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Li X, Li C, Zhou L, Wang Q, Yao J, Zhang X, Yu Y, Li R, Zhou H, Tu Y. Global phylogeography and genomic characterization of bla KPC and bla NDM-positive clinical Klebsiella aerogenes isolates from China, 2016-2022. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 923:171560. [PMID: 38458455 DOI: 10.1016/j.scitotenv.2024.171560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/03/2024] [Accepted: 03/05/2024] [Indexed: 03/10/2024]
Abstract
Carbapenem-resistant Klebsiella aerogenes (CRKA), being one of the members of carbapenem-resistant Enterobacteriaceae (CRE), has caused great public health concern, but with fewer studies compared to other CRE members. Furthermore, studies on phylogenetic analysis based on whole genome Single-Nucleotide Polymorphism (SNP) of CRKA were limited. Here, 20 CRKA isolates (11 blaKPC-2-bearing and 9 blaNDM-1/5-harboring) were characterized by antimicrobial susceptibility testing, conjugation assay, whole genome sequencing (WGS) and bioinformatics analysis. Additionally, the phylogeographic relationships of K. aerogenes were further investigated from public databases. All isolates were multidrug-resistant (MDR) bacteria, and they demonstrated susceptibility to colistin. Most blaKPC-2 or blaNDM-1/5-carrying plasmids were found to be conjugative. Phylogenetic analysis revealed the clonal dissemination of K. aerogenes primarily occurred within clinical settings. Notably, some strains in this study showed the potential for clonal transmission, sharing few SNPs between K. aerogenes and KPC- and/or NDM-positive K. aerogenes isolated from various countries. The STs of K. aerogenes strains had significant diversity. WGS analysis showed that the IncFIIK plasmid was the most prevalent carrier of blaKPC-2, and, blaNDM-1/5 were detected on the IncX3 plasmids. The Tn6296 and Tn3000 transposons were most common vehicles for facilitating the transmission of blaKPC-2 and blaNDM-1/5, respectively. This study highlights the importance of continuous screening and surveillance by WGS for analysis of drug-resistant strains in hospital settings, and provide clinical information that supports epidemiological and public health research on human pathogens.
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Affiliation(s)
- Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Changan Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Longjie Zhou
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Qiaojun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiayao Yao
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Xiaofan Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, China
| | - Yunsong Yu
- Center for General Practice Medicine, Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, 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, Jiangsu 225009, China.
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China.
| | - Yuexing Tu
- Department of Critical Care Medicine, Tongde Hospital of Zhejiang Province, #234 Gucui Road, Hangzhou, Zhejiang 310012, China.
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Wang Y, Sapula SA, Whittall JJ, Blaikie JM, Lomovskaya O, Venter H. Identification and characterization of CIM-1, a carbapenemase that adds to the family of resistance factors against last resort antibiotics. Commun Biol 2024; 7:282. [PMID: 38454015 PMCID: PMC10920655 DOI: 10.1038/s42003-024-05940-0] [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: 05/02/2023] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
The increasing rate of carbapenem-resistant bacteria within healthcare environments is an issue of great concern that needs urgent attention. This resistance is driven by metallo-β-lactamases (MBLs), which can catalyse the hydrolysis of almost all clinically available β-lactams and are resistant to all the clinically utilized β-lactamase inhibitors. In this study, an uncharacterized MBL is identified in a multidrug resistant isolate of the opportunistic pathogen, Chryseobacterium indologenes. Sequence analysis predicts this MBL (CIM-1) to be a lipoprotein with an atypical lipobox. Characterization of CIM-1 reveals it to be a high-affinity carbapenemase with a broad spectrum of activity that includes all cephalosporins and carbapenems. Results also shown that CIM-1 is potentially a membrane-associated MBL with an uncharacterized lipobox. Using prediction tools, we also identify more potentially lipidated MBLs with non-canonical lipoboxes highlighting the necessity of further investigation of lipidated MBLs.
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Affiliation(s)
- Yu Wang
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
- School of Biomedical Science, University of Adelaide, Adelaide, Australia
| | - Sylvia A Sapula
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Jonathan J Whittall
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | - Jack M Blaikie
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia
| | | | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, Australia.
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Ma L, Qu Y, Wang W, Wang D. Characterization of Klebsiella pneumoniae carrying the blaNDM-1 gene in IncX3 plasmids and the rare In1765 in an IncFIB-IncHI1B plasmid. Front Cell Infect Microbiol 2024; 13:1324846. [PMID: 38274736 PMCID: PMC10808583 DOI: 10.3389/fcimb.2023.1324846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Background Today, the blaNDM gene is widely distributed on several plasmids from a variety of Gram-negative bacteria, primarily in transposons and gene cassettes within their multidrug-resistant (MDR) regions. This has led to the global dissemination of the blaNDM gene. Methods The determination of class A beta-lactamase, class B and D carbapenemases was performed according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). Antimicrobial susceptibility testing was performed using both the BioMerieux VITEK2 system and antibiotic paper diffusion methods. Plasmid transfer was then evaluated by conjugation experiments and plasmid electroporation assays. To comprehensively analyze the complete genome of K. pneumoniae strain F11 and to investigate the presence of mobile genetic elements associated with antibiotic resistance and virulence genes, Nanopore and Illumina sequencing platforms were used, and bioinformatics methods were applied to analyze the obtained data. Results Our findings revealed that K. pneumoniae strain F11 carried class A beta-lactamase and classes B+D carbapenemases, and exhibited resistance to commonly used antibiotics, particularly tigecycline and ceftazidime/avibactam, due to the presence of relevant resistance genes. Plasmid transfer assays demonstrated successful recovery of plasmids pA_F11 and pB_F11, with average conjugation frequencies of 2.91×10-4 and 1.56×10-4, respectively. However, plasmids pC_F11 and pD_F11 failed in both conjugation and electroporation experiments. The MDR region of plasmid pA_F11 contained rare In1765, TnAs2, and TnAs3 elements. The MDR2 region of plasmid pB_F11 functioned as a mobile genetic "island" and lacked the blaNDM-1 gene, serving as a "bridge" connecting the early composite structure of bleMBL and blaNDM-1 to the recent composite structure. Additionally, the MDR1 region of plasmid pB_F11 comprised In27, TnAs1, TnAs3, and Tn2; and plasmid pC_F11 harbored the recent composite structure of bleMBL and blaNDM-1 within Tn3000 which partially contained partial Tn125. Conclusion This study demonstrated that complex combinations of transposons and integron overlaps, along with the synergistic effects of different drug resistance and virulence genes, led to a lack of effective therapeutic agents for strain F11, therefore its dissemination and prevalence should be strictly controlled.
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Affiliation(s)
- Liman Ma
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Ying Qu
- Department of Clinical Medicine Laboratory, Taizhou Municipal Hospital Affiliated with Taizhou University, Taizhou, Zhejiang, China
| | - Wenji Wang
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
- School of Life Sciences, Taizhou University, Taizhou, Zhejiang, China
| | - Dongguo Wang
- School of Medicine, Taizhou University, Taizhou, Zhejiang, China
- Department of Central Laboratory, Taizhou Municipal Hospital affiliated with Taizhou University, Taizhou, Zhejiang, China
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Shaw LP, Neher RA. Visualizing and quantifying structural diversity around mobile resistance genes. Microb Genom 2023; 9:001168. [PMID: 38117673 PMCID: PMC10763510 DOI: 10.1099/mgen.0.001168] [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: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/22/2023] Open
Abstract
Understanding the evolution of mobile genes is important for understanding the spread of antimicrobial resistance (AMR). Many clinically important AMR genes have been mobilized by mobile genetic elements (MGEs) on the kilobase scale, such as integrons and transposons, which can integrate into both chromosomes and plasmids and lead to rapid spread of the gene through bacterial populations. Looking at the flanking regions of these mobile genes in diverse genomes can highlight common structures and reveal patterns of MGE spread. However, historically this has been a largely descriptive process, relying on gene annotation and expert knowledge. Here we describe a general method to visualize and quantify the structural diversity around genes using pangraph to find blocks of homologous sequence. We apply this method to a set of 12 clinically important beta-lactamase genes and provide interactive visualizations of their flanking regions at https://liampshaw.github.io/flanking-regions. We show that nucleotide-level variation in the mobile gene itself generally correlates with increased structural diversity in its flanking regions, demonstrating a relationship between rates of mutational evolution and rates of structural evolution, and find a bias for greater structural diversity upstream. Our framework is a starting point to investigate general rules that apply to the horizontal spread of new genes through bacterial populations.
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Affiliation(s)
- Liam P. Shaw
- Department of Biology, University of Oxford, Oxford, UK
- Department of Biosciences, University of Durham, Durham, UK
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Zhang Y, Xu D, He Z, Han J, Qu D. Characterization and fitness cost analysis of two plasmids carrying different subtypes of bla NDM in aquaculture farming. Food Microbiol 2023; 115:104327. [PMID: 37567620 DOI: 10.1016/j.fm.2023.104327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 06/09/2023] [Accepted: 06/16/2023] [Indexed: 08/13/2023]
Abstract
In recent years, the blaNDM gene, which mediate resistance to carbapenems, has disseminated all over the world, and has also been detected in animals. Understanding the dissemination and accumulation of antibiotic resistance genes (ARGs) in a human-impacted environment is essential to solve the food safety problems caused by antibiotics. In this study, two strains of carbapenem bacteria carrying blaNDM were screened from 244 strains isolated from two T. sinensis farms in Zhejiang province, China. After their plasmids were isolated and sequenced, their structure and gene environment were analyzed and the mechanism of blaNDM gene transfer was explored. The study measured the fitness cost of plasmids carrying different blaNDM subtypes by four biological characteristics experiments. The results showed that the fitness cost of IncC plasmid carrying blaNDM-1 was higher than that of IncX3 plasmid carrying blaNDM-5. Furthermore, the real-time PCR showed that the decrease of transcription level of fitness-related genes lead to the different fitness cost of plasmids carrying different blaNDM subtypes. Fitness of many blaNDM-harboring plasmids enhanced the further dissemination of this gene and increase the risk of blaNDM gene spreading in aquatic environment, and thus further investigation of carbapenem-resistant bacterias among food animals are in urgent need.
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Affiliation(s)
- Yaru Zhang
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Dingting Xu
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 311100, Zhejiang, China
| | - Ze He
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jianzhong Han
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Daofeng Qu
- Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China.
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6
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Castanheira M, Mendes RE, Gales AC. Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex. Clin Infect Dis 2023; 76:S166-S178. [PMID: 37125466 PMCID: PMC10150277 DOI: 10.1093/cid/ciad109] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.
