNDM-36, -37 were identified from a patient with refractory urinary tract infection (UTI) in China. We conducted antimicrobial susceptibility testing (AST), enzyme kinetics analysis, conjugation experiment, whole-genome sequencing (WGS), and bioinformatics analysis to characterize the blaNDM-36, -37 enzymes and their carrying strains. The blaNDM-36, -37 harboring E. coli isolates belonged to ST227, O9:H10 serotype and exhibited intermediate or resistance to all β-lactams tested except aztreonam and aztreonam/avibactam. The genes of blaNDM-36, -37 were located on a conjugative IncHI2-type plasmid. NDM-37 differed from NDM-5 by a single amino acid substitution (His261Tyr). NDM-36 differed from NDM-37 by an additional missense mutation (Ala233Val). NDM-36 had increased hydrolytic activity toward ampicillin and cefotaxime relative to NDM-37 and NDM-5, while NDM-37 and NDM-36 had lower catalytic activity toward imipenem but higher activity against meropenem in comparison to NDM-5. This is the first report of co-occurrence of two novel blaNDM variants in E. coli isolated from the same patient. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of NDM enzymes.
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Affiliation(s)
- Wanshan Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Bo Zhu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Wen Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China
| | - Qian Wang
- Department of Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xiaodi Cui
- School of Clinical Medicine, Jining Medical University, Jining, China
| | - Yujiao Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiutao Dong
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaofeng Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Jianping Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Fang Cheng
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Xiaohong Shi
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No. 1 Friendship Road, Yuzhong District, Chongqing, China.
| | - Mingju Hao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, No. 16766 Jingshi Road, Lixia District, Jinan, China.
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Hajikhani B, Sameni F, Ghazanfari K, Abdolali B, Yazdanparast A, Asarehzadegan Dezfuli A, Nasiri MJ, Goudarzi M, Dadashi M. Prevalence of blaNDM-producing Acinetobacter baumannii strains isolated from clinical samples around the world; a systematic review. GENE REPORTS 2023. [DOI: 10.1016/j.genrep.2022.101728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Diversity of Bacterial Clones and Plasmids of NDM-1 Producing Escherichia coli Clinical Isolates in Central Greece. Microorganisms 2023; 11:microorganisms11020516. [PMID: 36838481 PMCID: PMC9959086 DOI: 10.3390/microorganisms11020516] [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: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The objective of the present study was to genetically characterize ten NDM-1 producing Escherichia coli isolates, recovered from patients in a hospital in Central Greece during the period 2017 to 2021.The isolates were studied by whole genome sequencing to obtain multi-locus sequencing typing (MLST), identification of blaNDM1-environment, resistome and plasmid content. MLST analysis showed the presence of eight sequence types: ST46* (two isolates), ST46, ST744, ST998, ST410, ST224, ST4380, ST683 and ST12 (one isolate each). Apart of the presence of blaNDM-1, the isolates carried a combination of various to β-lactams encoding resistance genes: blaTEM-1B, blaCTX-15, blaOXA-1, blaVIM-1, blaSHV-5, blaOXA-16, blaOXA-10 and blaVEB-1. Additionally, plurality of resistance genes to aminoglycosides, macrolides, rifamycin, phenicols, sulfonamides and tetracycline was detected. The presence of multiple replicons was observed, with predominance of IncFII and IncFIB. Analysis of blaNDM-1 genetic environment of the isolates showed that seven had 100% identity with the pS-3002cz plasmid (Accession Number KJ 958927), two with the pB-3002cz plasmid (Accession Number KJ958926) and one with the pEc19397-131 plasmid (Accession Number MG878866). Τhis latter plasmid was derived by the fusion of two, previously identified, plasmids, pAMPD2 and pLK75 (Accession Numbers CP078058 and KJ440076, respectively). The diversity of clones and plasmids of NDM-1 producing E. coli isolated from patients in Greece indicates a continuous horizontal gene transfer.
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11
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Dwivedi A, Kumar CB, Kumar A, Soni M, Sahu V, Awasthi A, Rathore G. Molecular characterization of carbapenem resistant E. coli of fish origin reveals the dissemination of NDM-5 in freshwater aquaculture environment by the high risk clone ST167 and ST361. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49314-49326. [PMID: 36773268 DOI: 10.1007/s11356-023-25639-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/26/2023] [Indexed: 02/12/2023]
Abstract
Aquatic environment can act as reservoir and disseminator of antimicrobial resistance and resistant pathogens. Novel high-risk carbapenem resistant E. coli (CREC) are continuously emerging worldwide; however, the occurrence of CREC in freshwater aquaculture environment is largely unexplored. To fill this gap, large scale sampling of freshwater pond sites and retail fish markets was done between Oct 2020 and Oct 2021 to investigate the CREC contamination in fish. The frequency of CREC contamination in the freshwater fish was 6.99% (95% CI: 3.78-10.20%). All the isolates were MDR and harbored carbapenemase encoding gene, blaNDM-5 along with other antimicrobial resistance genes (ARGs), blaTEM (64.7%), blaCTX-M-15 (35.3%), blaOXA-1 (5.9%), tet(A) (100%), sul1 (94.1%), qnrS (82.3%), cat1 (35.3%), and cat2 (23.5%). The isolates belonged to phylogroup C and showed low virulence gene profile. ERIC-PCR grouped the isolates into five clusters (I-V). The isolates of clusters I, II, and III were identified as ST167 (76.4%) and of cluster IV as ST361 (17.6%). This is the first report documenting the contamination of NDM-5 producing E. coli ST167 and ST361 of clinical/livestock lineage in freshwater fish from India. The blaNDM-5 was significantly associated with ARGs, tet(A), and sul1; and plasmid replicons, IncF, IncI1, and IncP, signifying the presence of blaNDM-5 and associated ARGs on these transferable plasmids. These findings were validated by the successful conjugal transfer of blaNDM-5 and associated ARGs into non-CREC strain (J53). Our study highlights the ability of CREC to disseminate antimicrobial resistance which has health implications and environmental concerns.
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Affiliation(s)
- Arti Dwivedi
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India.,Department of Biotechnology, Maharaja Agrasen University, Baddi, Solan, Himachal Pradesh, India
| | - Chandra Bhushan Kumar
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Anil Kumar
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Mayank Soni
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Vikash Sahu
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Abhishek Awasthi
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Solan, Himachal Pradesh, India
| | - Gaurav Rathore
- Fish Health Management and Exotics Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India.
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12
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Zwittink RD, Wielders CC, Notermans DW, Verkaik NJ, Schoffelen AF, Witteveen S, Ganesh VA, de Haan A, Bos J, Bakker J, Schneeberger-van der Linden C, Kuijper EJ, de Greeff SC, Hendrickx AP. Multidrug-resistant organisms in patients from Ukraine in the Netherlands, March to August 2022. Euro Surveill 2022; 27:2200896. [PMID: 36695467 PMCID: PMC9808315 DOI: 10.2807/1560-7917.es.2022.27.50.2200896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Since March 2022, there has been an emergence of multidrug-resistant organisms (MDRO) in the Netherlands in patients originating from Ukraine (58 patients, 75 isolates). For about half of these patients, recent hospitalisation in Ukraine was reported. Genomic surveillance revealed that the majority of the MDRO represent globally spread epidemic lineages and that 60% contain New Delhi metallo-β-lactamase (NDM) genes. Professionals should be aware of an increase in such MDRO associated with migration and medical evacuation of people from Ukraine.
