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Conte D, Mesa D, Krul D, Bail L, Ito CAS, Palmeiro JK, Dalla-Costa LM. Comparative genomics of IncQ1 plasmids carrying bla GES variants from clinical and environmental sources in Brazil. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105644. [PMID: 39038632 DOI: 10.1016/j.meegid.2024.105644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/08/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024]
Abstract
IncQ-type plasmids have become important vectors in the dissemination of blaGES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different blaGES variants from human and environmental sources. The blaGES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored blaGES-7 in a class 1 integron (In2061), recently described by our group, and K. variicola carried blaGES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS6100 truncating the 3'-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of blaGES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.
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Affiliation(s)
- Danieli Conte
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil.
| | - Dany Mesa
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Damaris Krul
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
| | - Larissa Bail
- Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | | | - Jussara Kasuko Palmeiro
- Departamento de Análises Clínicas, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil; Laboratório de Microbiologia Molecular Aplicada, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Libera Maria Dalla-Costa
- Faculdades Pequeno Príncipe, Curitiba, Paraná, Brazil; Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, Paraná, Brazil
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Long TF, Zhou SY, Huang ZL, Li G, Zhong Q, Zhang XJ, Li YY, Chen CP, Xia LJ, Wei R, Wan L, Gao A, Ren H, Liao XP, Liu YH, Chen L, Sun J. Innovative Delivery System Combining CRISPR-Cas12f for Combatting Antimicrobial Resistance in Gram-Negative Bacteria. ACS Synth Biol 2024; 13:1831-1841. [PMID: 38863339 DOI: 10.1021/acssynbio.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Antimicrobial resistance poses a significant global challenge, demanding innovative approaches, such as the CRISPR-Cas-mediated resistance plasmid or gene-curing system, to effectively combat this urgent crisis. To enable successful curing of antimicrobial genes or plasmids through CRISPR-Cas technology, the development of an efficient broad-host-range delivery system is paramount. In this study, we have successfully designed and constructed a novel functional gene delivery plasmid, pQ-mini, utilizing the backbone of a broad-host-range Inc.Q plasmid. Moreover, we have integrated the CRISPR-Cas12f system into the pQ-mini plasmid to enable gene-curing in broad-host of bacteria. Our findings demonstrate that pQ-mini facilitates the highly efficient transfer of genetic elements to diverse bacteria, particularly in various species in the order of Enterobacterales, exhibiting a broader host range and superior conjugation efficiency compared to the commonly used pMB1-like plasmid. Notably, pQ-mini effectively delivers the CRISPR-Cas12f system to antimicrobial-resistant strains, resulting in remarkable curing efficiencies for plasmid-borne mcr-1 or blaKPC genes that are comparable to those achieved by the previously reported pCasCure system. In conclusion, our study successfully establishes and optimizes pQ-mini as a broad-host-range functional gene delivery vector. Furthermore, in combination with the CRISPR-Cas system, pQ-mini demonstrates its potential for broad-host delivery, highlighting its promising role as a novel antimicrobial tool against the growing threat of antimicrobial resistance.
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Affiliation(s)
- Teng-Fei Long
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Shi-Ying Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Zi-Lei Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Gong Li
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Qin Zhong
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Jing Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Yuan-Yuan Li
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Cai-Ping Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Li-Juan Xia
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ran Wei
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Lei Wan
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ang Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Hao Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Xiao-Ping Liao
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Ya-Hong Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Liang Chen
- Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14214, United States
| | - Jian Sun
- Guangdong Laboratory for Lingnan Modern Agriculture, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P. R. China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics, Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, P. R. China
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Wang Y, Dagan T. The evolution of antibiotic resistance islands occurs within the framework of plasmid lineages. Nat Commun 2024; 15:4555. [PMID: 38811529 PMCID: PMC11137137 DOI: 10.1038/s41467-024-48352-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 04/25/2024] [Indexed: 05/31/2024] Open
Abstract
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
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Affiliation(s)
- Yiqing Wang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany.
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Mumtaz MN, Irfan M, Siraj S, Khan A, Khan H, Imran M, Khan IA, Khan A. Whole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan. J Infect Public Health 2024; 17:271-282. [PMID: 38134602 DOI: 10.1016/j.jiph.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/18/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
BACKGROUND Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan. METHODOLOGY We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation. RESULTS MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan. Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis. CONCLUSION This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.
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Affiliation(s)
- Mah Noor Mumtaz
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Sami Siraj
- Institute of Pharmaceutical Sciences, Khyber Medical University (KMU), Peshawar, Pakistan
| | - Aslam Khan
- Department of Pathology, Medical Teaching Institution MTI, Hayatabad Medical Complex (HMC), Peshawar, Pakistan
| | - Hizbullah Khan
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Muhammad Imran
- Research center for Advanced Materials Science (RCAMS), Chemistry Department, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan (AWKUM), Mardan, Pakistan.
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Tokuda M, Shintani M. Microbial evolution through horizontal gene transfer by mobile genetic elements. Microb Biotechnol 2024; 17:e14408. [PMID: 38226780 PMCID: PMC10832538 DOI: 10.1111/1751-7915.14408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024] Open
Abstract
Mobile genetic elements (MGEs) are crucial for horizontal gene transfer (HGT) in bacteria and facilitate their rapid evolution and adaptation. MGEs include plasmids, integrative and conjugative elements, transposons, insertion sequences and bacteriophages. Notably, the spread of antimicrobial resistance genes (ARGs), which poses a serious threat to public health, is primarily attributable to HGT through MGEs. This mini-review aims to provide an overview of the mechanisms by which MGEs mediate HGT in microbes. Specifically, the behaviour of conjugative plasmids in different environments and conditions was discussed, and recent methodologies for tracing the dynamics of MGEs were summarised. A comprehensive understanding of the mechanisms underlying HGT and the role of MGEs in bacterial evolution and adaptation is important to develop strategies to combat the spread of ARGs.