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Affiliation(s)
| | | | - Ana C Gales
- Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [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: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Noel HR, Petrey JR, Palmer LD. Mobile genetic elements in Acinetobacter antibiotic-resistance acquisition and dissemination. Ann N Y Acad Sci 2022; 1518:166-182. [PMID: 36316792 PMCID: PMC9771954 DOI: 10.1111/nyas.14918] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Pathogenic Acinetobacter species, most notably Acinetobacter baumannii, are a significant cause of healthcare-associated infections worldwide. Acinetobacter infections are of particular concern to global health due to the high rates of multidrug resistance and extensive drug resistance. Widespread genome sequencing and analysis has determined that bacterial antibiotic resistance is often acquired and disseminated through the movement of mobile genetic elements, including insertion sequences (IS), transposons, integrons, and conjugative plasmids. In Acinetobacter specifically, resistance to carbapenems and cephalosporins is highly correlated with IS, as many ISAba elements encode strong outwardly facing promoters that are required for sufficient expression of β-lactamases to confer clinical resistance. Here, we review the role of mobile genetic elements in antibiotic resistance in Acinetobacter species through the framework of the mechanism of resistance acquisition and with a focus on experimentally validated mechanisms.
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Affiliation(s)
- Hannah R. Noel
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Jessica R. Petrey
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
| | - Lauren D. Palmer
- Department of Microbiology and Immunology University of Illinois Chicago Chicago Illinois USA
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9
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Ejaz H, Qamar MU, Junaid K, Younas S, Taj Z, Bukhari SNA, Abdalla AE, Abosalif KOA, Ahmad N, Saleem Z, Salem EHM. The Molecular Detection of Class B and Class D Carbapenemases in Clinical Strains of Acinetobacter calcoaceticus-baumannii Complex: The High Burden of Antibiotic Resistance and the Co-Existence of Carbapenemase Genes. Antibiotics (Basel) 2022; 11:antibiotics11091168. [PMID: 36139948 PMCID: PMC9494970 DOI: 10.3390/antibiotics11091168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/13/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex (CRACB) in clinical environments is a significant global concern. These critical pathogens have shown resistance to a broad spectrum of antibacterial drugs, including carbapenems, mostly due to the acquisition of various β-lactamase genes. Clinical samples (n = 1985) were collected aseptically from multiple sources and grown on blood and MacConkey agar. Isolates and antimicrobial susceptibility were confirmed with the VITEK-2 system. The modified Hodge test confirmed the CRACB phenotype, and specific PCR primers were used for the molecular identification of blaOXA and blaNDM genes. Of the 1985 samples, 1250 (62.9%) were culture-positive and 200 (43.9%) were CRACB isolates. Of these isolates, 35.4% were recovered from pus samples and 23.5% from tracheal secretions obtained from patients in intensive care units (49.3%) and medical wards (20.2%). An antibiogram indicated that 100% of the CRACB isolates were resistant to β-lactam antibiotics and β-lactam inhibitors, 86.5% to ciprofloxacin, and 83.5% to amikacin, while the most effective antibiotics were tigecycline and colistin. The CRACB isolates displayed resistance to eight different AWaRe classes of antibiotics. All isolates exhibited the blaOXA-51 gene, while blaOXA-23 was present in 94.5%, blaVIM in 37%, and blaNDM in 14% of the isolates. The blaOXA-51, blaOXA-23, and blaOXA-24 genes co-existed in 13 (6.5%) isolates. CRACB isolates with co-existing blaOXA-23, blaOXA-24, blaNDM, blaOXA-51 and blaVIM genes were highly prevalent in clinical samples from Pakistan. CRACB strains were highly critical pathogens and presented resistance to virtually all antibacterial drugs, except tigecycline and colistin.
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Affiliation(s)
- Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
- Correspondence: (H.E.); (M.U.Q.)
| | - Muhammad Usman Qamar
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad 38000, Pakistan
- Correspondence: (H.E.); (M.U.Q.)
| | - Kashaf Junaid
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Sonia Younas
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zeeshan Taj
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Syed Nasir Abbas Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Abualgasim E. Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Khalid O. A. Abosalif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Naveed Ahmad
- Department of Pharmaceutics, College of Pharmacy, Jouf University, Sakaka 72388, Saudi Arabia
| | - Zikria Saleem
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Eman H. M. Salem
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Menoufia University, Shebin El-Koom 32511, Egypt
- Department of Microbiology, King AbdulAziz Specialist Hospital, Sakaka 72341, Saudi Arabia
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10
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Zheng Z, Xu Y, Ye L, Chan EWC, Chen S. Genomic insights into the emergence and spread of NDM-1-producing Vibrio spp. isolates in China. J Antimicrob Chemother 2022; 77:3039-3049. [PMID: 35978475 DOI: 10.1093/jac/dkac276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Carbapenemase-producing Vibrio spp., which exhibit an XDR phenotype, have become increasingly prevalent and pose a severe threat to public health. OBJECTIVES To investigate the genetic characteristics of NDM-1-producing Vibrio spp. isolates and the dissemination mechanisms of blaNDM-1 in Vibrio. METHODS A total of 1363 non-duplicate Vibrio spp. isolates collected from shrimp samples in China were subjected to antimicrobial susceptibility tests and screened for blaNDM-1. The blaNDM-1-positive isolates were further characterized by PFGE, MLST, conjugation and WGS using Illumina and Nanopore platforms. Plasmid stability and fitness cost were assessed using Escherichia coli J53, Klebsiella pneumoniae Kpt80 and Salmonella spp. SA2051 as recipient strains. RESULTS In total, 13 blaNDM-1-positive isolates were identified, all exhibiting MDR. WGS analysis revealed that the 13 blaNDM-1 genes were all associated with a derivative of Tn125. Plasmid analysis revealed that six blaNDM-1 genes were located in IncC plasmids and the other seven were carried by plasmids of two different novel types. Conjugation and plasmid stability assays showed that only the IncC plasmids could be transferred to all the recipient strains and could be stably maintained in the hosts. CONCLUSIONS The emergence of the novel plasmids has contributed to the variable genetic contexts of blaNDM-1 in Vibrio spp. and IncC plasmids harbouring the blaNDM-1 gene could facilitate the spread of such genes between Vibrio spp. and other zoonotic pathogens, leading to a rapid dissemination of blaNDM-1 in bacterial pathogens worldwide.
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Affiliation(s)
- Zhiwei Zheng
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Yating Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.,State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hum Hung, Hong Kong
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
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Gong Y, Lu Y, Xue D, Wei Y, Li Q, Li G, Lu S, Wang J, Wang Y, Peng Y, Zhao Y. Emergence of a Carbapenem-Resistant Klebsiella pneumoniae Isolate Co-harbouring Dual bla NDM- 6 -Carrying Plasmids in China. Front Microbiol 2022; 13:900831. [PMID: 35663874 PMCID: PMC9158518 DOI: 10.3389/fmicb.2022.900831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The widespread emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) with limited therapeutic options has become a global concern. In this study, a K. pneumoniae strain called KP2e was recovered from a human case of fatal septic shock in a Chinese hospital. Polymerase chain reaction and sequencing, antimicrobial susceptibility testing, conjugation experiments, S1 nuclease-pulsed field gel electrophoresis/southern blot, whole genome sequencing and comparative genomics were performed to investigate the phenotypic and molecular characteristics of this isolate. KP2e possessed the NDM-6-encoding gene and exhibited resistance to almost all β-lactams except for monobactam. This strain belonged to sequence type 4024, the complete genome of which was composed of one chromosome and three plasmids. Furthermore, blaNDM–6 coexisted on two self-transmissible plasmids, which were assigned to types IncFIB and IncN. A structure of IS26-composite transposon capturing an identical Tn125 remnant (ΔISAba125-blaNDM–6-bleMBL-trpF-dsbC-cutA-groES-ΔgroEL) was identified in the two plasmids, and this conserved blaNDM-surrounding genetic context was similar to that of few IncN plasmids found in other regions of China. Our research appears to be the first description of a clinical strain that emerged co-harbouring dual blaNDM-carrying plasmids, and the first report of NDM-6-positive CRKP in China. These findings demonstrated that IncN is a key medium in the evolution and expanding dissemination of blaNDM genes among various species, which indicates that close monitoring and rapid detection of blaNDM-harbouring plasmids is necessary.
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Affiliation(s)
- Yali Gong
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Medical University, Chongqing, China
| | - Yifei Lu
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Medical University, Chongqing, China
| | - Dongdong Xue
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Medical University, Chongqing, China
| | - Yu Wei
- Department of Radiology, Southwest Hospital, Army Medical University, Chongqing, China
| | - Qimeng Li
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Medical University, Chongqing, China
| | - Gang Li
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
| | - Yunying Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Yizhi Peng
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Chongqing Key Laboratory for Disease Proteomics, Army Medical University, Chongqing, China
| | - Yan Zhao
- Department of Microbiology, College of Basic Medical Sciences, Army Medical University, Chongqing, China
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12
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Intra- and interpopulation transposition of mobile genetic elements driven by antibiotic selection. Nat Ecol Evol 2022; 6:555-564. [PMID: 35347261 DOI: 10.1038/s41559-022-01705-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/17/2022] [Indexed: 12/30/2022]
Abstract
The spread of genes encoding antibiotic resistance is often mediated by horizontal gene transfer (HGT). Many of these genes are associated with transposons, a type of mobile genetic element that can translocate between the chromosome and plasmids. It is widely accepted that the translocation of antibiotic resistance genes onto plasmids potentiates their spread by HGT. However, it is unclear how this process is modulated by environmental factors, especially antibiotic treatment. To address this issue, we asked whether antibiotic exposure would select for the transposition of resistance genes from chromosomes onto plasmids and, if so, whether antibiotic concentration could tune the distribution of resistance genes between chromosomes and plasmids. We addressed these questions by analysing the transposition dynamics of synthetic and natural transposons that encode resistance to different antibiotics. We found that stronger antibiotic selection leads to a higher fraction of cells carrying the resistance on plasmids because the increased copy number of resistance genes on multicopy plasmids leads to higher expression of those genes and thus higher cell survival when facing antibiotic selection. Once they have transposed to plasmids, antibiotic resistance genes are primed for rapid spread by HGT. Our results provide quantitative evidence for a mechanism by which antibiotic selection accelerates the spread of antibiotic resistance in microbial communities.