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Affiliation(s)
- Romy D Zwittink
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Cornelia Ch Wielders
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Daan W Notermans
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Nelianne J Verkaik
- SWAB Working Group Surveillance of Antibiotic Resistance, Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Annelot F Schoffelen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sandra Witteveen
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Varisha A Ganesh
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Angela de Haan
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jeroen Bos
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jacinta Bakker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Ed J Kuijper
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Sabine C de Greeff
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Antoni Pa Hendrickx
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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13
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Li Y, Yan M, Xue F, Zhong W, Liu X, Chen X, Wu Y, Zhang J, Wang Q, Zheng B, Lv Y. In vitro and in vivo activities of a novel β-lactamase inhibitor combination imipenem/XNW4107 against recent clinical Gram-negative bacilli from China. J Glob Antimicrob Resist 2022; 31:1-9. [PMID: 35820591 DOI: 10.1016/j.jgar.2022.07.006] [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: 01/03/2022] [Revised: 03/22/2022] [Accepted: 07/05/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES XNW4107 is a novel β-lactamase inhibitor that possesses broad activity against serine-β-lactamases. XNW4107 in combination with imipenem exhibited potent in vitro activity against carbapenem-resistant bacteria and particularly against carbapenem-resistant Acinetobacter baumannii. This study aimed to evaluate the in vitro and in vivo antibacterial activities of imipenem/XNW4107. METHODS The minimum inhibitory concentrations, minimum bactericidal concentrations, time-kill curves, post-antibiotic effects, and spontaneous frequency of resistance were used to investigate the imipenem/XNW4107 in vitro activity. A mouse systemic infection model was used to evaluate the imipenem/XNW4107 in vivo efficacy. RESULTS MIC90 of imipenem/XNW4107 against imipenem-nonsusceptible A. baumannii (n = 106) was 8 mg/L, which was 16-fold lower than the MIC90 of imipenem; the resistance rate decreased from 90% to 20% applying the CLSI imipenem breakpoint. MIC90 of imipenem/XNW4107 against imipenem-resistant Klebsiella pneumoniae (n = 54) was 2 mg/L, which was 128-fold lower than the MIC90 of imipenem; 80% imipenem-nonsusceptible Pseudomonas aeruginosa (n = 101) exhibited MICs of imipenem/XNW4107 from 2 to 8 mg/L, which were 4- to 8-fold lower than the MICs of imipenem. Imipenem/XNW4107 was bactericidal against A. baumannii, K. pneumoniae, and Escherichia coli. The time-kill curves showed that increasing concentrations did not result in progressively increased killing at concentrations >4 × MIC. Imipenem/XNW4107 has a low potential for resistance development in tested strains except for K. pneumoniae. Imipenem/XNW4107 provided good protection against imipenem-resistant A. baumannii and K. pneumoniae in vivo. CONCLUSIONS The broad-spectrum profile and potent in vitro and in vivo antibacterial activities support imipenem/XNW4107 as a promising investigational candidate.
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Affiliation(s)
- Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Mengyao Yan
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Wei Zhong
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Xiao Liu
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Xi Chen
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Yuchuan Wu
- Suzhou Sinovent Pharmaceuticals Co., Ltd., Beijing, China
| | - Jia Zhang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Qing Wang
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Bo Zheng
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
| | - Yuan Lv
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China.
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14
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Habib A, Lo S, Villageois-Tran K, Petitjean M, Malik SA, Armand-Lefèvre L, Ruppé E, Zahra R. Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. PLoS One 2022; 17:e0270707. [PMID: 35802735 PMCID: PMC9269877 DOI: 10.1371/journal.pone.0270707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Carbapenems are considered last-line beta-lactams for the treatment of infections caused by multidrug-resistant Gram-negative bacteria. However, their activity is compromised by the rising prevalence of carbapenemase-producing Enterobacterales (CPE), which are especially marked in the Indian subcontinent. In Pakistan, previous reports have warned about the possible spread of CPE in the community, but data are still partial. This study was carried out to analyse the prevalence of CPE, the genetic characterisation, and phylogenetic links among the spreading CPE in the community. In this cohort study, we collected 306 rectal swabs from patients visiting Benazir Bhutto hospital, Rawalpindi. CPEs were screened by using ertapenem-supplemented MacConkey agar. Identification was performed by using conventional biochemical tests, and genomes were sequenced using Illumina chemistry. Antibiotic resistance genes, plasmid incompatibility groups, and Escherichia coli phylogroups were determined in silico. Sequence types were determined by using MLST tool. The prevalence of CPE carriage observed was 14.4% (44/306 samples). The most common carbapenemase-encoding gene was bla-NDM-5 (n = 58) followed by blaNDM-1 (n = 7), blaNDM (non-assigned variant, n = 4), blaOXA-181 (n = 3), blaOXA-232 (n = 3) and blaNDM-7 (n = 1). Most of the CPE were E. coli (55/64, 86%), and the genomic analysis revealed a pauciclonal diffusion of E. coli with ST167 (n = 14), 405 (n = 10), 940 (n = 8), 648 (n = 6) and 617 (n = 5). We obtained a second sample from 94 patients during their hospital stay in whom carriage was negative at admission and found that 7 (7.4%) acquired a CPE. Our results indicate that the prevalence of CPE carriage in the Pakistani urban community was high and driven by the dissemination of some E. coli clones, with ST167 being the most frequent. The high CPE carriage in the community poses a serious public health threat and calls for implementation of adequate preventive measures.
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Affiliation(s)
- Amina Habib
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Stéphane Lo
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Khanh Villageois-Tran
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Beaujon, Clichy, France
| | | | - Shaheen Akhtar Malik
- Accident and Emergency Department, Benazir Bhutto Hospital, Rawalpindi, Pakistan
| | - Laurence Armand-Lefèvre
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, Paris, France
- APHP, Laboratoire de Bactériologie, Hôpital Bichat, Paris, France
| | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- * E-mail:
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15
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Farzana R, Jones LS, Rahman MA, Sands K, van Tonder AJ, Portal E, Criollo JM, Parkhill J, Guest MF, Watkins WJ, Pervin M, Boostrom I, Hassan B, Mathias J, Kalam MA, Walsh TR. Genomic Insights Into the Mechanism of Carbapenem Resistance Dissemination in Enterobacterales From a Tertiary Public Heath Setting in South Asia. Clin Infect Dis 2022; 76:119-133. [PMID: 35412593 PMCID: PMC9825829 DOI: 10.1093/cid/ciac287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 01/12/2023] Open
Abstract
SUMMARY 10.6% patients were CRE positive. Only 27% patients were prescribed at least 1 antibiotic to which infecting pathogen was susceptible. Burn and ICU admission and antibiotics exposures facilitate CRE acquisition. Escherichia coli ST167 was the dominant CRE clone. BACKGROUND Given the high prevalence of multidrug resistance (MDR) across South Asian (SA) hospitals, we documented the epidemiology of carbapenem-resistant Enterobacterales (CRE) infections at Dhaka Medical College Hospital between October 2016 and September 2017. METHODS We enrolled patients and collected epidemiology and outcome data. All Enterobacterales were characterized phenotypically and by whole-genome sequencing. Risk assessment for the patients with CRE was performed compared with patients with carbapenem-susceptible Enterobacterales (CSE). RESULTS 10.6% of all 1831 patients with a clinical specimen collected had CRE. In-hospital 30-day mortality was significantly higher with CRE [50/180 (27.8%)] than CSE [42/312 (13.5%)] (P = .001); however, for bloodstream infections, this was nonsignificant. Of 643 Enterobacterales isolated, 210 were CRE; blaNDM was present in 180 isolates, blaOXA-232 in 26, blaOXA-181 in 24, and blaKPC-2 in 5. Despite this, ceftriaxone was the most commonly prescribed empirical antibiotic and only 27% of patients were prescribed at least 1 antibiotic to which their infecting pathogen was susceptible. Significant risk factors for CRE isolation included burns unit and intensive care unit admission, and prior exposure to levofloxacin, amikacin, clindamycin, and meropenem. Escherichia coli ST167 was the dominant CRE clone. Clustering suggested clonal transmission of Klebsiella pneumoniae ST15 and the MDR hypervirulent clone, ST23. The major trajectories involved in horizontal gene transfer were IncFII and IncX3, IS26, and Tn3. CONCLUSIONS This is the largest study from an SA public hospital combining outcome, microbiology, and genomics. The findings indicate the urgent implementation of targeted diagnostics, appropriate antibiotic use, and infection-control interventions in SA public institutions.