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Affiliation(s)
- Maho Tokuda
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
| | - Masaki Shintani
- Department of Environment and Energy Systems, Graduate School of Science and TechnologyShizuoka UniversityHamamatsuJapan
- Research Institute of Green Science and TechnologyShizuoka UniversityHamamatsuJapan
- Japan Collection of MicroorganismsRIKEN BioResource Research CenterIbarakiJapan
- Graduate School of Integrated Science and TechnologyShizuoka UniversityHamamatsuJapan
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Sun H, Li H, Zhang X, Liu Y, Chen H, Zheng L, Zhai Y, Zheng H. The honeybee gut resistome and its role in antibiotic resistance dissemination. Integr Zool 2023; 18:1014-1026. [PMID: 36892101 DOI: 10.1111/1749-4877.12714] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
There is now general concern about widespread antibiotic resistance, and growing evidence indicates that gut microbiota is critical in providing antibiotic resistance. Honeybee is an important pollinator; the incidence of antibiotic resistance genes in honeybee gut causes potential risks to not only its own health but also to public and animal health, for its potential disseminator role, thus receiving more attention from the public. Recent analysis results reveal that the gut of honeybee serves as a reservoir of antibiotic resistance genes, probably due to antibiotics application history in beekeeping and horizontal gene transfer from the highly polluted environment. These antibiotic resistance genes accumulate in the honeybee gut and could be transferred to the pathogen, even having the potential to spread during pollination, tending, social interactions, etc. Newly acquired resistance traits may cause fitness reduction in bacteria whereas facilitating adaptive evolution as well. This review outlines the current knowledge about the resistome in honeybee gut and emphasizes its role in antibiotic resistance dissemination.
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Affiliation(s)
- Huihui Sun
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Sanya Institute of China Agricultural University, Sanya, China
| | - Hu Li
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan Liu
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Chen
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Li Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and Insect Pests, Jinan, China
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7
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Shelenkov A, Mikhaylova Y, Voskanyan S, Egorova A, Akimkin V. Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates. Microorganisms 2023; 11:1314. [PMID: 37317293 DOI: 10.3390/microorganisms11051314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Shushanik Voskanyan
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Anna Egorova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
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Shintani M, Suzuki H, Nojiri H, Suzuki M. Reconsideration of the previously classified incompatibility groups of plasmids, IncP-1 and IncP-11. Environ Microbiol 2023. [PMID: 36744408 DOI: 10.1111/1462-2920.16345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
This study presents the reassessment of earlier published data with reference to the article published in Environmental Microbiology entitled 'IncP-type plasmids carrying genes for antibiotic resistance or aromatic compound degradation are prevalent in sequenced Aromatoleum and Thauera strains' by Lo et al. This correspondence clarifies misperceptions of plasmids classified under incompatibility (Inc) groups IncP-1 and IncP-11.
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Affiliation(s)
- Masaki Shintani
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Hamamatsu, Shizuoka, Japan.,Research Institute of Green Science and Technology, Shizuoka University, Hamamatsu, Shizuoka, Japan.,Japan Collection of Microorganisms, RIKEN BioResource Research Center, Ibaraki, Japan
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Hideaki Nojiri
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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Major N, Jechalke S, Nesme J, Goreta Ban S, Černe M, Sørensen SJ, Ban D, Grosch R, Schikora A, Schierstaedt J. Influence of sewage sludge stabilization method on microbial community and the abundance of antibiotic resistance genes. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 154:126-135. [PMID: 36242814 DOI: 10.1016/j.wasman.2022.09.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Municipal sewage sludge (MSS) and other biosolids are of high interest for agriculture. These nutrient-rich organic materials can potentially serve as organic fertilizers. Besides an increase of organic matter in soil, other positive effects were shown after their application. Especially the positive influence on circular economy increased the attention paid to management of MSS in recent years. Unfortunately, the use of sewage sludge has some drawbacks. Biosolids are frequently polluted with heavy metals, xenobiotic organic compounds and industrial chemicals, which may be hazardous for the environment and humans. Here, we investigated the influence of stabilization method and the size of wastewater treatment plant on the structure of microbial communities as well as the abundance of antibiotic resistance genes (ARG) and mobile genetic elements (MGE). All tested ARG and MGE were detectable in almost all of the samples. Interestingly, the presence of MGE as well as particular heavy metals correlated positively with the presence of several ARG. We conclude that the distribution of ARG and MGE in biosolids originated from municipal wastewater treatment plants, cannot be explained by the size of the facility or the applied stabilization method. Moreover, we postulate that the presence of pollutants and long-term impacts should be assessed prior to a possible use of sewage sludge as fertilizer.
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Affiliation(s)
- Nikola Major
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Sven Jechalke
- Institute for Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Joseph Nesme
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | | | - Marko Černe
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Søren J Sørensen
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Dean Ban
- Institute of Agriculture and Tourism, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Rita Grosch
- Leibniz Institute of Vegetable and Ornamental Crops, Department Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Adam Schikora
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany.