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13
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Teixeira P, Tacão M, Henriques I. Occurrence and distribution of Carbapenem-resistant Enterobacterales and carbapenemase genes along a highly polluted hydrographic basin. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 300:118958. [PMID: 35131334 DOI: 10.1016/j.envpol.2022.118958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
We determined the distribution and temporal variation of Carbapenem Resistant Enterobacterales (CRE), carbapenemase-encoding genes and other antibiotic resistance genes (ARGs) in a highly polluted river (Lis River; Portugal), also assessing the potential influence of water quality to this distribution. Water samples were collected in two sampling campaigns performed one year apart (2018/2019) from fifteen sites and water quality was analyzed. CRE were isolated and characterized. The abundance of four ARGs (blaNDM, blaKPC, tetA, blaCTX-M), two Microbial Source Tracking (MST) indicators (HF183 and Pig-2-Bac) and the class 1 integrase gene (IntI1) was measured by qPCR. RESULTS: confirmed the poor quality of the Lis River water, particularly in sites near pig farms. A collection of 23 CRE was obtained: Klebsiella (n = 19), Enterobacter (n = 2) and Raoultella (n = 2). PFGE analysis revealed a clonal relationship between isolates obtained in different sampling years and sites. All CRE isolates exhibited multidrug resistance profiles. Klebsiella and Raoultella isolates carried blaKPC while Enterobacter harbored blaNDM. Conjugation experiments were successful for only four Klebsiella isolates. All ARGs were detected by qPCR on both sampling campaigns. An increase in ARGs and IntI1 abundances was detected in sites located downstream of wastewater treatment plants. Strong correlations were observed between blaCTX-M, IntI1 and the human-pollution marker HF183, and also between tetA and the pig-pollution marker Pig-2-bac, suggesting that both human- and animal-derived pollution in the Lis River are a potential source of ARGs. Plus, water quality parameters related to eutrophication and land use were significantly correlated with ARGs abundances. Our findings demonstrated that the Lis River encloses high levels of antibiotic resistant bacteria and ARGs, including CRE and carbapenemase-encoding genes. Overall, this study provides a better understanding on the impacts of water pollution resulting from human and animal activities on the resistome of natural aquatic systems.
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Affiliation(s)
- Pedro Teixeira
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal
| | - Marta Tacão
- Biology Department and CESAM (Centre for Marine and Environmental Studies), University of Aveiro, Aveiro, Portugal, University of Aveiro, Aveiro, Portugal.
| | - Isabel Henriques
- University of Coimbra, Centre for Functional Ecology and Department of Life Sciences, Faculty of Science and Technology, Coimbra, Portugal
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14
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Acman M, Wang R, van Dorp L, Shaw LP, Wang Q, Luhmann N, Yin Y, Sun S, Chen H, Wang H, Balloux F. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene bla NDM. Nat Commun 2022; 13:1131. [PMID: 35241674 PMCID: PMC8894482 DOI: 10.1038/s41467-022-28819-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
The mobile resistance gene blaNDM encodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections. The blaNDM gene is globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within highly recombining and transposon-rich genomic regions, which leads to the dynamics underlying the global dissemination of blaNDM to remain poorly resolved. Here, we compile a dataset of over 6000 bacterial genomes harbouring the blaNDM gene, including 104 newly generated PacBio hybrid assemblies from clinical and livestock-associated isolates across China. We develop a computational approach to track structural variants surrounding blaNDM, which allows us to identify prevalent genomic contexts, mobile genetic elements, and likely events in the gene's global spread. We estimate that blaNDM emerged on a Tn125 transposon before 1985, but only reached global prevalence around a decade after its first recorded observation in 2005. The Tn125 transposon seems to have played an important role in early plasmid-mediated jumps of blaNDM, but was overtaken in recent years by other elements including IS26-flanked pseudo-composite transposons and Tn3000. We found a strong association between blaNDM-carrying plasmid backbones and the sampling location of isolates. This observation suggests that the global dissemination of the blaNDM gene was primarily driven by successive between-plasmid transposon jumps, with far more restricted subsequent plasmid exchange, possibly due to adaptation of plasmids to their specific bacterial hosts.
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Affiliation(s)
- Mislav Acman
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Ruobing Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
| | - Liam P Shaw
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Qi Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Nina Luhmann
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London, WC1E 6BT, UK
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15
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Khabthani S, Rolain JM, Merhej V. Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants. Int J Mol Sci 2022; 23:ijms23042137. [PMID: 35216256 PMCID: PMC8874588 DOI: 10.3390/ijms23042137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/06/2022] [Accepted: 02/12/2022] [Indexed: 02/04/2023] Open
Abstract
Background: The emergence and diffusion of strains of pathogenic bacteria resistant to antibiotics constitutes a real public health challenge. Antibiotic resistance genes (ARGs) can be carried by both pathogenic and non-pathogenic bacteria, including commensal bacteria from the human microbiota, which require special monitoring in the fight against antimicrobial resistance. Methods: We analyzed the proteomes of 335 new bacterial species from human microbiota to estimate its whole range of ARGs using the BLAST program against ARGs reference databases. Results: We found 278 bacteria that harbor a total of 883 potential ARGs with the following distribution: 264 macrolides-lincosamides-streptogramin, 195 aminoglycosides, 156 tetracyclines, 58 β-lactamases, 58 fosfomycin, 51 glycopeptides, 36 nitroimidazoles, 33 phenicols and 32 rifamycin. Furthermore, evolutionary analyses revealed the potential horizontal transfer with pathogenic bacteria involving mobile genetic elements such as transposase and plasmid. We identified many ARGs that may represent new variants in fosfomycin and β-lactams resistance. Conclusion: These findings show that new bacterial species from human microbiota should be considered as an important reservoir of ARGs that can be transferred to pathogenic bacteria. In vitro analyses of their phenotypic potential are required to improve our understanding of the functional role of this bacterial community in the development of antibiotic resistance.
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Affiliation(s)
- Sami Khabthani
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Marc Rolain
- Faculté de Pharmacie, Aix-Marseille Université, 13005 Marseille, France; (S.K.); (J.-M.R.)
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Vicky Merhej
- IHU Méditerranée Infection, Institut de Recherche Pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Faculté de Sciences Médicales et Paramédicales, Aix-Marseille Université, 13005 Marseille, France
- Correspondence:
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16
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Li X, He J, Jiang Y, Peng M, Yu Y, Fu Y. Genetic Characterization and Passage Instability of a Hybrid Plasmid Co-Harboring blaIMP-4 and blaNDM-1 Reveal the Contribution of Insertion Sequences During Plasmid Formation and Evolution. Microbiol Spectr 2021; 9:e0157721. [PMID: 34908434 PMCID: PMC8672901 DOI: 10.1128/spectrum.01577-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/04/2021] [Indexed: 01/20/2023] Open
Abstract
Carbapenemase is the predominant enzyme in the mechanism leading to Enterobacterales resistance to carbapenems, but only a limited number of isolates harbor double classes/types of carbapenemase. Here, an IMP-4 and NDM-1 producer named Klebsiella michiganensis 7525 is reported, and the co-harboring plasmid is further characterized. K. michiganensis 7525 was positive for the blaIMP-4 and blaNDM-1 genes by the NG-Test Carba-5 method and PCR followed by sequencing, and both were located on the same plasmid (designated pKOX7525_1) according to S1-PFGE with Southern blot experiments. pKOX7525_1 was capable of transconjugation with an efficiency of 4.3 × 10-8 in a filter mating experiment. Whole-genome sequencing and bioinformatics analysis confirmed that the plasmid was novel, clustered to the incompatibility type of IncHIB/IncFIA/IncR and presented high similarity to a blaIMP-4-carrying IncHIB plasmid (pA) published with 79% coverage and 100% sequence identify. In contrast, a large-fragment insertion and inversion mediated by IS26 was observed on the plasmid, which introduced a genetic hybrid zone with multiple resistance genes, including blaNDM-1, to the plasmid. In the transconjugants, the presence of pKOX7525_1 had a negative impact on bacterial fitness. In vitro evolution experiments showed that pKOX7525_1 in the transconjugant could not be stably inherited after 10 days of passage and that blaNDM-1 could be lost during repeated laboratory passage. Our study not only reports a novel plasmid co-harboring blaIMP-4 and blaNDM-1 but also highlights the putative pathway of plasmid formation and evolution by means of genetic rearrangement through sequence insertion and homologue recombination, which may have critical value for plasmid research and increase awareness of carbapenem-resistant Enterobacteriaceae (CRE). IMPORTANCE In this study, we characterized a novel plasmid from a carbapenem-resistant K. michiganensis (CRKM) isolate, which harbors two metallo-β-lactamases (MBLs), IMP-4 and NDM-1, is capable of transconjugation and contains three replicons. Our results first expand the diversity of plasmids co-harboring carbapenemase genes in Enterobacterales, which exhibits epidemic importance in bacterial resistance. Additionally, we investigated the origin and formation of this MBL double-positive plasmid based on comparative genomics analysis, which indicated that IS26 plays a vital role through continuous genetic rearrangements. Moreover, this plasmid is unstable in transconjugants during passage at the multidrug-resistant (MDR) region of blaNDM-1, with fluctuating stability under varying antibiotic selection, highlighting auspicious considerations regarding recognition of the complexity and plasticity of plasmids in evolution and re-emphasizing clinical infection control inspired by CRE.