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Affiliation(s)
- Refath Farzana
- Correspondence: R. Farzana, Department of Zoology, University of Oxford, Oxford, United Kingdom; Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, UK ()
| | - Lim S Jones
- Public Health Wales Microbiology, University Hospital of Wales, Cardiff, United Kingdom
| | | | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Andries J van Tonder
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Edward Portal
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jose Munoz Criollo
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Martyn F Guest
- Advanced Research Computing @Cardiff (ARCCA), Cardiff University, Cardiff, United Kingdom
| | - W John Watkins
- Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Monira Pervin
- Department of Virology, Dhaka Medical College, Dhaka, Bangladesh
| | - Ian Boostrom
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Brekhna Hassan
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jordan Mathias
- Department of Medical Microbiology, Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Md Abul Kalam
- Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Timothy R Walsh
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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16
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Moser AI, Keller PM, Campos-Madueno EI, Poirel L, Nordmann P, Endimiani A. A Patient With Multiple Carbapenemase Producers Including an Unusual Citrobacter sedlakii Hosting an IncC bla NDM-1- and armA-carrying Plasmid. Pathog Immun 2022; 6:119-134. [PMID: 34988342 PMCID: PMC8714174 DOI: 10.20411/pai.v6i2.482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background. Patients colonized with multiple species of carbapenemase-producing Enterobacterales (CPE) are increasingly observed. This phenomenon can be due to the high local prevalence of these pathogens, the presence of important host risk factors, and the great genetic promiscuity of some carbapenemase genes. Methods. We analyzed 4 CPE (Escherichia coli, Klebsiella pneumoniae, Providencia stuartii, Citrobacter sedlakii), 1 extended-spectrum cephalosporin-resistant K. pneumoniae (ESC-R-Kp), and 1 carbapenemase-producing Acinetobacter baumannii simultaneously isolated from a patient transferred from Macedonia. Susceptibility tests were performed using a microdilution MIC system. The complete genome sequences were obtained by using both short-read and long-read whole-genome sequencing technologies. Results. All CPE presented high-level resistance to all aminoglycosides due to the expression of the armA 16S rRNA methylase. In C. sedlakii and E. coli (ST69), both the carbapenemase blaNDM-1 and armA genes were located on an identical IncC plasmid of type 1a. The K. pneumoniae (ST268) and P. stuartii carried chromosomal blaNDM-1 and blaOXA-48, respectively, while the ESC-R-Kp (ST395) harbored a plasmid-located blaCTX-M-15. In the latter 3 isolates, armA-harboring IncC plasmids similar to plasmids found in C. sedlakii and E. coli were also detected. The A. baumannii strain possessed the blaOXA-40 carbapenemase gene. Conclusions. The characterization of the genetic organization of IncC-type plasmids harbored by 3 different species from the same patient offered insights into the evolution of these broad-host-range plasmids. Moreover, we characterized here the first complete genome sequence of a carbapenemase-producing C. sedlakii strain, providing a reference for future studies on this rarely reported species.
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Affiliation(s)
- Aline I Moser
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Peter M Keller
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
| | - Edgar I Campos-Madueno
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laurent Poirel
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Patrice Nordmann
- Emerging Antibiotic Resistance Unit, Medical and Molecular Microbiology, Department of Medicine, University of Fribourg, Fribourg, Switzerland.,French INSERM European Unit, University of Fribourg (LEA-IAME), Fribourg, Switzerland.,National Reference Center for Emerging Antibiotic Resistance (NARA), Fribourg, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases (IFIK), University of Bern, Bern, Switzerland
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17
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Grevskott DH, Ghavidel FZ, Svanevik CS, Marathe NP. Resistance profiles and diversity of β-lactamases in Escherichia coli strains isolated from city-scale sewage surveillance in Bergen, Norway mimic clinical prevalence. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 226:112788. [PMID: 34571418 DOI: 10.1016/j.ecoenv.2021.112788] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
The aim of this study was to examine antibiotic resistance profiles and diversity of β-lactamases in Escherichia coli present within the population and the potential spread of resistant E. coli into the receiving environment using city-scale sewage surveillance. In E. coli isolates from ECC plates without antibiotics from ten influent samples (n = 300), highest resistance was observed against ampicillin (16.6%), sulfamethoxazole (9.7%) and trimethoprim (9.0%), while in effluent samples (n = 262) it was against sulfamethoxazole (11.8%), ampicillin (11.5%) and tetracycline (8.8%). All isolates (n = 123) obtained on cefotaxime-containing plates were multidrug-resistant. Several clinically important antibiotic resistance genes (ARGs) were detected in 46 E. coli isolates subjected to whole-genome sequencing, including carbapenemases like NDM-6, VIM-1 and OXA-48-variant, as well as tigecycline resistance gene tet(X4). CTX-M-15 was the most prevalent (42.9%) extended-spectrum β-lactamase among cefotaxime-resistant isolates, followed by CTX-M-27 (31.4%) and CTX-M-14 (17.1%), resembling clinical prevalence in Norway. Most of the sequenced isolates carried other clinically relevant ARGs, such as dfrA17, sul1, sul2, tet(A), aph(6)-Id, aph(3'')-Ib and aadA5. Sixteen different sequence types (STs) were identified, including ST131 (39.1%), ST38 (10.9%) and ST69 (8.7%). One E. coli isolate belonging to novel ST (ST11874) carried multiple virulence factors including genotoxin, salmochelin, aerobactin and yersiniabactin, suggesting that this isolate has potential to cause health concerns in future. Our study reveals presence of clinically relevant ARGs like blaNDM-6 and tet(X4) in pathogenic strains, which have so far not been reported from the clinics in Norway. Our study may thus, provide a framework for population-based surveillance of antibiotic resistance.
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Affiliation(s)
- Didrik H Grevskott
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Fatemeh Z Ghavidel
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Cecilie S Svanevik
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway
| | - Nachiket P Marathe
- Department of Contaminants and Biohazards, Institute of Marine Research (IMR), Bergen, Norway.