| | - Jasper Schierstaedt
- Leibniz Institute of Vegetable and Ornamental Crops, Department Plant-Microbe Systems, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
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Yang X, Zhang T, Lei CW, Wang Q, Huang Z, Chen X, Wang HN. Florfenicol and oxazolidone resistance status in livestock farms revealed by short- and long-read metagenomic sequencing. Front Microbiol 2022; 13:1018901. [PMID: 36338088 PMCID: PMC9632178 DOI: 10.3389/fmicb.2022.1018901] [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: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 12/03/2022] Open
Abstract
Antibiotic resistance genes (ARGs) as a novel type of environmental pollutant pose a health risk to humans. Oxazolidinones are one of the most important antibiotics for the treatment of Gram-positive bacterial infections in humans. Although oxazolidinones are not utilized in the livestock industry, florfenicol is commonly used on farms to treat bacterial infections, which may contribute to the spread of the cfr, optrA, and poxtA genes on farms. Using metagenomics sequencing, we looked into the antibiotic resistome context of florfenicol and oxazolidinone in 10 large-scale commercial farms in China. We identified 490 different resistance genes and 1,515 bacterial genera in the fecal samples obtained from 10 farms. Florfenicol-resistant Kurthia, Escherichia, and Proteus were widely present in these samples. The situation of florfenicol and oxazolidone resistance in pig farms is even more severe. The total number of genes and the abundance of drug resistance genes were higher in pigs than in chickens, including optrA and poxtA. All the samples we collected had a high abundance of fexA and floR. Through nanopore metagenomic analysis of the genetic environment, we found that plasmids, integrative and conjugative element (ICE), and transposons (Tn7-like and Tn558) may play an important role in the spread of floR, cfr, and optrA. Our findings suggest that florfenicol and oxazolidinone resistance genes have diverse genetic environments and are at risk of co-transmission with, for example, tetracycline and aminoglycoside resistance genes. The spread of florfenicol- and oxazolidinone–resistant bacteria on animal farms should be continuously monitored.
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Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary. Antibiotics (Basel) 2022; 11:antibiotics11101441. [PMID: 36290099 PMCID: PMC9598914 DOI: 10.3390/antibiotics11101441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/26/2022] Open
Abstract
The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a blaOXA-48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations.
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12
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Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11101364. [PMID: 36290022 PMCID: PMC9598329 DOI: 10.3390/antibiotics11101364] [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: 09/21/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3′)-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates.
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Novel Insights into blaGES Mobilome Reveal Extensive Genetic Variation in Hospital Effluents. Microbiol Spectr 2022; 10:e0246921. [PMID: 35880869 PMCID: PMC9430818 DOI: 10.1128/spectrum.02469-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mobile genetic elements contribute to the emergence and spread of multidrug-resistant bacteria by enabling the horizontal transfer of acquired antibiotic resistance among different bacterial species and genera. This study characterizes the genetic backbone of blaGES in Aeromonas spp. and Klebsiella spp. isolated from untreated hospital effluents. Plasmids ranging in size from 9 to 244 kb, sequenced using Illumina and Nanopore platforms, revealed representatives of plasmid incompatibility groups IncP6, IncQ1, IncL/M1, IncFII, and IncFII-FIA. Different GES enzymes (GES-1, GES-7, and GES-16) were located in novel class 1 integrons in Aeromonas spp. and GES-5 in previously reported class 1 integrons in Klebsiella spp. Furthermore, in Klebsiella quasipneumoniae, blaGES-5 was found in tandem as a coding sequence that disrupted the 3' conserved segment (CS). In Klebsiella grimontii, blaGES-5 was observed in two different plasmids, and one of them carried multiple IncF replicons. Three Aeromonas caviae isolates presented blaGES-1, one Aeromonas veronii isolate presented blaGES-7, and another A. veronii isolate presented blaGES-16. Multilocus sequence typing (MLST) analysis revealed novel sequence types for Aeromonas and Klebsiella species. The current findings highlight the large genetic diversity of these species, emphasizing their great adaptability to the environment. The results also indicate a public health risk because these antimicrobial-resistant genes have the potential to reach wastewater treatment plants and larger water bodies. Considering that they are major interfaces between humans and the environment, they could spread throughout the community to clinical settings. IMPORTANCE In the "One Health" approach, which encompasses human, animal, and environmental health, emerging issues of antimicrobial resistance are associated with hospital effluents that contain clinically relevant antibiotic-resistant bacteria along with a wide range of antibiotic concentrations, and lack regulatory status for mandatory prior and effective treatment. blaGES genes have been reported in aquatic environments despite the low detection of these genes among clinical isolates within the studied hospitals. Carbapenemase enzymes, which are relatively unusual globally, such as GES type inserted into new integrons on plasmids, are worrisome. Notably, K. grimontii, a newly identified species, carried two plasmids with blaGES-5, and K. quasipneumoniae carried two copies of blaGES-5 at the same plasmid. These kinds of plasmids are primarily responsible for multidrug resistance among bacteria in both clinical and natural environments, and they harbor resistant genes against antibiotics of key importance in clinical therapy, possibly leading to a public health problem of large proportion.