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Affiliation(s)
- Xi Li
- Centre of Laboratory Medicine, Zhejiang Provincial People’s Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Minfei Peng
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, China
- Department of Clinical Laboratory, Taizhou Hospital of Zhejiang Province, Linhai, Zhejiang Province, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, Zhejiang Province, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Fu
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang Province, China
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17
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Zafer MM, Hussein AFA, Al-Agamy MH, Radwan HH, Hamed SM. Genomic Characterization of Extensively Drug-Resistant NDM-Producing Acinetobacter baumannii Clinical Isolates With the Emergence of Novel bla ADC-257. Front Microbiol 2021; 12:736982. [PMID: 34880837 PMCID: PMC8645854 DOI: 10.3389/fmicb.2021.736982] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023] Open
Abstract
Acinetobacter baumannii has become a major challenge to clinicians worldwide due to its high epidemic potential and acquisition of antimicrobial resistance. This work aimed at investigating antimicrobial resistance determinants and their context in four extensively drug-resistant (XDR) NDM-producing A. baumannii clinical isolates collected between July and October 2020 from Kasr Al-Ainy Hospital, Cairo, Egypt. A total of 20 A. baumannii were collected and screened for acquired carbapenemases (blaNDM, blaVIM and blaIMP) using PCR. Four NDM producer A. baumannii isolates were identified and selected for whole-genome sequencing, in silico multilocus sequence typing, and resistome analysis. Antimicrobial susceptibility profiles were determined using disk diffusion and broth microdilution tests. All blaNDM-positive A. baumannii isolates were XDR. Three isolates belonged to high-risk international clones (IC), namely, IC2 corresponding to ST570Pas/1701Oxf (M20) and IC9 corresponding to ST85Pas/ST1089Oxf (M02 and M11). For the first time, we report blaNDM-1 gene on the chromosome of an A. baumannii strain that belongs to sequence type ST164Pas/ST1418Oxf. Together with AphA6, blaNDM-1 was bracketed by two copies of ISAba14 in ST85Pas isolates possibly facilitating co-transfer of amikacin and carbapenem resistance. A novel blaADC allele (blaADC-257) with an upstream ISAba1 element was identified in M19 (ST/CC164Pas and ST1418Oxf/CC234Oxf). blaADC genes harbored by M02 and M11 were uniquely interrupted by IS1008. Tn2006-associated blaOXA-23 was carried by M20. blaOXA-94 genes were preceded by ISAba1 element in M02 and M11. AbGRI3 was carried by M20 hosting the resistance genes aph(3`)-Ia, aac(6`)-Ib`, catB8, ant(3``)-Ia, sul1, armA, msr(E), and mph(E). Nonsynonymous mutations were identified in the quinolone resistance determining regions (gyrA and parC) of all isolates. Resistance to colistin in M19 was accompanied by missense mutations in lpxACD and pmrABC genes. The current study provided an insight into the genomic background of XDR phenotype in A. baumannii recovered from patients in Egypt. WGS revealed strong association between resistance genes and diverse mobile genetic elements with novel insertion sites and genetic organizations.
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Affiliation(s)
- Mai M Zafer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ahram Canadian University, Cairo, Egypt
| | - Amira F A Hussein
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mohamed H Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia.,Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo, Egypt
| | - Hesham H Radwan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
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18
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Haraoui LP. Networked collective microbiomes and the rise of subcellular 'units of life'. Trends Microbiol 2021; 30:112-119. [PMID: 34696928 DOI: 10.1016/j.tim.2021.09.011] [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] [Received: 03/31/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 10/20/2022]
Abstract
Microbiomes are generally conceived of as one element of a pair - their partner being the habitat they occupy. I call this common scientific practice 'pair-thinking'. Research into antimicrobial resistance and its underlying anthropogenic drivers highlights the growing footprint occupied by mobile genetic elements (MGEs). Furthermore, these MGEs are known to circulate widely between microbiomes. Using a pluralistic framework anchored within a processual microbial ontology, these observations point to a reframing of microbiomes as networked and collective, thus challenging pair-thinking. Such a shift has implications for the future of microbiome research, from conceptual and methodological perspectives, and exposes the impacts of anthropogenic forces on the evolution of microbiomes and the functions they carry out.
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Affiliation(s)
- Louis-Patrick Haraoui
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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19
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Ai W, Zhou Y, Wang B, Zhan Q, Hu L, Xu Y, Guo Y, Wang L, Yu F, Li X. Corrigendum: First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei. Front Microbiol 2021; 12:741628. [PMID: 34650541 PMCID: PMC8507845 DOI: 10.3389/fmicb.2021.741628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/03/2021] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2021.676113.].
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Affiliation(s)
- Wenxiu Ai
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qing Zhan
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Longhua Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanlei Xu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaolong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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20
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Zhang X, Wang L, Li D, Wang C, Guo Q, Wang M. Characterization of the novel plasmid-encoded MBL gene blaAFM-1, integrated into a blaIMP-45-bearing transposon Tn6485e in a carbapenem-resistant Pseudomonas aeruginosa clinical isolate. J Antimicrob Chemother 2021; 77:83-88. [PMID: 34545931 DOI: 10.1093/jac/dkab342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To characterize the novel subclass B1 MBL AFM-1, encoded by a blaIMP-45-bearing megaplasmid from a carbapenem-resistant Pseudomonas aeruginosa (CRPA) clinical isolate. METHODS CRPA HS17-127 and its transconjugant were discovered to carry blaAFM-1 in our previous study. blaAFM-1 and blaNDM-1 were cloned and expressed in Escherichia coli TOP10 and P. aeruginosa PAO1, respectively, to test the resistance phenotype. Kinetic studies were performed to elucidate the biochemical characteristics of the AFM-1 enzyme. Comparative genomic analysis was applied to investigate the genetic context of blaAFM-1. RESULTS PAO1 transconjugant TcHS17-127 exhibited carbapenem resistance with an imipenem MIC of 64 mg/L. E. coli transformants with cloned blaAFM-1 or blaNDM-1 had increased MICs of all β-lactams tested (except aztreonam) and imipenem MICs of 4-8 mg/L. Kinetic studies showed that AFM-1 had greater catalytic efficiency against cephalosporins than carbapenems. blaAFM-1 was located on a 486 963 bp IncP-2 plasmid, pHS17-127, containing a 57.3 kb MDR Tn1403-derivative transposon, Tn6485e, which is genetically closest to the blaIMP-45-bearing Tn6485 transposon but has acquired an extra ISCR27n3-blaAFM-1 module. Multicentre surveillance of 605 P. aeruginosa clinical isolates identified three blaAFM carriers from different STs. Two of them co-carried blaAFM-1 and blaIMP-45. A BLAST search against the NCBI database showed six blaAFM carriers on various plasmids and the chromosomes of different Gram-negative species. CONCLUSIONS The blaAFM-1 gene confers carbapenem resistance and has been captured in distinct species of non-fermenters. Co-carriage of blaAFM-1 and blaIMP-45 in an MDR transposon on a conjugative plasmid can be expected to promote further dissemination of blaMBLs.
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Affiliation(s)
- Xuefei Zhang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Leilei Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Dan Li
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Chen Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People's Republic of China, Shanghai, China
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21
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A Novel SXT/R391 Integrative and Conjugative Element Carries Two Copies of the blaNDM-1 Gene in Proteus mirabilis. mSphere 2021; 6:e0058821. [PMID: 34378988 PMCID: PMC8386438 DOI: 10.1128/msphere.00588-21] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The rapid spread of the blaNDM-1 gene is a major public health concern. Here, we describe the multidrug-resistant Proteus mirabilis strain XH1653, which contains a novel SXT/R391 integrative and conjugative element (ICE), harboring two tandem copies of blaNDM-1 and 21 other resistance genes. XH1653 was resistant to all antibiotics tested, apart from aztreonam. Whole-genome data revealed that two copies of blaNDM-1 embedded in the ISCR1 element are located in HS4 of the novel ICE, which we named ICEPmiChnXH1653. A circular intermediate of ICEPmiChnXH1653 was detected by PCR, and conjugation experiments showed that the ICE can be transferred to the Escherichia coli strain EC600 with frequencies of 1.5 × 10-7. In the recipient strain, the ICE exhibited a higher excision frequency and extrachromosomal copy number than the ICE in the donor strain. We also observed that the presence of ICEPmiChnXH1653 has a negative impact on bacterial fitness and leads to changes in the transcriptome of the host. In vitro evolution experiments under nonselective conditions showed that the two tandem copies of the ISCR1 element and the ISVsa3 element can be lost during repeated laboratory passage. This is the first report of a novel SXT/R391 ICE carrying two tandem copies of blaNDM-1, which also illustrates the role that ICEs may play as platforms for the accumulation and transmission of antibiotic resistance genes. IMPORTANCE The occurrence of carbapenemase-producing Proteus mirabilis, especially those strains producing NDM-1 and its variants, is a major public health concern worldwide. The integrative conjugative element (ICE) plays an important role in horizontal acquisition of resistance genes. In this study, we characterized a novel SXT/R391 ICE from a clinical P. mirabilis isolate that we named ICEPmiChnXH1653, which contains two tandem copies of the carbapenemase gene blaNDM-1. We performed an integrative approach to gain insights into different aspects of ICEPmiChnXH1653 evolution and biology and observed that ICEPmiChnXH1653 obtained the carbapenemase gene blaNDM-1 by ISCR1-mediated homologous recombination. Our study reveals that the transmission of blaNDM-1 by ISCR1 elements or ICEs may be an important contributor to the carbapenem resistance development across species, which could improve our understanding of horizontal gene transfer in clinical environments.
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Sanz-García F, Gil-Gil T, Laborda P, Ochoa-Sánchez LE, Martínez JL, Hernando-Amado S. Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat. Int J Mol Sci 2021; 22:8080. [PMID: 34360847 PMCID: PMC8347278 DOI: 10.3390/ijms22158080] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.
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Affiliation(s)
| | | | | | | | - José L. Martínez
- Centro Nacional de Biotecnología, CSIC, 28049 Madrid, Spain; (F.S.-G.); (T.G.-G.); (P.L.); (L.E.O.-S.); (S.H.-A.)
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23
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Trade-Offs between Antibacterial Resistance and Fitness Cost in the Production of Metallo-β-Lactamases by Enteric Bacteria Manifest as Sporadic Emergence of Carbapenem Resistance in a Clinical Setting. Antimicrob Agents Chemother 2021; 65:e0241220. [PMID: 33972250 DOI: 10.1128/aac.02412-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Meropenem is a clinically important antibacterial reserved for treatment of multiresistant infections. In meropenem-resistant bacteria of the family Enterobacterales, NDM-1 is considerably more common than IMP-1, despite both metallo-β-lactamases (MBLs) hydrolyzing meropenem with almost identical kinetics. We show that blaNDM-1 consistently confers meropenem resistance in wild-type Enterobacterales, but blaIMP-1 does not. The reason is higher blaNDM-1 expression because of its stronger promoter. However, the cost of meropenem resistance is reduced fitness of blaNDM-1-positive Enterobacterales. In parallel, from a clinical case, we identified multiple Enterobacter spp. isolates carrying a plasmid-encoded blaNDM-1 having a modified promoter region. This modification lowered MBL production to a level associated with zero fitness cost, but, consequently, the isolates were not meropenem resistant. However, we identified a Klebsiella pneumoniae isolate from this same clinical case carrying the same blaNDM-1 plasmid. This isolate was meropenem resistant despite low-level NDM-1 production because of a ramR mutation reducing envelope permeability. Overall, therefore, we show how the resistance/fitness trade-off for MBL carriage can be resolved. The result is sporadic emergence of meropenem resistance in a clinical setting.