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18
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Li F, Ye K, Li X, Ye L, Guo L, Wang L, Yang J. Genetic characterization of Carbapenem-Resistant Escherichia coli from China, 2015-2017. BMC Microbiol 2021; 21:248. [PMID: 34535075 PMCID: PMC8449468 DOI: 10.1186/s12866-021-02307-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular characteristics of carbapenem-resistant Escherichia coli (CREco) remain unclear. METHODS We conducted a multi-center bacterial resistance monitoring project from 2015 to 2017.The minimum inhibitory concentrations ofCREco were determined bybroth microdilution method. The genome sequencing of CREcoisolates was performed, and single-nucleotide polymorphism (SNP) was analyzed. RESULTS A total of 144CREcoisolatescollected from 10 cities in China were involved in this study. ST167 (n = 43) is the most popular type, followed by ST410(n = 14), ST131(n = 9). There were 102 (70.83%) CREco isolates that produced various NDMs, including NDM-1 (n = 16), NDM-4(n = 1), NDM-5(n = 79), NDM-6(n = 2) and NDM-9(n = 4). In addition, 15 isolates produced KPC-2, three isolates wereIMP-4 positive, and three isolates produced OXA-48. Genetic relatedness and phylogenetic analysis showed that isolates with the same ST had a high degree of homology. Some STs (including ST167, ST410, ST131, ST46, ST405 and ST617) exhibited a trend of outbreak. CONCLUSIONS The majority of CREco belonged to ST167, followed by ST410 and ST131, and most of them carried various NDM-coding genes. The spread of high-risk clones of CREco has occurred in different regions of China.
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Affiliation(s)
- Fengtian Li
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Kun Ye
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Xin Li
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Liyan Ye
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Ling Guo
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Lifeng Wang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiyong Yang
- Laboratory Medicine Department, First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China.
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19
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Zhao QY, Zhu JH, Cai RM, Zheng XR, Zhang LJ, Chang MX, Lu YW, Fang LX, Sun J, Jiang HX. IS 26 Is Responsible for the Evolution and Transmission of blaNDM-Harboring Plasmids in Escherichia coli of Poultry Origin in China. mSystems 2021; 6:e0064621. [PMID: 34254816 PMCID: PMC8407110 DOI: 10.1128/msystems.00646-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/19/2021] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae are some of the most important pathogens responsible for nosocomial infections, which can be challenging to treat. The blaNDM carbapenemase genes, which are expressed by New Delhi metallo-β-lactamase (NDM)-producing Escherichia coli isolates, have been found in humans, environmental samples, and multiple other sources worldwide. Importantly, these genes have also been found in farm animals, which are considered an NDM reservoir and an important source of human infections. However, the dynamic evolution of blaNDM genetic contexts and blaNDM-harboring plasmids has not been directly observed, making it difficult to assess the extent of horizontal dissemination of the blaNDM gene. In this study, we detected NDM-1 (n = 1), NDM-5 (n = 24), and NDM-9 (n = 8) variants expressed by E. coli strains isolated from poultry in China from 2016 to 2017. By analyzing the immediate genetic environment of the blaNDM genes, we found that IS26 was associated with multiple types of blaNDM multidrug resistance regions, and we identified various IS26-derived circular intermediates. Importantly, in E. coli strain GD33, we propose that IncHI2 and IncI1 plasmids can fuse when IS26 is present. Our analysis of the IS26 elements flanking blaNDM allowed us to propose an important role for IS26 elements in the evolution of multidrug-resistant regions (MRRs) and in the dissemination of blaNDM. To the best of our knowledge, this is the first description of the dynamic evolution of blaNDM genetic contexts and blaNDM-harboring plasmids. These findings could help proactively limit the transmission of these NDM-producing isolates from food animals to humans. IMPORTANCE Carbapenem resistance in members of the order Enterobacterales is a growing public health problem that is associated with high mortality in developing and industrialized countries. Moreover, in the field of veterinary medicine, the occurrence of New Delhi metallo-β-lactamase-producing Escherichia coli isolates in animals, especially food-producing animals, has become a growing concern in recent years. The wide dissemination of blaNDM is closely related to mobile genetic elements (MGEs) and plasmids. Although previous analyses have explored the association of many different MGEs with mobilization of blaNDM, little is known about the evolution of various genetic contexts of blaNDM in E. coli. Here, we report the important role of IS26 in forming multiple types of blaNDM multidrug resistance cassettes and the dynamic recombination of plasmids bearing blaNDM. These results suggest that significant attention should be paid to monitoring the transmission and further evolution of blaNDM-harboring plasmids among E. coli strains of food animal origin.
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Affiliation(s)
- Qiu-Yun Zhao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jia-Hang Zhu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Run-Mao Cai
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xing-Run Zheng
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Li-Juan Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Man-Xia Chang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yue-Wei Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jian Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Hong-Xia Jiang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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20
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Feng Y, Xue G, Feng J, Yan C, Cui J, Gan L, Zhang R, Zhao H, Xu W, Li N, Liu S, Du S, Zhang W, Yao H, Tai J, Ma L, Zhang T, Qu D, Wei Y, Yuan J. Rapid Detection of New Delhi Metallo-β-Lactamase Gene Using Recombinase-Aided Amplification Directly on Clinical Samples From Children. Front Microbiol 2021; 12:691289. [PMID: 34367092 PMCID: PMC8339468 DOI: 10.3389/fmicb.2021.691289] [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: 04/06/2021] [Accepted: 06/30/2021] [Indexed: 11/26/2022] Open
Abstract
New Delhi metallo-β-lactamase, a metallo-β-lactamase carbapenemase type, mediates resistance to most β-lactam antibiotics including penicillins, cephalosporins, and carbapenems. Therefore, it is important to detect blaNDM genes in children’s clinical samples as quickly as possible and analyze their characteristics. Here, a recombinase-aided amplification (RAA) assay, which operates in a single one-step reaction tube at 39°C in 5−15 min, was established to target blaNDM genes in children’s clinical samples. The analytical sensitivity of the RAA assay was 20 copies, and the various bacterial types without blaNDM genes did not amplify. This method was used to detect blaNDM genes in 112 children’s stool samples, 10 of which were tested positive by both RAA and standard PCR. To further investigate the characteristics of carbapenem-resistant bacteria carrying blaNDM in children, 15 carbapenem-resistant bacteria (Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, Citrobacter freundii, Klebsiella oxytoca, Acinetobacter junii, and Proteus mirabilis) were isolated from the 10 samples. Notably, more than one bacterial type was isolated from three samples. Most of these isolates were resistant to cephalosporins, cefoperazone-sulbactam, piperacillin-tazobactam, ticarcillin-clavulanic acid, aztreonam, co-trimoxazole, and carbapenems. blaNDM–1 and blaNDM–5 were the two main types in these samples. These data show that the RAA assay has potential to be a sensitive and rapid blaNDM gene screening test for clinical samples. The common existence of blaNDM and multi-drug resistance genes presents major challenges for pediatric treatment.