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Hull DM, Harrell E, Harden L, Thakur S. Multidrug resistance and virulence genes carried by mobile genomic elements in Salmonella enterica isolated from live food animals, processed, and retail meat in North Carolina, 2018–2019. Int J Food Microbiol 2022; 378:109821. [DOI: 10.1016/j.ijfoodmicro.2022.109821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/02/2022] [Accepted: 06/19/2022] [Indexed: 11/25/2022]
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15
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Sun H, Mu X, Zhang K, Lang H, Su Q, Li X, Zhou X, Zhang X, Zheng H. Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids. MICROBIOME 2022; 10:69. [PMID: 35501925 PMCID: PMC9063374 DOI: 10.1186/s40168-022-01268-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND The spread of antibiotic resistance genes (ARGs) has been of global concern as one of the greatest environmental threats. The gut microbiome of animals has been found to be a large reservoir of ARGs, which is also an indicator of the environmental antibiotic spectrum. The conserved microbiota makes the honeybee a tractable and confined ecosystem for studying the maintenance and transfer of ARGs across gut bacteria. Although it has been found that honeybee gut bacteria harbor diverse sets of ARGs, the influences of environmental variables and the mechanism driving their distribution remain unclear. RESULTS We characterized the gut resistome of two closely related honeybee species, Apis cerana and Apis mellifera, domesticated in 14 geographic locations across China. The composition of the ARGs was more associated with host species rather than with geographical distribution, and A. mellifera had a higher content of ARGs in the gut. There was a moderate geographic pattern of resistome distribution, and several core ARG groups were found to be prevalent among A. cerana samples. These shared genes were mainly carried by the honeybee-specific gut members Gilliamella and Snodgrassella. Transferrable ARGs were frequently detected in honeybee guts, and the load was much higher in A. mellifera samples. Genomic loci of the bee gut symbionts containing a streptomycin resistance gene cluster were nearly identical to those of the broad-host-range IncQ plasmid, a proficient DNA delivery system in the environment. By in vitro conjugation experiments, we confirmed that the mobilizable plasmids could be transferred between honeybee gut symbionts by conjugation. Moreover, "satellite plasmids" with fragmented genes were identified in the integrated regions of different symbionts from multiple areas. CONCLUSIONS Our study illustrates that the gut microbiota of different honeybee hosts varied in their antibiotic resistance structure, highlighting the role of the bee microbiome as a potential bioindicator and disseminator of antibiotic resistance. The difference in domestication history is highly influential in the structuring of the bee gut resistome. Notably, the evolution of plasmid-mediated antibiotic resistance is likely to promote the probability of its persistence and dissemination. Video Abstract.
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Affiliation(s)
- Huihui Sun
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xiaohuan Mu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kexun Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Haoyu Lang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qinzhi Su
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Xingan Li
- Key Laboratory for Bee Genetics and Breeding, Jilin Provincial Institute of Apicultural Sciences, Jilin, 132000, China
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100083, China.
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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Plasmid-Mediated Quinolone Resistance (PMQR) in Two Clinical Strains of Salmonella enterica Serovar Corvallis. Microorganisms 2022; 10:microorganisms10030579. [PMID: 35336154 PMCID: PMC8953408 DOI: 10.3390/microorganisms10030579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 01/27/2023] Open
Abstract
Non-typhoid serovars of Salmonella enterica are one of the main causes of bacterial food-borne infections worldwide. For the treatment of severe cases of salmonellosis in adults, fluoroquinolones are amongst the drugs of choice. They are categorized by the World Health Organization (WHO) as “critically important with highest priority in human medicine”. In the present study, two clinical S. enterica serovar Corvallis isolates (HUA 5/18 and HUA 6/18) from a Spanish hospital, selected on the basis of fluoroquinolone resistance, were characterized. The MICs of ciprofloxacin, determined by E-test, were 0.5 and 0.75 µg/mL for HUA 5/18 and HUA 6/18, respectively, and both were also resistant to pefloxacin but susceptible to nalidixic acid. Whole genome sequencing (WGS) of the isolates was performed with Illumina platform, and different bioinformatics tools were used for sequence analysis. The two isolates belonged to ST1541, and had the Thr57Ser substitution in the ParC protein which is also found in ciprofloxacin susceptible isolates. However, they harbored identical ColE plasmids of 10 kb carrying the qnrS1 gene. In these plasmids, the gene was flanked by defective versions of IS2-like and ISKra4-like insertion sequences. HUA 5/18 and HUA 6/18 were also phenotypically resistant to streptomycin, sulfonamides and tetracycline, with the responsible genes: strA, strB, sul2 and tet(A) genes, being located on a IncQ1 plasmid. ColE plasmids with the qnrS1 gene are widely spread among multiple serovars of S. enterica from different samples and countries. These mobilizable plasmids are playing an important role in the worldwide spread of qnrS1. Thus, their detection in hospitals is a cause of concern which deserves further attention.
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17
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Ramstad SN, Brandal LT, Taxt AM, Wasteson Y, Bjørnholt JV, Naseer U. Prevalence of genotypic antimicrobial resistance in clinical Shiga toxin-producing Escherichia coli in Norway, 2018 to 2020. J Med Microbiol 2021; 70. [PMID: 34870582 PMCID: PMC8744279 DOI: 10.1099/jmm.0.001454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction Shiga toxin-producing Escherichia coli (STEC) can cause severe to fatal disease in humans. Antimicrobial treatment is sometimes necessary, but contraindicated due to undesirable clinical outcome. However, recent studies have shown promising outcomes following antimicrobial treatment. Before the establishment of a possible antimicrobial treatment strategy for STEC infections, the prevalence of antimicrobial resistance in STEC needs to be determined. Gap statement The resistance status of Norwegian clinical STEC is not known and should be assessed. Aim We aim to characterize genotypic antimicrobial resistance determinants in clinical STEC in Norway, and determine the prevalence of genotypic resistance in order to inform possible antimicrobial treatment options for STEC infections. Methodology We included all clinical STEC submitted to the Norwegian Reference Laboratory from March 2018 to April 2020. All samples were whole-genome sequenced and screened for genotypic antimicrobial resistance,virulence determinants and plasmid incompatibility groups. We performed phylogenetic clustering of STEC by core-genome multi-locus sequence typing, and statistical association analyses between isolate characteristics and genotypic resistance. Results A total of 459 STEC were analysed. For 385 (83.9 %) STEC we did not identify any antimicrobial resistance determinants. Seventy-four STEC (16.1 %) harboured antimicrobial resistance determinants against one or more antimicrobial classes. The most frequent genotypic resistance was identified against aminoglycosides (10.5 %). Thirty-nine STEC (8.5 %) had a multi-drug resistance (MDR) genotype. Genotypic resistance was more prevalent in non-O157 than O157 STEC (P=0.02). A positive association was seen between genotypic resistance and the low-virulent STEC O117:H7 phylogenetic cluster (no. 14) (P<0.001). Genotypic resistance was not significantly associated to high-virulent STEC. STEC O146:H28 and isolates harbouring the plasmid replicon type IncQ1 were positively associated with MDR. Conclusion The overall prevalence of genotypic resistance in clinical STEC in Norway is low (16.1 %). Genotypic resistance is more prevalent in non-O157 strains compared to O157 strains, and not significantly associated to high-virulent STEC. Resistance to antimicrobials suggested for treatment, especially azithromycin is low and may present an empiric treatment alternative for severe STEC infections.