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Bahr G, González LJ, Vila AJ. Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design. Chem Rev 2021; 121:7957-8094. [PMID: 34129337 PMCID: PMC9062786 DOI: 10.1021/acs.chemrev.1c00138] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antimicrobial resistance is one of the major problems in current practical medicine. The spread of genes coding for resistance determinants among bacteria challenges the use of approved antibiotics, narrowing the options for treatment. Resistance to carbapenems, last resort antibiotics, is a major concern. Metallo-β-lactamases (MBLs) hydrolyze carbapenems, penicillins, and cephalosporins, becoming central to this problem. These enzymes diverge with respect to serine-β-lactamases by exhibiting a different fold, active site, and catalytic features. Elucidating their catalytic mechanism has been a big challenge in the field that has limited the development of useful inhibitors. This review covers exhaustively the details of the active-site chemistries, the diversity of MBL alleles, the catalytic mechanism against different substrates, and how this information has helped developing inhibitors. We also discuss here different aspects critical to understand the success of MBLs in conferring resistance: the molecular determinants of their dissemination, their cell physiology, from the biogenesis to the processing involved in the transit to the periplasm, and the uptake of the Zn(II) ions upon metal starvation conditions, such as those encountered during an infection. In this regard, the chemical, biochemical and microbiological aspects provide an integrative view of the current knowledge of MBLs.
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Affiliation(s)
- Guillermo Bahr
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Lisandro J. González
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
| | - Alejandro J. Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET, Universidad Nacional de Rosario, Ocampo y Esmeralda S/N, 2000 Rosario, Argentina
- Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000 Rosario, Argentina
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25
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Kong LH, Xiang R, Wang YL, Wu SK, Lei CW, Kang ZZ, Chen YP, Ye XL, Lai Y, Wang HN. Integration of the blaNDM-1 carbapenemase gene into a novel SXT/R391 integrative and conjugative element in Proteus vulgaris. J Antimicrob Chemother 2021; 75:1439-1442. [PMID: 32155266 DOI: 10.1093/jac/dkaa068] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/07/2020] [Accepted: 02/04/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To characterize the genetic environment of the carbapenem resistance determinant in Proteus vulgaris of swine origin. METHODS The carbapenem-resistant P. vulgaris strain BC22 was isolated from a faecal swab from a diseased pig with diarrhoea in Sichuan Province of China in 2018. The presence of carbapenemase genes was screened by PCR. WGS and bioinformatics analysis were performed to analyse the genetic environment of the carbapenem resistance determinant. RESULTS P. vulgaris strain BC22 was found to harbour the carbapenemase gene blaNDM-1. WGS data revealed that blaNDM-1 was located in a truncated ISAba125 composite transposon. The carbapenem resistance gene blaNDM-1 and 20 other resistance genes, including the multiresistance gene cfr and the bifunctional aminoglycoside/quinolone resistance gene aac(6')-lb-cr, were located in a novel SXT/R391 integrative and conjugative element (ICE). This new SXT/R391 ICE of 148.7 kb was chromosomally located, and could be transferred to Escherichia coli. CONCLUSIONS Here, we report a carbapenemase gene, blaNDM-1, integrated into an SXT/R391 ICE. Our study highlights that this SXT/R391 ICE may facilitate the dissemination of clinically important resistance genes such as blaNDM-1, cfr and aac(6')-lb-cr.
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Affiliation(s)
- Ling-Han Kong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Rong Xiang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yu-Long Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Shun-Kang Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Chang-Wei Lei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Zhuang-Zhuang Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yan-Peng Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Xiao-Lan Ye
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Yan Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Hong-Ning Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan Province, People's Republic of China.,Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
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26
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Ai W, Zhou Y, Wang B, Zhan Q, Hu L, Xu Y, Guo Y, Wang L, Yu F, Li X. First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei. Front Microbiol 2021; 12:676113. [PMID: 34220761 PMCID: PMC8252965 DOI: 10.3389/fmicb.2021.676113] [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: 03/04/2021] [Accepted: 04/27/2021] [Indexed: 11/30/2022] Open
Abstract
Many antimicrobial resistance genes usually located on transferable plasmids are responsible for multiple antimicrobial resistance among multidrug-resistant (MDR) Gram-negative bacteria. The aim of this study is to characterize a carbapenemase-producing Enterobacter hormaechei 1575 isolate from the blood sample in a tertiary hospital in Wuhan, Hubei Province, China. Antimicrobial susceptibility test showed that 1575 was an MDR isolate. The whole genome sequencing (WGS) and comparative genomics were used to deeply analyze the molecular information of the 1575 and to explore the location and structure of antibiotic resistance genes. The three key resistance genes (blaSFO–1, blaNDM–1, and mcr-9) were verified by PCR, and the amplicons were subsequently sequenced. Moreover, the conjugation assay was also performed to determine the transferability of those resistance genes. Plasmid files were determined by the S1 nuclease pulsed-field gel electrophoresis (S1-PFGE). WGS revealed that p1575-1 plasmid was a conjugative plasmid that possessed the rare coexistence of blaSFO–1, blaNDM–1, and mcr-9 genes and complete conjugative systems. And p1575-1 belonged to the plasmid incompatibility group IncHI2 and multilocus sequence typing ST102. Meanwhile, the pMLST type of p1575-1 was IncHI2-ST1. Conjugation assay proved that the MDR p1575-1 plasmid could be transferred to other recipients. S1-PFGE confirmed the location of plasmid with molecular weight of 342,447 bp. All these three resistant genes were flanked by various mobile elements, indicating that the blaSFO–1, blaNDM–1, and mcr-9 could be transferred not only by the p1575-1 plasmid but also by these mobile elements. Taken together, we report for the first time the coexistence of blaSFO–1, blaNDM–1, and mcr-9 on a transferable plasmid in a MDR clinical isolate E. hormaechei, which indicates the possibility of horizontal transfer of antibiotic resistance genes.
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Affiliation(s)
- Wenxiu Ai
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qing Zhan
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Longhua Hu
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanlei Xu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaolong Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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27
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Starkova P, Lazareva I, Avdeeva A, Sulian O, Likholetova D, Ageevets V, Lebedeva M, Gostev V, Sopova J, Sidorenko S. Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-β-Lactamase in Klebsiella pneumoniae in Russia. Antibiotics (Basel) 2021; 10:691. [PMID: 34207702 PMCID: PMC8226487 DOI: 10.3390/antibiotics10060691] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/23/2022] Open
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a new threat to healthcare. In this study, we analyzed nine CR-hvKp isolates of different sequence-types (ST) recovered from patients with nosocomial infections in two hospitals in Saint Petersburg. Whole-genome sequencing showed that eight of them harbored large mosaic plasmids carrying resistance to carbapenems and hypervirulence simultaneously, and four different types of hybrid plasmids were identified. BLAST analysis showed a high identity with two hybrid plasmids originating in the UK and Czech Republic. We demonstrated that hybrid plasmids emerged due to the acquisition of resistance genes by virulent plasmids. Moreover, one of the hybrid plasmids carried a novel New Delhi metallo-beta-lactamase (NDM) variant, differing from NDM-1 by one amino acid substitution (D130N), which did not provide significant evolutionary advantages compared to NDM-1. The discovery of structurally similar plasmids in geographically distant regions suggests that the actual distribution of hybrid plasmids carrying virulence and resistance genes is much wider than expected.
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Affiliation(s)
- Polina Starkova
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
- National Research Institute of Information Technologies, Mechanics and Optics, 191002 Saint Petersburg, Russia
| | - Irina Lazareva
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
| | - Alisa Avdeeva
- Department of Microbiology, Saint Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Ofeliia Sulian
- Saint Petersburg State Academy of Veterinary Medicine, 196084 Saint Petersburg, Russia;
| | - Darya Likholetova
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
| | - Vladimir Ageevets
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
| | - Marina Lebedeva
- Bryansk Interregional Veterinary Laboratory, Suponevo, 241520 Bryansk, Russia;
| | - Vladimir Gostev
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
| | - Julia Sopova
- Center of Transgenesis and Genome Editing, Saint Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Plant Genetics and Biotechnology, Saint Petersburg Branch of Vavilov Institute of General Genetics, 119991 Saint Petersburg, Russia
| | - Sergey Sidorenko
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 Saint Petersburg, Russia; (P.S.); (I.L.); (D.L.); (V.A.); (V.G.)
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, 195067 Saint Petersburg, Russia
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28
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NDM-1-encoding plasmid in Acinetobacter chengduensis isolated from coastal water. INFECTION GENETICS AND EVOLUTION 2021; 93:104926. [PMID: 34020069 DOI: 10.1016/j.meegid.2021.104926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/03/2021] [Accepted: 05/15/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Acinetobacter spp. may cause difficult-to-treat nosocomial infections due to acquisition of carbapenemases, including New Delhi metallo-β-lactamase (NDM). This genus has been pointed out as a possible actor in the early dissemination of blaNDM, and this gene has been documented in a variety of species. OBJECTIVE Here we describe an Acinetobacter chengduensis (isolate FL51) carrying blaNDM recovered from coastal water in Brazil. METHODS In vitro techniques included antimicrobial susceptibility and minimum inhibitory concentration tests, PCR, plasmid profile and matting-out/transformation assays. In silico approaches comprised comparative genomic analyses using appropriate databases. RESULTS FL51 grew at room temperature in a variety of culture media, excluding MacConkey. It showed resistance to all beta-lactams tested and to ciprofloxacin. blaNDM-1 was identified, and a single replicon was observed in plasmid profile. In silico DNA hybridization revealed Acinetobacter FL51 as being Acinetobacter chengduensis. blaNDM-1 was flanked upstream by ISAba14-aphA6-ISAba125 and downstream by bleMBL-trpF-Δtat, inserted in a 41,068 bp non typeable plasmid named pNDM-FL51. This replicon showed high coverage and identity with other sequences present in plasmids deposited on the GenBank database, recovered almost exclusively from Acinetobacter spp., associated with hospital settings and animal sources. CONCLUSION We described a recently described environmental Acinetobacter species carrying a plasmid-borne blaNDM associated with a Tn125-like structure. Our findings suggest that replicon may play an important role in blaNDM dissemination among distinct settings within this genus and may support the theory of blaNDM emergence from an environmental Acinetobacter.