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Affiliation(s)
| | - Guanhua Xue
- Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Hanqin Zhao
- Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Nannan Li
- Capital Institute of Pediatrics, Beijing, China
| | - Shiyu Liu
- Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Capital Institute of Pediatrics, Beijing, China
| | | | - Hailan Yao
- Capital Institute of Pediatrics, Beijing, China
| | - Jun Tai
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Lijuan Ma
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing, China
| | - Dong Qu
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Yongxiang Wei
- Children's Hospital Affiliated to Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Capital Institute of Pediatrics, Beijing, China
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21
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Sumbana JJ, Santona A, Fiamma M, Taviani E, Deligios M, Zimba T, Lucas G, Sacarlal J, Rubino S, Paglietti B. Extraintestinal Pathogenic Escherichia coli ST405 Isolate Coharboring blaNDM-5 and blaCTXM-15: A New Threat in Mozambique. Microb Drug Resist 2021; 27:1633-1640. [PMID: 34077257 DOI: 10.1089/mdr.2020.0334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The development of carbapenem resistance in extraintestinal pathogenic Escherichia coli (ExPEC) has significant clinical implications, particularly in countries where second-line antimicrobials are not readily available, rendering treatments ineffective, and ExPEC infections untreatable. Thus, early detection of high-risk ExPEC lineages and raising awareness of the specific mechanisms underlying carbapenem resistance are mandatory for the selection of appropriate treatment options and the prevention of E. coli spread. This study aims to investigate the phenotypic and genotypic features of the first NDM-5 carbapenemase-producing ExPEC strain isolated from the blood of a patient admitted to the Maputo Central Hospital (MCH), in Mozambique. E. coli SSM100 isolate was identified by MALDI-TOF, it displayed high-level resistance to third generation cephalosporins, carbapenems, fluoroquinolones, and aminoglycosides, performing antimicrobial susceptibilities testing by VITEK 2 system. E. coli SSM100 isolate was classified through whole-genome sequencing as ST405-D-O102: H6, a globally distributed lineage associated with antimicrobial resistance, carrying the blaNDM-5 gene located on an F1:A1:B49 plasmid, coharboring blaCTX-M-15, blaTEM-1, aadA2, sul1, and dfrA12 genes. In addition, mutations in gyrA (S83L and D87N), parC (S80I and E84V), and parE (I529L) conferring fluoroquinolone resistance were also found. Moreover, SSM100 isolate carried 88 virulence genes, of which 28 are reported to be associated with UPEC. The emergence of NDM-5 carbapenemase in a pandemic ST405-D-O102:H6 clone in Mozambique is of great concern. Locations of extended-spectrum β-lactamase determinants and NDM-5 carbapenemase gene on IncF-plasmid can increase their spread reinforcing the need for antimicrobial surveillance and the urgent introduction of carbapenemase detection tests in diagnostic laboratories of the country.
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Affiliation(s)
- José João Sumbana
- Department of Biological Sciences, Eduardo Mondlane University, Maputo, Mozambique.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonella Santona
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Elisa Taviani
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Center of Biotechnology, Eduardo Mondlane University, Maputo, Mozambique
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | | | - Jahit Sacarlal
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo, Mozambique
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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22
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Grünzweil OM, Palmer L, Cabal A, Szostak MP, Ruppitsch W, Kornschober C, Korus M, Misic D, Bernreiter-Hofer T, Korath ADJ, Feßler AT, Allerberger F, Schwarz S, Spergser J, Müller E, Braun SD, Monecke S, Ehricht R, Walzer C, Smodlaka H, Loncaric I. Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals. Int J Mol Sci 2021; 22:ijms22115905. [PMID: 34072783 PMCID: PMC8199236 DOI: 10.3390/ijms22115905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.
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Affiliation(s)
- Olivia M. Grünzweil
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Lauren Palmer
- Marine Mammal Care Center, Los Angeles, CA 90731, USA;
| | - Adriana Cabal
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Michael P. Szostak
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Christian Kornschober
- Austrian Agency for Health and Food Safety (AGES), National Reference Centre for Salmonella, 8010 Graz, Austria;
| | - Maciej Korus
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Dusan Misic
- Department of Functional Food Products Development, Faculty of Biotechnology and Food Science, Wroclaw University of Environmental and Life Sciences, 51-630 Wroclaw, Poland; (M.K.); (D.M.)
| | - Tanja Bernreiter-Hofer
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna D. J. Korath
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Andrea T. Feßler
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute of Medical Microbiology and Hygiene, 1090 Vienna, Austria; (A.C.); (W.R.); (F.A.)
| | - Stefan Schwarz
- Centre for Infection Medicine, Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany; (A.T.F.); (S.S.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
| | - Elke Müller
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Sascha D. Braun
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
| | - Stefan Monecke
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute for Medical Microbiology and Hygiene, Technical University of Dresden, 01307 Dresden, Germany
| | - Ralf Ehricht
- Leibniz Institute of Photonic Technology (IPHT), 07745 Jena, Germany; (E.M.); (S.D.B.); (S.M.); (R.E.)
- InfectoGnostics Research Campus, 07743 Jena, Germany
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Chris Walzer
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, 1160 Vienna, Austria;
- Health Program, Wildlife Conservation Society, Bronx, New York City, NY 10460, USA
| | - Hrvoje Smodlaka
- College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA;
| | - Igor Loncaric
- Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria; (O.M.G.); (M.P.S.); (T.B.-H.); (A.D.J.K.); (J.S.)
- Correspondence: ; Tel.: +43-125-077-2115
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23
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Activity of β-Lactam Antibiotics against Metallo-β-Lactamase-Producing Enterobacterales in Animal Infection Models: a Current State of Affairs. Antimicrob Agents Chemother 2021; 65:AAC.02271-20. [PMID: 33782001 DOI: 10.1128/aac.02271-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metallo-β-lactamases (MBLs) result in resistance to nearly all β-lactam antimicrobial agents, as determined by currently employed susceptibility testing methods. However, recently reported data demonstrate that variable and supraphysiologic zinc concentrations in conventional susceptibility testing media compared with physiologic (bioactive) zinc concentrations may be mediating discordant in vitro-in vivo MBL resistance. While treatment outcomes in patients appear suggestive of this discordance, these limited data are confounded by comorbidities and combination therapy. To that end, the goal of this review is to evaluate the extent of β-lactam activity against MBL-harboring Enterobacterales in published animal infection model studies and provide contemporary considerations to facilitate the optimization of current antimicrobials and development of novel therapeutics.
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24
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Costa A, Figueroa-Espinosa R, Gaudenzi F, Lincopan N, Fuga B, Ghiglione B, Gutkind G, Di Conza J. Co-Occurrence of NDM-5 and RmtB in a Clinical Isolate of Escherichia coli Belonging to CC354 in Latin America. Front Cell Infect Microbiol 2021; 11:654852. [PMID: 33996632 PMCID: PMC8117236 DOI: 10.3389/fcimb.2021.654852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/14/2021] [Indexed: 11/15/2022] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-producing isolates are usually resistant to most β-lactams and other antibiotics as a result of the coexistence of several resistance markers, and they cause a variety of infections associated to high mortality rates. Although NDM-1 is the most prevalent one, other variants are increasing their frequency worldwide. In this study we describe the first clinical isolate of NDM-5- and RmtB-producing Escherichia coli in Latin America. E. coli (Ec265) was recovered from a urine sample of a female outpatient. Phenotypical and genotypical characterization of resistance markers and conjugation assays were performed. Genetic analysis of Ec265 was achieved by whole genome sequencing. Ec265 belonging to ST9693 (CC354), displayed resistance to most β-lactams (including carbapenems), aminoglycosides (gentamicin and amikacin), and quinolones. Several resistance genes were found, including blaNDM-5 and rmtB, located on a conjugative plasmid. blaNDM-5 genetic context is similar to others found around the world. Co-transfer of multiple antimicrobial resistance genes represents a particular challenge for treatment in clinical settings, whereas the spread of pathogens resistant to last resort antibiotics should raise an alarm in the healthcare system worldwide.