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Affiliation(s)
- Silje N Ramstad
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424 Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lin T Brandal
- Department of Infectious Diseases and Prevention, Norwegian Institute of Public Health, Oslo, Norway.,ECDC fellowship Programme, Public Health Microbiology path (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Arne M Taxt
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424 Oslo, Norway.,Department of Infectious Diseases and Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Yngvild Wasteson
- Department of Paraclinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
| | - Jørgen V Bjørnholt
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956 Nydalen, 0424 Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Umaer Naseer
- Department of Infectious Diseases and Prevention, Norwegian Institute of Public Health, Oslo, Norway
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18
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Bearson SMD. Salmonella in Swine: Prevalence, Multidrug Resistance, and Vaccination Strategies. Annu Rev Anim Biosci 2021; 10:373-393. [PMID: 34699256 DOI: 10.1146/annurev-animal-013120-043304] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An estimated 1.3 million Salmonella infections and 420 deaths occur annually in the United States, with an estimated economic burden of $3.7 billion. More than 50% of US swine operations test positive for Salmonella according to the National Animal Health Monitoring System, and 20% of Salmonella from swine are multidrug resistant (resistant to ≥3 antimicrobial classes) as reported by the National Antimicrobial Resistance Monitoring System. This review on Salmonella in swine addresses the current status of these topics by discussing antimicrobial resistance and metal tolerance in Salmonella and the contribution of horizontal gene transfer. A major challenge in controlling Salmonella is that Salmonella is a foodborne pathogen in humans but is often a commensal in food animals and thereby establishes an asymptomatic reservoir state in such animals, including swine. As food animal production systems continue to expand and antimicrobial usage becomes more limited, the need for Salmonella interventions has intensified. A promising mitigation strategy is vaccination against Salmonella in swine to limit animal, environmental, and food contamination. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shawn M D Bearson
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, Agricultural Research Center, US Department of Agriculture, Ames, Iowa, USA;
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19
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McMillan EA, Nguyen LHT, Hiott LM, Sharma P, Jackson CR, Frye JG, Chen CY. Genomic Comparison of Conjugative Plasmids from Salmonella enterica and Escherichia coli Encoding Beta-Lactamases and Capable of Mobilizing Kanamycin Resistance Col-like Plasmids. Microorganisms 2021; 9:microorganisms9112205. [PMID: 34835331 PMCID: PMC8623487 DOI: 10.3390/microorganisms9112205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella enterica and Escherichia coli are important human pathogens that frequently contain plasmids, both large and small, carrying antibiotic resistance genes. Large conjugative plasmids are known to mobilize small Col plasmids, but less is known about the specificity of mobilization. In the current study, six S. enterica and four E. coli strains containing large plasmids were tested for their ability to mobilize three different kanamycin resistance Col plasmids (KanR plasmids). Large conjugative plasmids from five isolates, four S. enterica and one E. coli, were able to mobilize KanR plasmids of various types. Plasmids capable of mobilizing the KanR plasmids were either IncI1 or IncX, while IncI1 and IncX plasmids with no evidence of conjugation had disrupted transfer regions. Conjugative plasmids of similar types mobilized similar KanR plasmids, but not all conjugative plasmid types were capable of mobilizing all of the KanR plasmids. These data describe some of the complexities and specificities of individual small plasmid mobilization.
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Affiliation(s)
- Elizabeth A. McMillan
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Athens, GA 30605, USA; (E.A.M.); (L.M.H.); (C.R.J.)
| | - Ly-Huong T. Nguyen
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Molecular Characterization of Foodborne Pathogens Research Unit, Wyndmoor, PA 19038, USA; (L.-H.T.N.); (C.-Y.C.)
| | - Lari M. Hiott
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Athens, GA 30605, USA; (E.A.M.); (L.M.H.); (C.R.J.)
| | - Poonam Sharma
- Institute of Biosecurity and Microbial Forensics, Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA;
| | - Charlene R. Jackson
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Athens, GA 30605, USA; (E.A.M.); (L.M.H.); (C.R.J.)
| | - Jonathan G. Frye
- U.S. Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, Athens, GA 30605, USA; (E.A.M.); (L.M.H.); (C.R.J.)
- Correspondence:
| | - Chin-Yi Chen
- U.S. Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Molecular Characterization of Foodborne Pathogens Research Unit, Wyndmoor, PA 19038, USA; (L.-H.T.N.); (C.-Y.C.)
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20
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Mohsin M, Hassan B, Martins WMBS, Li R, Abdullah S, Sands K, Walsh TR. Emergence of plasmid-mediated tigecycline resistance tet(X4) gene in Escherichia coli isolated from poultry, food and the environment in South Asia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147613. [PMID: 33992939 DOI: 10.1016/j.scitotenv.2021.147613] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
The recent emergence of mobile-tigecycline resistance tet(X) genes in human and animals in China seriously threats the clinical utility of tigecycline. Here we focused on the isolation and molecular characterization of plasmid-mediated tigecycline resistance tet(X4)-positive E. coli from different sources in Pakistan using MinION and Illumina sequencing. The tet(X4) gene was detected in four E. coli isolates from poultry, chicken meat, wild bird and the slaughterhouse wastewater in Pakistan. Co-existence of colistin resistance mcr-1 gene was also detected in three isolates. The four isolates belonged to different sequence types and the tet(X4) gene was located on plasmids ranging from 12,331 bp to 113,610 bp belonging to IncFII and IncQ replicon types with two genetic contexts ISCR2-tet(X4)-abh-ISCR2-lysR-floR-virD2 and ΔISCR2-abh-tet(X4)-ISCR2-virD2-floR, respectively. In all the four E. coli strains, tet(X4) was transferable by conjugation to E. coli J53 host strain. In addition, three of four strains transferred tet(X4) to a wild-type carbapenem resistant E. coli strain. To our knowledge, this is the first report of the emergence of plasmid-mediated tet(X4) gene from Pakistan. The convergence of tigecycline and colistin resistance in South Asia is a serious threat to human health.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan.