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Qamar MU, Lopes BS, Hassan B, Khurshid M, Shafique M, Atif Nisar M, Mohsin M, Nawaz Z, Muzammil S, Aslam B, Ejaz H, Toleman MA. The present danger of New Delhi metallo-β-lactamase: a threat to public health. Future Microbiol 2020; 15:1759-1778. [PMID: 33404261 DOI: 10.2217/fmb-2020-0069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The evolution of antimicrobial-resistant Gram-negative pathogens is a substantial menace to public health sectors, notably in developing countries because of the scarcity of healthcare facilities. New Delhi metallo-β-lactamase (NDM) is a potent β-lactam enzyme able to hydrolyze several available antibiotics. NDM was identified from the clinical isolates of Klebsiella pneumoniae and Escherichia coli from a Swedish patient in New Delhi, India. This enzyme horizontally passed on to various Gram-negative bacteria developing resistance against a variety of antibiotics which cause treatment crucial. These bacteria increase fatality rates and play an integral role in the economic burden. The efficient management of NDM-producing isolates requires the coordination between each healthcare setting in a region. In this review, we present the prevalence of NDM in children, fatality and the economic burden of resistant bacteria, the clonal spread of NDM harboring bacteria and modern techniques for the detection of NDM producing pathogens.
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Affiliation(s)
- Muhammad Usman Qamar
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Bruno S Lopes
- School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, AB24 3DR, Scotland, UK
| | - Brekhna Hassan
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, CF10 3AT, Cardiff, UK
| | - Mohsin Khurshid
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Muhammad Shafique
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Muhammad Atif Nisar
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
- College of Science and Engineering, Flinders University, 5042, Australia
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture Faisalabad, 38000, Pakistan
| | - Zeeshan Nawaz
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Saima Muzammil
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Bilal Aslam
- Department of Microbiology, Faculty of Life Sciences, Government College University Faisalabad, 38000, Pakistan
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Jouf, 72388, Saudi Arabia
| | - Mark A Toleman
- Department of Medical Microbiology & Infectious Diseases, Institute of Infection & Immunity, School of Medicine, Cardiff University, CF10 3AT, Cardiff, UK
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30
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Hammer-Dedet F, Jumas-Bilak E, Licznar-Fajardo P. The Hydric Environment: A Hub for Clinically Relevant Carbapenemase Encoding Genes. Antibiotics (Basel) 2020; 9:antibiotics9100699. [PMID: 33076221 PMCID: PMC7602417 DOI: 10.3390/antibiotics9100699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/06/2020] [Accepted: 10/10/2020] [Indexed: 12/31/2022] Open
Abstract
Carbapenems are β-lactams antimicrobials presenting a broad activity spectrum and are considered as last-resort antibiotic. Since the 2000s, carbapenemase producing Enterobacterales (CPE) have emerged and are been quickly globally spreading. The global dissemination of carbapenemase encoding genes (CEG) within clinical relevant bacteria is attributed in part to its location onto mobile genetic elements. During the last decade, carbapenemase producing bacteria have been isolated from non-human sources including the aquatic environment. Aquatic ecosystems are particularly impacted by anthropic activities, which conduce to a bidirectional exchange between aquatic environments and human beings and therefore the aquatic environment may constitute a hub for CPE and CEG. More recently, the isolation of autochtonous aquatic bacteria carrying acquired CEG have been reported and suggest that CEG exchange by horizontal gene transfer occurred between allochtonous and autochtonous bacteria. Hence, aquatic environment plays a central role in persistence, dissemination and emergence of CEG both within environmental ecosystem and human beings, and deserves to be studied with particular attention.
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Affiliation(s)
- Florence Hammer-Dedet
- UMR 5569 HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France; (F.H.-D.); (E.J.-B.)
| | - Estelle Jumas-Bilak
- UMR 5569 HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France; (F.H.-D.); (E.J.-B.)
- Département d’Hygiène Hospitalière, CHU Montpellier, 34090 Montpellier, France
| | - Patricia Licznar-Fajardo
- UMR 5569 HydroSciences Montpellier, Université de Montpellier, CNRS, IRD, 34090 Montpellier, France; (F.H.-D.); (E.J.-B.)
- Département d’Hygiène Hospitalière, CHU Montpellier, 34090 Montpellier, France
- Correspondence:
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Baraniak A, Machulska M, Żabicka D, Literacka E, Izdebski R, Urbanowicz P, Bojarska K, Herda M, Kozińska A, Hryniewicz W, Gniadkowski M. Towards endemicity: large-scale expansion of the NDM-1-producing Klebsiella pneumoniae ST11 lineage in Poland, 2015-16. J Antimicrob Chemother 2020; 74:3199-3204. [PMID: 31406993 DOI: 10.1093/jac/dkz315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/12/2019] [Accepted: 06/22/2019] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVES In 2015 and 2016 Poland recorded rapid proliferation of New Delhi MBL (NDM)-producing Enterobacterales, with at least 470 and 1780 cases, respectively. We addressed the roles of the Klebsiella pneumoniae ST11 NDM-1 outbreak genotype, already spreading in 2012-14, and of newly imported organisms in this increase. METHODS The study included 2136 NDM-positive isolates identified between April 2015 and December 2016, following transfer of patients with K. pneumoniae ST147 NDM-1 from Tunisia to Warsaw in March 2015. The isolates were screened by PCR mapping for variants of blaNDM-carrying Tn125-like elements. Selected isolates were typed by PFGE and MLST. NDM-encoding plasmids were analysed by nuclease S1/hybridization, transfer assays, PCR-based replicon typing and PCR mapping. RESULTS The organisms were mainly K. pneumoniae containing the Tn125A variant of the ST11 epidemic lineage (n = 2094; ∼98%). Their representatives were of the outbreak pulsotype and ST11, and produced NDM-1, encoded by specific IncFII (pKPX-1/pB-3002cz)-like plasmids. The isolates were recovered in 145 healthcare centres in 13/16 administrative regions, predominantly the Warsaw area. The 'Tunisian' genotype K. pneumoniae ST147 NDM-1 Tn125F comprised 18 isolates (0.8%) from eight institutions. The remaining 24 isolates, mostly K. pneumoniae and Escherichia coli of diverse STs, produced NDM-1 or NDM-5 specified by various Tn125 derivatives and plasmids. CONCLUSIONS The K. pneumoniae ST11 NDM-1 outbreak has dramatically expanded in Poland since 2012, which may bring about a countrywide endemic situation in the near future. In addition, the so-far limited K. pneumoniae ST147 NDM-1 outbreak plus multiple NDM imports from different countries were observed in 2015-16.
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Affiliation(s)
- A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - M Machulska
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - E Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - K Bojarska
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - M Herda
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - A Kozińska
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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Roach D, Waalkes A, Abanto J, Zunt J, Cucho C, Soria J, Salipante SJ. Whole Genome Sequencing of Peruvian Klebsiella pneumoniae Identifies Novel Plasmid Vectors Bearing Carbapenem Resistance Gene NDM-1. Open Forum Infect Dis 2020; 7:ofaa266. [PMID: 32760750 PMCID: PMC7395672 DOI: 10.1093/ofid/ofaa266] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/25/2020] [Indexed: 01/07/2023] Open
Abstract
Background Klebsiella pneumoniae is a bacterial pathogen with increasing rates of resistance to carbapenem antibiotics, but the population structure and genetic drivers of carbapenem-resistant K pneumoniae (CRKP) remain underexplored in developing countries. Carbapenem-resistant K pneumoniae were recently introduced into Peru but have grown rapidly in prevalence, enabling study of this pathogen as it expands into an unaffected environment. Methods In this study, using whole genome sequencing, we show that 3 distinct lineages encompass almost all CRKP identified in the hospital where it was first reported in Peru. Results The most prevalent lineage, ST348, has not been described outside of Europe, raising concern for global dissemination. We identified metallo- β -lactamase NDM-1 as the primary carbapenem resistance effector, which was harbored on a novel vector resulting from recombination between 2 different plasmids, pKP1-NDM-1 and pMS7884A. Conclusions This study is the first of its kind performed in Peru, and it furthers our understanding of the landscape of CRKP infections in Latin America.
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Affiliation(s)
- David Roach
- University of Washington School of Medicine, Department of Internal Medicine, Seattle, Washington, USA.,University of Washington School of Medicine, Department of Global Health, Seattle, Washington, USA
| | - Adam Waalkes
- University of Washington School of Medicine, Department of Laboratory Medicine, Seattle, Washington, USA
| | | | - Joseph Zunt
- University of Washington School of Medicine, Department of Internal Medicine, Seattle, Washington, USA.,University of Washington School of Medicine, Department of Global Health, Seattle, Washington, USA
| | | | | | - Stephen J Salipante
- University of Washington School of Medicine, Department of Laboratory Medicine, Seattle, Washington, USA
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Ramirez MS, Bonomo RA, Tolmasky ME. Carbapenemases: Transforming Acinetobacter baumannii into a Yet More Dangerous Menace. Biomolecules 2020; 10:biom10050720. [PMID: 32384624 PMCID: PMC7277208 DOI: 10.3390/biom10050720] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023] Open
Abstract
Acinetobacter baumannii is a common cause of serious nosocomial infections. Although community-acquired infections are observed, the vast majority occur in people with preexisting comorbidities. A. baumannii emerged as a problematic pathogen in the 1980s when an increase in virulence, difficulty in treatment due to drug resistance, and opportunities for infection turned it into one of the most important threats to human health. Some of the clinical manifestations of A. baumannii nosocomial infection are pneumonia; bloodstream infections; lower respiratory tract, urinary tract, and wound infections; burn infections; skin and soft tissue infections (including necrotizing fasciitis); meningitis; osteomyelitis; and endocarditis. A. baumannii has an extraordinary genetic plasticity that results in a high capacity to acquire antimicrobial resistance traits. In particular, acquisition of resistance to carbapenems, which are among the antimicrobials of last resort for treatment of multidrug infections, is increasing among A. baumannii strains compounding the problem of nosocomial infections caused by this pathogen. It is not uncommon to find multidrug-resistant (MDR, resistance to at least three classes of antimicrobials), extensively drug-resistant (XDR, MDR plus resistance to carbapenems), and pan-drug-resistant (PDR, XDR plus resistance to polymyxins) nosocomial isolates that are hard to treat with the currently available drugs. In this article we review the acquired resistance to carbapenems by A. baumannii. We describe the enzymes within the OXA, NDM, VIM, IMP, and KPC groups of carbapenemases and the coding genes found in A. baumannii clinical isolates.