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Affiliation(s)
- Agustina Costa
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Roque Figueroa-Espinosa
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Florencia Gaudenzi
- Laboratorio de Bacteriología, Hospital Central de San Isidro "Dr. Melchor Ángel Posse, ", Martínez, Argentina
| | - Nilton Lincopan
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Barbara Ghiglione
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriel Gutkind
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - José Di Conza
- Laboratorio de Resistencia Bacteriana, Instituto de Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
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25
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Ramakrishnan V, Marialouis XA, Sankarasubramanian J, Santhanam A, Balakrishnan AS. Whole Genomic analysis of a clinical isolate of Uropathogenic Escherichia coli strain of Sequence Type - 101 carrying the drug resistance NDM-7 in IncX3 plasmid. Bioinformation 2021; 17:126-131. [PMID: 34393427 PMCID: PMC8340689 DOI: 10.6026/97320630017126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/31/2020] [Accepted: 01/26/2021] [Indexed: 11/30/2022] Open
Abstract
The emerging NDM-producing Enterobactereciae is a major threat to public health. The association of NDM-7 with sequence type 101 E.coli is identified in very few numbers. Therefore, it is of interest to analyse the whole genome sequence of NDM-producing uropathogenic E. coli XA31 that was found to carry numerous drug resistance genes of different antibiotic classes. The isolate E. coli belongs to ST-101 carrying blaNDM-7 coexisting with several resistance genes blaOXA-1, blaTEM1-A, blaCTX-M15, aac(6')-Ib-cr, catB3, tetB. Resfinder predicts this and four other plasmid replicons were identified using the Plasfinder in the CGE platform. The high transferable IncX3 plasmid was found to carry the NDM-7 gene. Thus, we the report the combination of NDM-7-ST101-IncX3 in India. The combination of this epidemic clone with NDM-7 is highly required to develop an effective infection control strategy.
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Affiliation(s)
- Venkatesan Ramakrishnan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Xavier Alexander Marialouis
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
- National Institute of Pharmaceutical Education and Research, 168, Manicktala Main Road, Kolkata 700054, West Bengal, India
| | - Jagadesan Sankarasubramanian
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
| | - Amutha Santhanam
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
- National Centre for Nanoscience and Nanotechnology, University of Madras, Guindy Campus, Chennai 600025, Tamil Nadu, India
| | - Anand Setty Balakrishnan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai 625021, Tamil Nadu, India
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26
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Touati A, Manseur L, Mehidi I, Mairi A. Epidemiological and Genetic Features of Plasmids Carrying blaNDM Genes: An In Silico Analysis with Emphasis on Replicon Types, and Resistome. Microb Drug Resist 2021; 27:1232-1242. [PMID: 33417812 DOI: 10.1089/mdr.2020.0427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase that has been disseminated worldwide. Plasmids harboring the blaNDM gene belonged to many incompatibility groups, of which IncX3, IncF, and IncA/C were the most represented. This in silico study aimed at analyzing a set of 649 plasmids carrying NDM-type carbapenemase (pNDMs) previously assigned in GenBank. Materials and Methods: The selected plasmids were analyzed by ResFinder (antibiotic resistome identification), BacMet (metal/biocides resistome identification), PlasmidFinder/PLSDB (replicon typing), TAfinder (toxin-antitoxin system [TAS] identification), and OriTfinder (prediction of the transferability). Results: We found that Escherichia coli and Klebsiella pneumoniae amounted to about 68.6% of all reported species. The distribution of these plasmids by samples showed a diversity of origins. Many plasmids carried different genes encoding resistance to antibiotics, heavy metals, and biocides with different frequencies. The TAfinder allowed the identification of a TAS in 292 plasmids (45%). Twenty-four different incompatibility groups were predicted, of which IncX3 (34.2%; n = 222), IncC (10.9%, n = 71), and IncFII (9.9%, n = 64) were the most often described. Besides, 23.6% (n = 151) of pNDMs were recognized as multireplicon plasmids. Conclusion: This study has shown the importance of plasmids in the dissemination of the NDM carbapenemase and raises the importance of monitoring these elements to better understand the evolution of the antibiotic resistance threat.
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Affiliation(s)
- Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Lyticia Manseur
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Imene Mehidi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Assia Mairi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
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Wang M, Wang W, Niu Y, Liu T, Li L, Zhang M, Li Z, Su W, Liu F, Zhang X, Xu H. A Clinical Extensively-Drug Resistant (XDR) Escherichia coli and Role of Its β-Lactamase Genes. Front Microbiol 2020; 11:590357. [PMID: 33362736 PMCID: PMC7758502 DOI: 10.3389/fmicb.2020.590357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
An extensively-drug resistant (XDR) Escherichia coli W60 was isolated from the urine sample of a patient. The genetic basis for its XDR phenotype was investigated, particularly the basis for its resistance toward β-lactam/BLI (β-Lactamase Inhibitor) combinations. Following determination of the XDR phenotype, third generation genomic sequencing was performed to identify genetic structures in E. coli W60. Further cloning analysis was performed to identify determinants of β-lactam/BLI combination resistance. It was found that E. coli W60 is resistant to nearly all of the tested antibiotics including all commonly used β-lactam/BLI combinations. Analysis of the genomic structures in E. coli W60 showed two novel transferable plasmids are responsible for the resistance phenotypes. Further genetic analysis showed bla NDM-5 leads to high resistance to β-lactam/BLI combinations, which was enhanced by co-expressing ble MBL. pECW602 harbors a truncated bla TEM that is not functional due to the loss of the N-terminal signal peptide coding region. Research performed in this work leads to several significant conclusions: the XDR phenotype of E. coli W60 can be attributed to the presence of transferable multidrug resistance plasmids; NDM-5 confers high resistance to β-lactam/BLI combinations; co-expression of ble MBL enhances resistance caused by NDM-5; the signal peptides of TEM type β-lactamases are essential for their secretion and function. Findings of this work show the danger of transferable multidrug resistance plasmids and metallo-β-lactamases, both of which should be given more attention in the analysis and treatment of multidrug resistant pathogens.
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Affiliation(s)
- Mingyu Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenjia Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yu Niu
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Ting Liu
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Ling Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Mengge Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ziyun Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Wenya Su
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Fangyue Liu
- Shandong Shian Chemical Co., Ltd., Dezhou, China
| | - Xuhua Zhang
- Laboratory Medicine Center, The Second Hospital of Shandong University, Jinan, China
| | - Hai Xu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
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Pharmacodynamics of the Novel Metallo-β-Lactamase Inhibitor ANT2681 in Combination with Meropenem for the Treatment of Infections Caused by NDM-Producing Enterobacteriaceae. Antimicrob Agents Chemother 2020; 64:AAC.01076-20. [PMID: 32778549 DOI: 10.1128/aac.01076-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Enterobacteriaceae that produce metallo-β-lactamases (MBLs) are an emerging threat to public health. The metallo-β-lactamase inhibitor (MBLi) ANT2681 inhibits the enzymatic activity of MBLs through interaction with the dinuclear zinc ion cluster present in the active site that is common to these enzymes. ANT2681 is being codeveloped, with meropenem as the partner β-lactam, as a novel combination therapy for infections caused by MBL-producing bacteria. The pharmacokinetics/pharmacodynamics of meropenem-ANT2681 were studied in a murine neutropenic thigh model of NDM-producing Enterobacteriaceae Dose-ranging studies were performed with both meropenem and ANT2681. Dose fractionation experiments were performed to identify the relevant pharmacodynamic index of ANT2681 when coadministered with meropenem. A background of meropenem at 50 mg/kg of body weight every 4 h (q4h) subcutaneously (s.c.) had minimal antibacterial effect. On this background, half-maximal effect was observed with an ANT2681 dose of 89 mg/kg q4h intravenously (i.v.). The dose fractionation study showed that area under the concentration-time curve (AUC) was the relevant pharmacodynamic index for the inhibitor. The magnitude of the meropenem-ANT2681 exposure required to achieve stasis was explored using 5 NDM-producing strains. A 3-dimensional surface fitted to the pharmacodynamic data from the 5 strains suggested that stasis was achieved with an fT > potentiated meropenem MIC of 40% and ANT2681 AUC of 700 mg · h/liter. These data and analyses provide the underpinning evidence for the combined use of meropenem and ANT2681 for clinical infections.