| | - Brekhna Hassan
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Willames M B S Martins
- School of Medicine, Department of Medical Microbiology, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Ruichao Li
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, PR China
| | - Sabahat Abdullah
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Kirsty Sands
- Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, United Kingdom
| | - Timothy R Walsh
- Ineos Oxford Institute of Antimicrobial Research, Department of Zoology, University of Oxford, United Kingdom.
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21
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Chang MX, Zhang JF, Sun YH, Li RS, Lin XL, Yang L, Webber MA, Jiang HX. Contribution of Different Mechanisms to Ciprofloxacin Resistance in Salmonella spp. Front Microbiol 2021; 12:663731. [PMID: 34025618 PMCID: PMC8137344 DOI: 10.3389/fmicb.2021.663731] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/09/2021] [Indexed: 11/28/2022] Open
Abstract
Development of fluoroquinolone resistance can involve several mechanisms that include chromosomal mutations in genes (gyrAB and parCE) encoding the target bacterial topoisomerase enzymes, increased expression of the AcrAB-TolC efflux system, and acquisition of transmissible quinolone-resistance genes. In this study, 176 Salmonella isolates from animals with a broad range of ciprofloxacin MICs were collected to analyze the contribution of these different mechanisms to different phenotypes. All isolates were classified according to their ciprofloxacin susceptibility pattern into five groups as follows: highly resistant (HR), resistant (R), intermediate (I), reduced susceptibility (RS), and susceptible (S). We found that the ParC T57S substitution was common in strains exhibiting lowest MICs of ciprofloxacin while increased MICs depended on the type of GyrA mutation. The ParC T57S substitution appeared to incur little cost to bacterial fitness on its own. The presence of PMQR genes represented an route for resistance development in the absence of target-site mutations. Switching of the plasmid-mediated quinolone resistance (PMQR) gene location from a plasmid to the chromosome was observed and resulted in decreased ciprofloxacin susceptibility; this also correlated with increased fitness and a stable resistance phenotype. The overexpression of AcrAB-TolC played an important role in isolates with small decreases in susceptibility and expression was upregulated by MarA more often than by RamA. This study increases our understanding of the relative importance of several resistance mechanisms in the development of fluoroquinolone resistance in Salmonella from the food chain.
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Affiliation(s)
- Man-Xia Chang
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jin-Fei Zhang
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yin-Huan Sun
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Rong-Sheng Li
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Ling Lin
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ling Yang
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hong-Xia Jiang
- Guangdong Key Laboratory of Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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22
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Hill D, Morra MJ, Stalder T, Jechalke S, Top E, Pollard AT, Popova I. Dairy manure as a potential source of crop nutrients and environmental contaminants. J Environ Sci (China) 2021; 100:117-130. [PMID: 33279025 DOI: 10.1016/j.jes.2020.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/15/2020] [Accepted: 07/15/2020] [Indexed: 06/12/2023]
Abstract
Although animal manure is applied to agricultural fields for its nutrient value, it may also contain potential contaminants. To determine the variability in such contaminants as well as in valuable nutrients, nine uncomposted manure samples from Idaho dairies collected during 2.5 years were analyzed for macro- and micro-nutrients, hormones, phytoestrogens, antibiotics, veterinary drugs, antibiotic resistance genes, and genetic elements involved in the spread of antibiotic resistance. Total N ranged from 6.8 to 30.7 (C:N of 10 to 21), P from 2.4 to 9.0, and K from 10.2 to 47.7 g/kg manure. Zn (103 - 348 mg/kg) was more abundant than Cu (56 - 127 mg/kg) in all samples. Phytoestrogens were the most prevalent contaminants detected, with concentrations fluctuating over time, reflecting animal diets. This is the first study to document the presence of flunixin, a non-steroidal anti-inflammatory drug, in solid stacked manure from regular dairy operations. Monensin was the most frequently detected antibiotic. Progesterones and sulfonamides were regularly detected. We also investigated the relative abundance of several types of plasmids involved in the spread of antibiotic resistance in clinical settings. Plasmids belonging to the IncI, IncP, and IncQ1 incompatibility groups were found in almost all manure samples. IncQ1 plasmids, class 1 integrons, and sulfonamide resistance genes were the most widespread and abundant genetic element surveyed, emphasizing their potential role in the spread of antibiotic resistance. The benefits associated with amending agricultural soils with dairy manure must be carefully weighed against the potential negative consequences of any manure contaminants.
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Affiliation(s)
- Danika Hill
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Matthew J Morra
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | | | - Sven Jechalke
- Justus Liebig University Giessen, Institute for Phytopathology, 35392 Gießen, Germany
| | - Eva Top
- Department of Biology, University of Idaho, ID 83844-3051, USA
| | - Anne T Pollard
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA
| | - Inna Popova
- Department of Soil & Water Systems, University of Idaho, ID 83844-2340, USA.