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Affiliation(s)
- Maria Soledad Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
| | - Robert A. Bonomo
- Medical Service and GRECC, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH 44106, USA;
- Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, Proteomics and Bioinformatics; Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- WRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH 44106, USA
| | - Marcelo E. Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, CA 92831, USA;
- Correspondence: ; Tel.: +657-278-5263
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FARAJZADEH SHEIKH A, SHAHIN M, SHOKOOHIZADEH L, GHANBARI F, SOLGI H, SHAHCHERAGHI F. Emerge of NDM-1-Producing Multidrug-Resistant Pseudomonas aeruginosa and Co-Harboring of Carbapenemase Genes in South of Iran. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:959-967. [PMID: 32953684 PMCID: PMC7475625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND New Delhi metallo-beta-lactamase-1 (NDM-1) is one of the most important emerging antibiotic resistance. Co-harboring three or four carbapenemases is rare and only a few reports exist in the literature. We described the characteristics of the large epidemic outbreaks and reports co-producing blaNDM-1 with the other carbapenemase genes in P. aeruginosa isolates. METHODS This present cross-sectional research was conducted on 369 P. aeruginosa isolates obtained from burn and general hospitals within years 2013 to 2016. Beta-lactamase classes A, B and D genes were identified by PCR method. Modified hodge test (MHT), double-disk potentiation tests (DDPT) and double disk synergy test (DDST) were performed for detection carbapenemase and metallo beta-lactamase (MBL) production of blaNDM-1 positive P. aeruginos isolates. RESULTS From 236 carbapenem-resistant P. aeruginosa (CRPA), 116 isolates have had MBL genes and twenty-nine isolates were found positive for blaNDM-1 . In CRPA isolates, blaIMP-1 , blaVIM-2 and blaOXA-10 were identified in 27.5%, 21.1% and 32.2% of isolates respectively, while co-producing blaNDM-1 , blaIMP-1 , blaOXA-10 , co-producing blaNDM-1 , blaVIM-2 , blaOXA-10 and co-producing blaIMP-1 , blaVIM-2 were determined in 11 (4.6%), 8 (3.4%) and 27 (11.4%) of isolates respectively. CONCLUSION The finding of this co-existence of multiple carbapenemase resistance genes is threating for public health. Dipicolinic acid is a superior MBL inhibitor in DDPT antique than EDTA in DDST method for the detection of MBL-blaNDM-1 producing P. aeruginosa.
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Affiliation(s)
- Ahmad FARAJZADEH SHEIKH
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran,Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mojtaba SHAHIN
- Department of Medical Laboratory Sciences, Faculty of Medical Sciences, Arak Branch, Islamic Azad University, Arak, Iran,Corresponding Author:
| | - Leili SHOKOOHIZADEH
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamedan, Iran
| | - Fahimeh GHANBARI
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamid SOLGI
- Department of Bacteriology, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fereshteh SHAHCHERAGHI
- Department of Bacteriology, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Distinct Mechanisms of Dissemination of NDM-1 Metallo-β-Lactamase in Acinetobacter Species in Argentina. Antimicrob Agents Chemother 2020; 64:AAC.00324-20. [PMID: 32122888 DOI: 10.1128/aac.00324-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 01/10/2023] Open
Abstract
A 4-year surveillance of carbapenem-resistant Acinetobacter spp. isolates in Argentina identified 40 strains carrying bla NDM-1 Genome sequencing revealed that most were Acinetobacter baumannii, whereas seven represented other Acinetobacter spp. The A. baumannii genomes were closely related, suggesting recent spread. bla NDM-1 was located in the chromosome of A. baumannii strains and on a plasmid in non-A. baumannii strains. A resistance gene island carrying bla PER-7 and other resistance determinants was found on a plasmid in some A. baumannii strains.
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36
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Abouelfetouh A, Torky AS, Aboulmagd E. Role of plasmid carrying bla NDM in mediating antibiotic resistance among Acinetobacter baumannii clinical isolates from Egypt. 3 Biotech 2020; 10:170. [PMID: 32206504 PMCID: PMC7076099 DOI: 10.1007/s13205-020-2157-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/28/2020] [Indexed: 01/01/2023] Open
Abstract
We investigated antibiotic resistance levels among blaNDM-positive (n = 9) and -negative (n = 65) A. baumannii clinical isolates collected in 2010 and 2015 from Alexandria Main University Hospital, Egypt using disc diffusion and minimum inhibitory concentration (MIC) determination. Plasmids from blaNDM-positive isolates were transformed into a carbapenem-susceptible A. baumannii (CS-AB) isolate to assess the role of plasmid transfer in mediating carbapenem resistance. Imipenem, meropenem, and ertapenem MIC90 values against blaNDM-positive isolates were 128, > 256, and 256 µg/mL, respectively. Plasmid isolation and polymerase chain reaction revealed that blaNDM was plasmid mediated. The plasmids were electroporated into the cells of a CS-AB isolate at an efficiency of 1.3 × 10–8 to 2.6 × 10–7, transforming them to blaNDM-positive carbapenem-resistant cells with an imipenem MIC increase of 256-fold. In addition to carbapenem resistance, the blaNDM-positive isolates also exhibited higher levels of cephalosporins, tetracycline, aminoglycosides, fluoroquinolones, and colistin resistance than the blaNDM-negative isolates. Acquisition of blaNDM-carrying plasmids dramatically increased imipenem resistance among A. baumannii isolates. Intriguingly, blaNDM-positive isolates also showed a high degree of resistance to antibiotics of different classes. The potential co-existence of different resistance determinants on A. baumannii plasmids and their possible transfer owing to the natural competence of the pathogen are especially alarming. More effective infection control and antibiotic stewardship programs are needed to curb the spread and treat such infections in both hospital and community settings.
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Affiliation(s)
- Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 1 Khartoum Sq., Azarita, Alexandria, 21521 Egypt
| | - Aisha S. Torky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 1 Khartoum Sq., Azarita, Alexandria, 21521 Egypt
| | - Elsayed Aboulmagd
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, 1 Khartoum Sq., Azarita, Alexandria, 21521 Egypt
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Zalucki YM, Jen FEC, Pegg CL, Nouwens AS, Schulz BL, Jennings MP. Evolution for improved secretion and fitness may be the selective pressures leading to the emergence of two NDM alleles. Biochem Biophys Res Commun 2020; 524:555-560. [DOI: 10.1016/j.bbrc.2020.01.135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/24/2020] [Indexed: 01/07/2023]
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38
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Detection of blaOXA-23 and blaNDM-1 carbapenemase among clinical isolates of A. baumannii in Tabriz, north-west of Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2019.100555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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39
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Toleman MA. The Future of Peritoneal Dialysis in a Moving Landscape of Bacterial Resistance. Perit Dial Int 2020; 37:134-140. [DOI: 10.3747/pdi.2016.00038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Mark A. Toleman
- Department of Infection and Immunity School of Medicine, Cardiff University The Heath hospital, Heath Park Cardiff, UK
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40
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Shen X, Liu L, Yu J, Cao X, Zhan Q, Guo Y, Wang L, Yu F. Coexistence of bla NDM-1 and rmtC on a Transferrable Plasmid of a Novel ST192 Klebsiella aerogenes Clinical Isolate. Infect Drug Resist 2019; 12:3883-3891. [PMID: 31853191 PMCID: PMC6916698 DOI: 10.2147/idr.s228130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/02/2019] [Indexed: 01/14/2023] Open
Abstract
Introduction The occurrence and development of antibiotic resistance are mainly caused by the spread of large plasmids carrying multiple antibiotic resistance genes. Recently, the association between 16S rRNA methyltransferase genes and β-lactamase genes carried by the same plasmid is of concern. Methods The Klebsiella aerogenes 1564 was isolated from the catheter tip of a patient in a tertiary hospital, Shanghai, China. The presence of the bla NDM-1 and rmtC genes were assessed by PCR. Complete sequence of plasmid p1564 was determined. The K. aerogenes 1564 was characterized by antimicrobial susceptibility testing, Carbapenemase phenotype confirmation testing, conjugation experiment, S1-PFGE and multilocus sequence typing (MLST). Results Herein, we found that a New Delhi Metallo-β-lactamase-1 gene (bla NDM-1) and a 16S rRNA methyltransferase gene (rmtC) coexisted on a transferrable plasmid of a carbapenem-resistant K. aerogenes clinical isolate. The K. aerogenes clinical isolate was found to belong to a novel sequence type 192 (ST192) determined by MLST. The sequencing results of the plasmid p1564 carrying bla NDM-1 gene and rmtC gene showed that the size and guanine-cytosine content of the plasmid were 136, 902 bp and 51.8%, with 164 putative ORFs and two multidrug resistance gene islands. In addition to bla NDM-1and rmtC, the plasmid contained bleomycin resistance gene (ble MBL), CMY-6β-lactamase gene (bla CMY-6), quaternary ammonium compound resistance gene (sugE), truncated quaternary ammonium compound resistance gene (qacEΔ1), aminoglycoside resistance gene (aacA4) and sulfonamide resistance gene (sul1). By comparison, p1564 has high homology with pHS36-NDM from Salmonella enterica subsp. enterica serovar Stanley reported in China, with similar size and both belonging to plasmid incompatibility group A/C. Conclusion The present study demonstrated for the first time the co-existence of rmtC and bla NDM-1 in a novel ST192 K. aerogenes. The spread of plasmids harboring both bla NDM-1 and rmtC may occur among Enterobacteriaceae in China.
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Affiliation(s)
- Xiaofei Shen
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Li Liu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Jingyi Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Xingwei Cao
- Jiangxi Provincial Key Laboratory of Medicine, Clinical Laboratory of the Second Affiliated Hospital of Nanchang University, Nanchang 330006, People's Republic of China
| | - Qing Zhan
- Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang 330006, People's Republic of China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Liangxing Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
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Abstract
Antimicrobial resistance (AMR) is on the rise and spreading rapidly worldwide. Low- and middle-income countries, because of weak health systems, are particularly vulnerable to this increase. Population mobility further fuels the globalization of AMR, with travelers and migrants at significant risk of harboring drug-resistant organisms. This article provides an overview of the factors that contribute to the emergence, spread, and persistence of AMR, particularly antibiotic-resistance, in the tropics. Also addressed are clinical implications of this emergent global crisis for migrants and travelers, using specific scenarios commonly encountered in those populations.
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Hadjadj L, Baron SA, Diene SM, Rolain JM. How to discover new antibiotic resistance genes? Expert Rev Mol Diagn 2019; 19:349-362. [PMID: 30895843 DOI: 10.1080/14737159.2019.1592678] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.