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Gupta V, Singh M, Datta P, Goel A, Singh S, Prasad K, Chander J. Detection of various beta-Lactamases in Escherichia coli and Klebsiella sp.: A study from Tertiary Care Centre of North India. Indian J Med Microbiol 2020; 38:390-396. [PMID: 33154252 DOI: 10.4103/ijmm.ijmm_20_253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Objective The emergence of carbapenem-resistant Escherichia coli and Klebsiella species is a global threat. We aimed to compare two phenotypic methods and evaluate the genotypic method for the detection of beta-lactamases produced by E. coli and Klebsiella spp. Materials and Methods One hundred and twenty-six E. coli and Klebsiella isolates were examined for phenotypic production of beta-lactamases by using disc diffusion, combined disc test (CDT) and modified carbapenem inactivation method (mCIM). All strains were also studied for the presence of various genes by polymerase chain reaction. Results Out of 126 isolates, 96% of the isolates were extended-spectrum β-lactamase (ESBL) producers based on the presence of various ESBL genes. CDT method showed higher number of total (89%) carbapenemases in comparison to mCIM (81%). Among carbapenemases none of the isolates were Klebsiella pneumoniae carbapenemase producer by CDT, while 69% isolates were metallo-beta-lactamase (MBL) producers. Another method, mCIM/ethylene diamine tetraacetic acid mCIM showed 100% agreement for MBL detection. As regards, AmpC and class D carbapenemases; 0.04% and 16% positivity was detected, respectively, based on CDT method. Molecular analysis revealed 91% of the isolates harbouring carbapenemase genes. blaNDMwas the most common gene detected followed byblaOXA-48. Nine of the blaNDM-positive isolates also possessed blaOXA-48gene. Conclusion Our finding shows high percentages of ESBL and carbapenemases in E. coli and Klebsiella spp. Among phenotypic methods, CDT seems to be a better choice as prevalence of carbapenemases shows lots of variation in our country. For Class B enzymes, both CDT and mCIM/eCIM can be used in the routine laboratories.
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Affiliation(s)
- Varsha Gupta
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Meenakshi Singh
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Priya Datta
- Department of Microbiology, Government Medical College and Hospital; Department of Parasitology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Anku Goel
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Sanjay Singh
- Department of Microbiology, Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kashinath Prasad
- Department of Microbiology, Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Jagdish Chander
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
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30
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New Delhi metallo-β-lactamase-1 inhibitors for combating antibiotic drug resistance: recent developments. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02580-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Argimón S, Masim MAL, Gayeta JM, Lagrada ML, Macaranas PKV, Cohen V, Limas MT, Espiritu HO, Palarca JC, Chilam J, Jamoralin MC, Villamin AS, Borlasa JB, Olorosa AM, Hernandez LFT, Boehme KD, Jeffrey B, Abudahab K, Hufano CM, Sia SB, Stelling J, Holden MTG, Aanensen DM, Carlos CC. Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines. Nat Commun 2020; 11:2719. [PMID: 32483195 PMCID: PMC7264328 DOI: 10.1038/s41467-020-16322-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022] Open
Abstract
National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.
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Affiliation(s)
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Melissa A L Masim
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - June M Gayeta
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Marietta L Lagrada
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Polle K V Macaranas
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Victoria Cohen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Marilyn T Limas
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Holly O Espiritu
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Janziel C Palarca
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Jeremiah Chilam
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Manuel C Jamoralin
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Alfred S Villamin
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Janice B Borlasa
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Agnettah M Olorosa
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Lara F T Hernandez
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Karis D Boehme
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - Benjamin Jeffrey
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
| | - Charmian M Hufano
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
- St. Luke's Medical Center-Global City, Taguig, Metro Manila, The Philippines
| | - Sonia B Sia
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | | | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Celia C Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines.
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32
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Critical analysis of antibacterial agents in clinical development. Nat Rev Microbiol 2020; 18:286-298. [PMID: 32152509 DOI: 10.1038/s41579-020-0340-0] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 12/26/2022]
Abstract
The antibacterial agents currently in clinical development are predominantly derivatives of well-established antibiotic classes and were selected to address the class-specific resistance mechanisms and determinants that were known at the time of their discovery. Many of these agents aim to target the antibiotic-resistant priority pathogens listed by the WHO, including Gram-negative bacteria in the critical priority category, such as carbapenem-resistant Acinetobacter, Pseudomonas and Enterobacterales. Although some current compounds in the pipeline have exhibited increased susceptibility rates in surveillance studies that depend on geography, pre-existing cross-resistance both within and across antibacterial classes limits the activity of many of the new agents against the most extensively drug-resistant (XDR) and pan-drug-resistant (PDR) Gram-negative pathogens. In particular, cross-resistance to unrelated classes may occur by co-selection of resistant strains, thus leading to the rapid emergence and subsequent spread of resistance. There is a continued need for innovation and new-class antibacterial agents in order to provide effective therapeutic options against infections specifically caused by XDR and PDR Gram-negative bacteria.
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Abstract
β-Lactam antibiotics have been widely used as therapeutic agents for the past 70 years, resulting in emergence of an abundance of β-lactam-inactivating β-lactamases. Although penicillinases in Staphylococcus aureus challenged the initial uses of penicillin, β-lactamases are most important in Gram-negative bacteria, particularly in enteric and nonfermentative pathogens, where collectively they confer resistance to all β-lactam-containing antibiotics. Critical β-lactamases are those enzymes whose genes are encoded on mobile elements that are transferable among species. Major β-lactamase families include plasmid-mediated extended-spectrum β-lactamases (ESBLs), AmpC cephalosporinases, and carbapenemases now appearing globally, with geographic preferences for specific variants. CTX-M enzymes include the most common ESBLs that are prevalent in all areas of the world. In contrast, KPC serine carbapenemases are present more frequently in the Americas, the Mediterranean countries, and China, whereas NDM metallo-β-lactamases are more prevalent in the Indian subcontinent and Eastern Europe. As selective pressure from β-lactam use continues, multiple β-lactamases per organism are increasingly common, including pathogens carrying three different carbapenemase genes. These organisms may be spread throughout health care facilities as well as in the community, warranting close attention to increased infection control measures and stewardship of the β-lactam-containing drugs in an effort to control selection of even more deleterious pathogens.