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Lewicka E, Mitura M, Steczkiewicz K, Kieracinska J, Skrzynska K, Adamczyk M, Jagura-Burdzy G. Unique Properties of the Alpha-Helical DNA-Binding Protein KfrA Encoded by the IncU Incompatibility Group Plasmid RA3 and Its Host-Dependent Role in Plasmid Maintenance. Appl Environ Microbiol 2021; 87:e01771-20. [PMID: 33097508 PMCID: PMC7783346 DOI: 10.1128/aem.01771-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/18/2020] [Indexed: 01/15/2023] Open
Abstract
KfrA, encoded on the broad-host-range RA3 plasmid, is an alpha-helical DNA-binding protein that acts as a transcriptional autoregulator. The KfrARA3 operator site overlaps the kfrA promoter and is composed of five 9-bp direct repeats (DRs). Here, the biological properties of KfrA were studied using both in vivo and in vitro approaches. Localization of the DNA-binding helix-turn-helix motif (HTH) was mapped to the N29-R52 region by protein structure modeling and confirmed by alanine scanning. KfrA repressor ability depended on the number and orientation of DRs in the operator, as well as the ability of the protein to oligomerize. The long alpha-helical tail from residues 54 to 355 was shown to be involved in self-interactions, whereas the region from residue 54 to 177 was involved in heterodimerization with KfrC, another RA3-encoded alpha-helical protein. KfrA also interacted with the segrosome proteins IncC (ParA) and KorB (ParB), representatives of the class Ia active partition systems. Deletion of the kfr genes from the RA3 stability module decreased the plasmid retention in diverse hosts in a species-dependent manner. The specific interactions of KfrA with DNA are essential not only for the transcriptional regulatory function but also for the accessory role of KfrA in stable plasmid maintenance.IMPORTANCE Alpha-helical coiled-coil KfrA-type proteins are encoded by various broad-host-range low-copy-number conjugative plasmids. The DNA-binding protein KfrA encoded on the RA3 plasmid, a member of the IncU incompatibility group, oligomerizes, forms a complex with another plasmid-encoded, alpha-helical protein, KfrC, and interacts with the segrosome proteins IncC and KorB. The unique mode of KfrA dimer binding to the repetitive operator is required for a KfrA role in the stable maintenance of RA3 plasmid in distinct hosts.
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Affiliation(s)
- Ewa Lewicka
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Monika Mitura
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Department of Bioinformatics, PAS, Warsaw, Poland
| | - Justyna Kieracinska
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Kamila Skrzynska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Malgorzata Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
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24
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Kim JW, Bugata V, Cortés-Cortés G, Quevedo-Martínez G, Camps M. Mechanisms of Theta Plasmid Replication in Enterobacteria and Implications for Adaptation to Its Host. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0026-2019. [PMID: 33210586 PMCID: PMC7724965 DOI: 10.1128/ecosalplus.esp-0026-2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 11/20/2022]
Abstract
Plasmids are autonomously replicating sequences that help cells adapt to diverse stresses. Theta plasmids are the most frequent plasmid class in enterobacteria. They co-opt two host replication mechanisms: replication at oriC, a DnaA-dependent pathway leading to replisome assembly (theta class A), and replication fork restart, a PriA-dependent pathway leading to primosome assembly through primer extension and D-loop formation (theta classes B, C, and D). To ensure autonomy from the host's replication and to facilitate copy number regulation, theta plasmids have unique mechanisms of replication initiation at the plasmid origin of replication (ori). Tight plasmid copy number regulation is essential because of the major and direct impact plasmid gene dosage has on gene expression. The timing of plasmid replication and segregation are also critical for optimizing plasmid gene expression. Therefore, we propose that plasmid replication needs to be understood in its biological context, where complex origins of replication (redundant origins, mosaic and cointegrated replicons), plasmid segregation, and toxin-antitoxin systems are often present. Highlighting their tight functional integration with ori function, we show that both partition and toxin-antitoxin systems tend to be encoded in close physical proximity to the ori in a large collection of Escherichia coli plasmids. We also propose that adaptation of plasmids to their host optimizes their contribution to the host's fitness while restricting access to broad genetic diversity, and we argue that this trade-off between adaptation to host and access to genetic diversity is likely a determinant factor shaping the distribution of replicons in populations of enterobacteria.
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Affiliation(s)
- Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Vega Bugata
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Gerardo Cortés-Cortés
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Giselle Quevedo-Martínez
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, 95064
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McMillan EA, Jackson CR, Frye JG. Transferable Plasmids of Salmonella enterica Associated With Antibiotic Resistance Genes. Front Microbiol 2020; 11:562181. [PMID: 33133037 PMCID: PMC7578388 DOI: 10.3389/fmicb.2020.562181] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Salmonella enterica is a common foodborne illness in the United States and globally. An increasing number of Salmonella infections are resistant to antibiotics, and many of the genes responsible for those resistances are carried by plasmids. Plasmids are important mediators of horizontal gene exchange, which could potentially increase the spread of antibiotic resistance (AR) genes. Twenty-eight different incompatibility groups of plasmids have been described in Enterobacteriaceae. Incompatibility groups differ in their accessory gene content, replication mechanisms, and their associations with Salmonella serotypes and animal sources. Plasmids also differ in their ability to conjugate or be mobilized, essential genes, and conditions required for transfer. It is important to understand the differences in gene content and transfer mechanisms to accurately determine the impact of plasmids on the dissemination and persistence of antibiotic resistance genes. This review will cover the most common plasmid incompatibility groups present in S. enterica with a focus on the transfer mechanisms and associated antibiotic resistance genes.