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Affiliation(s)
- Linda Hadjadj
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Sophie Alexandra Baron
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Seydina M Diene
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Jean-Marc Rolain
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France.,b IHU Méditerranée Infection , Marseille , France
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Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D, Wilksch J, Cao H, Haq IU, Dougan G, Strugnell RA. Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep 2019; 9:2392. [PMID: 30787414 PMCID: PMC6382945 DOI: 10.1038/s41598-019-38943-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/11/2019] [Indexed: 11/25/2022] Open
Abstract
Klebsiella pneumoniae is a major threat to public health with the emergence of isolates resistant to most, if not all, useful antibiotics. We present an in-depth analysis of 178 extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae collected from patients resident in a region of Pakistan, during the period 2010-2012, when the now globally-distributed carbapenemase bla-NDM-1 was being acquired by Klebsiella. We observed two dominant lineages, but neither the overall resistance profile nor virulence-associated factors, explain their evolutionary success. Phenotypic analysis of resistance shows few differences between the acquisition of resistance genes and the phenotypic resistance profile, including beta-lactam antibiotics that were used to treat ESBL-positive strains. Resistance against these drugs could be explained by inhibitor-resistant beta-lactamase enzymes, carbapenemases or ampC type beta-lactamases, at least one of which was detected in most, but not all relevant strains analysed. Complete genomes for six selected strains are reported, these provide detailed insights into the mobile elements present in these isolates during the initial spread of NDM-1. The unexplained success of some lineages within this pool of highly resistant strains, and the discontinuity between phenotypic resistance and genotype at the macro level, indicate that intrinsic mechanisms contribute to competitive advantage and/or resistance.
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Affiliation(s)
- Eva Heinz
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, CAMS, Jouf University, Al-Jouf, Saudi Arabia
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology, The Children's Hospital & The Institute of Child Health, Lahore, Pakistan
| | | | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Shruti Gujaran
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Derek Pickard
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ikram-Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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NDM Metallo-β-Lactamases and Their Bacterial Producers in Health Care Settings. Clin Microbiol Rev 2019; 32:32/2/e00115-18. [PMID: 30700432 DOI: 10.1128/cmr.00115-18] [Citation(s) in RCA: 375] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase able to hydrolyze almost all β-lactams. Twenty-four NDM variants have been identified in >60 species of 11 bacterial families, and several variants have enhanced carbapenemase activity. Klebsiella pneumoniae and Escherichia coli are the predominant carriers of bla NDM, with certain sequence types (STs) (for K. pneumoniae, ST11, ST14, ST15, or ST147; for E. coli, ST167, ST410, or ST617) being the most prevalent. NDM-positive strains have been identified worldwide, with the highest prevalence in the Indian subcontinent, the Middle East, and the Balkans. Most bla NDM-carrying plasmids belong to limited replicon types (IncX3, IncFII, or IncC). Commonly used phenotypic tests cannot specifically identify NDM. Lateral flow immunoassays specifically detect NDM, and molecular approaches remain the reference methods for detecting bla NDM Polymyxins combined with other agents remain the mainstream options of antimicrobial treatment. Compounds able to inhibit NDM have been found, but none have been approved for clinical use. Outbreaks caused by NDM-positive strains have been reported worldwide, attributable to sources such as contaminated devices. Evidence-based guidelines on prevention and control of carbapenem-resistant Gram-negative bacteria are available, although none are specific for NDM-positive strains. NDM will remain a severe challenge in health care settings, and more studies on appropriate countermeasures are required.
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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Gentilini F, Turba ME, Pasquali F, Mion D, Romagnoli N, Zambon E, Terni D, Peirano G, Pitout JDD, Parisi A, Sambri V, Zanoni RG. Hospitalized Pets as a Source of Carbapenem-Resistance. Front Microbiol 2018; 9:2872. [PMID: 30574124 PMCID: PMC6291488 DOI: 10.3389/fmicb.2018.02872] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
The massive and irrational use of antibiotics in livestock productions has fostered the occurrence and spread of resistance to “old class antimicrobials.” To cope with that phenomenon, some regulations have been already enforced in the member states of the European Union. However, a role of livestock animals in the relatively recent alerts on the rapid worldwide increase of resistance to last-choice antimicrobials as carbapenems is very unlikely. Conversely, these antimicrobials are increasingly administered in veterinary hospitals whose role in spreading bacteria or mobile genetic elements has not adequately been addressed so far. A cross-sectional study was carried out on 105 hospitalized and 100 non-hospitalized pets with the aim of measuring the prevalence of carbapenem-resistant Gram-negative bacteria (GNB) colonizing dogs and cats, either hospitalized or not hospitalized and estimating the relative odds. Stool samples were inoculated on MacConkey agar plates containing 1 mg/L imipenem which were then incubated aerobically at 37°C ± 1 for 48 h. Isolated bacteria were identified first by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and were confirmed by 16S rRNA sequencing. The genetic basis of resistance was investigated using PCR methods, gene or whole genome sequencing (WGS). The prevalence of pets harboring carbapenem-resistant bacteria was 11.4 and 1.0% in hospitalized and not-hospitalized animals, respectively, with an odds ratio of 12.8 (p < 0.01). One pet carried two diverse isolates. Overall, 14 gram-negative non-fermenting bacteria, specifically, one Acinetobacter radioresistens, five Acinetobacter baumannii, six Pseudomonas aeruginosa and two Stenotrophomonas maltophilia were isolated. The Acinetobacter species carried acquired carbapenemases genes encoded by blaNDM-1 and blaOXA-23. In contrast, Pseudomonas phenotypic resistance was associated with the presence of mutations in the oprD gene. Notably, inherent carbapenem-resistant isolates of S. maltophilia were also resistant to the first-line recommended chemotherapeutic trimethoprim/sulfamethoxazole. This study estimates the risk of colonization by carbapenem-resistant non-fermenting GNB in pets hospitalized in veterinary tertiary care centers and highlights their potential role in spreading resistance genes among the animal and human community. Public health authorities should consider extending surveillance systems and putting the release of critical antibiotics under more strict control in order to manage the infection/colonization of pets in veterinary settings.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | | | - Frederique Pasquali
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Domenico Mion
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Noemi Romagnoli
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
| | - Elisa Zambon
- Ospedale: Veterinario I Portoni Rossi s.r.l., Bologna, Italy
| | - Daniele Terni
- Ospedale: Veterinario I Portoni Rossi s.r.l., Bologna, Italy
| | - Gisele Peirano
- Unit of Microbiology, University of Calgary and Calgary Laboratory Services, Calgary, AB, Canada
| | | | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Vittorio Sambri
- The Great Romagna Hub Laboratory, Pievesestina, Italy.,Department of Experimental, Diagnostic and Specialty Medicine - DIMES, University of Bologna, Bologna, Italy
| | - Renato Giulio Zanoni
- Department of Veterinary Medical Sciences, University of Bologna, Bologna, Italy
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1172] [Impact Index Per Article: 195.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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Szymanek-Majchrzak K, Mlynarczyk A, Kuthan R, Sawicka-Grzelak A, Majchrzak K, Kawecki D, Kosieradzki M, Durlik M, Deborska-Materkowska D, Paczek L, Mlynarczyk G. Significance of Screening Tests and the Incidence of New Delhi Metallo-beta-lactamase-Producing Gram-negative Bacilli in the Surgery and Transplantation Wards of a Warsaw Medical Center During the Period From April 2014 to May 2017. Transplant Proc 2018; 50:2159-2163. [PMID: 30177130 DOI: 10.1016/j.transproceed.2018.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/16/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022]
Abstract
BACKGROUND The first New Delhi metallo-beta-lactamase (NDM)-producing bacteria were isolated in 2008 in the world, and in 2011 in Poland. Due to the high clonal diversity (17 types) of their blaNDM gene, encoded on (Tn125-like) mobile genetic elements, these strains usually exhibit resistance to nearly all available antibiotics, which is particularly dangerous for organ transplant recipients. PURPOSE To assess of the prevalence of Gram-negative NDM-positive bacilli in surgery/transplantation wards of a teaching hospital in Warsaw and to ascertain the significance of screening tests on the rates and nature of colonization. MATERIALS AND METHODS The evaluated strains were isolated from 30 patients (between April 2014 and May 2017). The species were identified with VITEK-MS, antibiotic susceptibility was determined with VITEK 2, disk-diffusion, and/or E-test methods, according to EUCAST guidelines. The presence of the blaNDM-1 gene was confirmed using the polymerase chain reaction technique. RESULTS AND CONCLUSIONS There were 77 blaNDM-1-positive Klebsiella pneumoniae strains isolated from 30 patients. Cultures from individual patients, mainly from rectal swabs (53.9%) and urine samples (39.8%), yielded 1-11 isolates. Fifteen patients were already colonized on admission, and the other 15 developed a symptomatic infection. In total, 24 (80%) patients were carriers, and their colonizations persisted for <1-20 months. Most isolates were susceptible only to colistin, gentamicin, amikacin, tigecycline, and/or sulfamethoxazole/trimethoprim. Gastrointestinal-tract-colonizing K pneumoniae are the main reservoir of the blaNDM-1 gene. Following the introduction of on-admission mandatory screening for carbapenem-resistant strains, the rates of NDM-producing K pneumoniae isolation increased (7.5-fold), while the rates of isolation from patients with symptomatic infections considerably decreased (2.8-fold).
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Affiliation(s)
- K Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland.
| | - A Mlynarczyk
- Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland
| | - R Kuthan
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - A Sawicka-Grzelak
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland
| | - K Majchrzak
- Department of Prosthetic Dentistry, Medical University of Warsaw, Warsaw, Poland
| | - D Kawecki
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - M Kosieradzki
- Department of General and Transplantation Surgery, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - M Durlik
- Department of Transplant Medicine and Nephrology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - D Deborska-Materkowska
- Department of Transplant Medicine and Nephrology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - L Paczek
- Department of Immunology, Transplantology and Internal Diseases, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - G Mlynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; Department of Medical Microbiology, The Infant Jesus Teaching Hospital, Warsaw, Poland
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Wilson H, Török ME. Extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacteriaceae. Microb Genom 2018; 4:e000197. [PMID: 30035710 PMCID: PMC6113871 DOI: 10.1099/mgen.0.000197] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 06/19/2018] [Indexed: 12/12/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global public-health emergency, which threatens the advances made by modern medical care over the past century. The World Health Organization has recently published a global priority list of antibiotic-resistant bacteria, which includes extended-spectrum β-lactamase-producing Enterobacteriaceae and carbapenemase-producing Enterobacteriaceae. In this review, we highlight the mechanisms of resistance and the genomic epidemiology of these organisms, and the impact of AMR.
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Affiliation(s)
- Hayley Wilson
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - M. Estée Török
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
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