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Takayama Y, Sekizuka T, Matsui H, Adachi Y, Eda R, Nihonyanagi S, Wada T, Matsui M, Suzuki S, Takaso M, Kitasato H, Kuroda M, Hanaki H. Characterization of the IncFII-IncFIB(pB171) Plasmid Carrying bla NDM-5 in Escherichia coli ST405 Clinical Isolate in Japan. Infect Drug Resist 2020; 13:561-566. [PMID: 32110066 PMCID: PMC7035895 DOI: 10.2147/idr.s232943] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/19/2020] [Indexed: 12/02/2022] Open
Abstract
Purpose New Delhi metallo-β-lactamase 5 (NDM-5) shows stronger resistance to carbapenems and broad-spectrum cephalosporins than NDM-1 because NDM-5 differs from NDM-1 by two amino acid substitutions. In this study, our aim was to characterize a NDM-5-producing Escherichia coli isolate KY1497 from a patient with urinary tract infection in Japan, who had no recent history of overseas travel. Patients and Methods NDM-5-producing E. coli isolate KY1497 was detected in the urine sample of a patient hospitalized in a tertiary hospital in Japan. The complete genome sequence of isolate KY1497 was determined by short- and long-read sequencing with hybrid assembly, followed by multilocus sequence typing (MLST), core-genome phylogeny analysis, plasmid analysis, and transconjugation experiments. Results KY1497 was classified as ST405 by MLST, and core-genome phylogeny exhibited the closest lineage to the clinical isolates in Nepal (IOMTU605) and Canada (FDAARGOS_448). KY1497 harbors blaNDM-5 in the IncFII-IncFIB(pB171) replicon plasmid (pKY1497_1, 123,767 base pairs). Plasmid analysis suggested that the cognate plasmids of pKY1497_1 have a minor plasmid background, rather than the globally disseminated IncX3 plasmid carrying blaNDM-5. Transconjugation analysis revealed that pKY1497_1 is transmissible to the recipient E. coli J53 strain. Conclusion We characterized a novel Inc replicon plasmid (IncFII-IncFIB[pB171]) carrying blaNDM-5 and its host E. coli strain. NDMs are associated with a high risk of infection worldwide because of their antibiotic resistance and untreatable and hard-to-treat infections. Other patients in the hospital showed negative results for carbapenem-resistant Enterobacteriaceae. As NDM-producing strains are only sporadically detected in Japan, attention should be provided to the community prevalence of NDM-producing E. coli strains to prevent nosocomial infections.
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Affiliation(s)
- Yoko Takayama
- Department of Infection Control and Infectious Diseases, Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Kanagawa, Japan.,Department of Infection Control and Prevention, Kitasato University Hospital, Kanagawa, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hidehito Matsui
- Infection Control Research Center, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Yuzuru Adachi
- Infection Control Research Center, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
| | - Ryotaro Eda
- Department of Microbiology, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
| | - Shin Nihonyanagi
- Department of Infection Control and Prevention, Kitasato University Hospital, Kanagawa, Japan
| | - Tatsuhiko Wada
- Department of Infection Control and Prevention, Kitasato University Hospital, Kanagawa, Japan
| | - Mari Matsui
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satowa Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masashi Takaso
- Department of Orthopaedic Surgery, Kitasato University School of Medicine, Kanagawa, Japan
| | - Hidero Kitasato
- Department of Microbiology, School of Allied Health Sciences, Kitasato University, Kanagawa, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hideaki Hanaki
- Infection Control Research Center, Kitasato Institute for Life Sciences, Kitasato University, Tokyo, Japan
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High Prevalence of CTX-M Type Extended-Spectrum Beta-Lactamase Genes and Detection of NDM-1 Carbapenemase Gene in Extraintestinal Pathogenic Escherichia coli in Cuba. Pathogens 2020; 9:pathogens9010065. [PMID: 31963265 PMCID: PMC7168674 DOI: 10.3390/pathogens9010065] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/21/2022] Open
Abstract
Increase of extraintestinal pathogenic Escherichia coli (ExPEC) showing resistance to beta-lactams is a major public health concern. This study was conducted as a first molecular epidemiological study on ExPEC in Cuba, regarding prevalence of extended-spectrum beta-lactamases (ESBLs) and carbapenemase genes. A total of 306 ExPEC isolates collected in medical institutions in 16 regions in Cuba (2014–2018) were analyzed for their genotypes and presence of genes encoding ESBL, carbapenemase, plasmid-mediated quinolone resistance (PMQR) determinants by PCR and sequencing. The most common phylogenetic group of ExPEC was B2 (49%), followed by D (23%), A (21%), and B1 (7%). Among ESBL genes detected, blaCTX-M was the most common and detected in 61% of ExPEC, with blaCTX-M-15 being dominant and distributed to all the phylogenetic groups. NDM-1 type carbapenemase gene was identified in two isolates of phylogenetic group B1-ST448. Phylogenetic group B2 ExPEC belonged to mostly ST131 (or its single-locus variant) with O25b allele, harboring blaCTX-M-27, and included an isolate of emerging type ST1193. aac (6’)-Ib-cr was the most prevalent PMQR gene (40.5%), being present in 54.5% of CTX-M-positive isolates. These results indicated high prevalence of CTX-M genes and the emergence of NDM-1 gene among recent ExPEC in Cuba, depicting an alarming situation.
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San N, Aung MS, Urushibara N, San T, Maw WW, Lwin MM, Mar TT, Myint YY, Thu PP, Hlaing MS, Ganesh B, Kobayashi N. Genetic Diversity of CMY Beta-Lactamase Genes in Clinical Isolates of Escherichia coli in Myanmar: Identification of Three Novel Types and Updated Phylogenetic Classification of blaCMY. Microb Drug Resist 2019; 26:497-504. [PMID: 31738628 DOI: 10.1089/mdr.2019.0234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The dissemination of CMY-type enzymes, one of the plasmid-mediated AmpC beta-lactamases, among Enterobacteriaceae has become an important public health concern. In this study, genetic diversity of CMY beta-lactamase genes was investigated for 50 blaCMY-positive isolates detected from 426 clinical isolates of Escherichia coli in Yangon, Myanmar. CMY genes were differentiated into 9 types, with blaCMY-42 being predominant (22 isolates, 44%), followed by blaCMY-2, blaCMY-6, blaCMY-146, and included three novel types (CMY-156, CMY-158, CMY-159). Among E. coli harboring blaCMY, phylogenetic group D-sequence type (ST)405 and A-ST410 were the most common genotypes, and blaCTX-M-15 was detected in 72% (36/50) of isolates. blaCMY-42 was distributed to phylogenetic groups A, B1, and D E. coli with 11 STs, which included 10 isolates harboring carbapenemase genes (blaNDM-4, blaNDM-5, or blaNDM-7). Phylogenetic analysis of all the blaCMY genes reported to date, including the three novel types in the present study, revealed the presence of at least four distinct genetic groups, that is, CMY-1, CMY-2, CMY-70, and CMY-98 group, showing less than 91% nucleotide sequence identities among different groups. CMY-2 group beta-lactamase genes, which contained by far the largest number of CMY types (89.7%) with extensive diversity, were divided into two clusters (I and II). While eight CMY types identified in the present study were classified into CMY-2 group cluster I, novel type CMY-159 was assigned into CMY-98 group with a Citrobacter freundii strain in Thailand.
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Affiliation(s)
- Nilar San
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Thida San
- Yangon Children's Hospital, Ministry of Health and Sports, Yangon, Myanmar
| | - Win Win Maw
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Mya Mya Lwin
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Thin Thin Mar
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Yi Yi Myint
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Pyae Phyo Thu
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | - Myat Su Hlaing
- Department of Microbiology, University of Medicine 2, Yangon, Myanmar
| | | | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan
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