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Affiliation(s)
- Elizabeth A McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, United States
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26
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Clinical and Molecular Description of a High-Copy IncQ1 KPC-2 Plasmid Harbored by the International ST15 Klebsiella pneumoniae Clone. mSphere 2020; 5:5/5/e00756-20. [PMID: 33028683 PMCID: PMC7568653 DOI: 10.1128/msphere.00756-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In many parts of the world, carbapenem resistance is a serious public health concern. In Brazil, carbapenem resistance in Enterobacterales is mostly driven by the dissemination of KPC-2-producing K. pneumoniae clones. Despite being endemic in this country, only a few reports providing both clinical and genomic data are available in Brazil, which limit the understanding of the real clinical impact caused by the dissemination of different clones carrying blaKPC-2 in Brazilian hospitals. Although several of these KPC-2-producer K. pneumoniae isolates belong to the clonal complex 258 and carry Tn4401 transposons located on large plasmids, a concomitant emergence and silent dissemination of small high-copy-number blaKPC-2 plasmids are of importance, as described in this study. Our data identify a small high-copy-number IncQ1 KPC plasmid, its clinical relevance, and the potential for conjugative transfer into several K. pneumoniae isolates, belonging to different international lineages, such as ST258, ST101, and ST15. This study provides the genomic characterization and clinical description of bloodstream infections (BSI) cases due to ST15 KPC-2 producer Klebsiella pneumoniae. Six KPC-K. pneumoniae isolates were recovered in 2015 in a tertiary Brazilian hospital and were analyzed by whole-genome sequencing (WGS) (Illumina MiSeq short reads). Of these, two isolates were further analyzed by Nanopore MinION sequencing, allowing complete chromosome and plasmid circularization (hybrid assembly), using Unicycler software. The clinical analysis showed that the 30-day overall mortality for these BSI cases was high (83%). The isolates exhibited meropenem resistance (MICs, 32 to 128 mg/liter), with 3/6 isolates resistant to polymyxin B. The conjugative properties of the blaKPC-2 plasmid and its copy number were assessed by standard conjugation experiments and sequence copy number analysis. We identified in all six isolates a small (8.3-kb), high-copy-number (20 copies/cell) non-self-conjugative IncQ plasmid harboring blaKPC-2 in a non-Tn4401 transposon. This plasmid backbone was previously reported to harbor blaKPC-2 only in Brazil, and it could be comobilized at a high frequency (10−4) into Escherichia coli J53 and into several high-risk K. pneumoniae clones (ST258, ST15, and ST101) by a common IncL/M helper plasmid, suggesting the potential of international spread. This study thus identified the international K. pneumoniae ST15 clone as a carrier of blaKPC-2 in a high-copy-number IncQ1 plasmid that is easily transmissible among other common Klebsiella strains. This finding is of concern since IncQ1 plasmids are efficient antimicrobial resistance determinant carriers across Gram-negative species. The spread of such carbapenemase-encoding IncQ1 plasmids should therefore be closely monitored. IMPORTANCE In many parts of the world, carbapenem resistance is a serious public health concern. In Brazil, carbapenem resistance in Enterobacterales is mostly driven by the dissemination of KPC-2-producing K. pneumoniae clones. Despite being endemic in this country, only a few reports providing both clinical and genomic data are available in Brazil, which limit the understanding of the real clinical impact caused by the dissemination of different clones carrying blaKPC-2 in Brazilian hospitals. Although several of these KPC-2-producer K. pneumoniae isolates belong to the clonal complex 258 and carry Tn4401 transposons located on large plasmids, a concomitant emergence and silent dissemination of small high-copy-number blaKPC-2 plasmids are of importance, as described in this study. Our data identify a small high-copy-number IncQ1 KPC plasmid, its clinical relevance, and the potential for conjugative transfer into several K. pneumoniae isolates, belonging to different international lineages, such as ST258, ST101, and ST15.
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Piotrowska M, Dziewit L, Ostrowski R, Chmielowska C, Popowska M. Molecular Characterization and Comparative Genomics of IncQ-3 Plasmids Conferring Resistance to Various Antibiotics Isolated from a Wastewater Treatment Plant in Warsaw (Poland). Antibiotics (Basel) 2020; 9:antibiotics9090613. [PMID: 32957637 PMCID: PMC7557826 DOI: 10.3390/antibiotics9090613] [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: 09/01/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
As small, mobilizable replicons with a broad host range, IncQ plasmids are widely distributed among clinical and environmental bacteria. They carry antibiotic resistance genes, and it has been shown that they confer resistance to β-lactams, fluoroquinolones, aminoglycosides, trimethoprim, sulphonamides, and tetracycline. The previously proposed classification system divides the plasmid group into four subgroups, i.e., IncQ-1, IncQ-2, IncQ-3, and IncQ-4. The last two subgroups have been poorly described so far. The aim of this study was to analyze five newly identified IncQ-3 plasmids isolated from a wastewater treatment plant in Poland and to compare them with all known plasmids belonging to the IncQ-3 subgroup whose sequences were retrieved from the NCBI database. The complete nucleotide sequences of the novel plasmids were annotated and bioinformatic analyses were performed, including identification of core genes and auxiliary genetic load. Furthermore, functional experiments testing plasmid mobility were carried out. Phylogenetic analysis based on three core genes (repA, mobA/repB, and mobC) revealed the presence of three main clusters of IncQ-3 replicons. Apart from having a highly conserved core, the analyzed IncQ-3 plasmids were vectors of antibiotic resistance genes, including (I) the qnrS2 gene that encodes fluoroquinolone resistance and (II) β-lactam, trimethoprim, and aminoglycoside resistance genes within integron cassettes.
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Affiliation(s)
- Marta Piotrowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Lukasz Dziewit
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Rafał Ostrowski
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Cora Chmielowska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Magdalena Popowska
- Department of Bacterial Physiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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28
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Protonotariou E, Poulou A, Politi L, Meletis G, Chatzopoulou F, Malousi A, Metallidis S, Tsakris A, Skoura L. Clonal outbreak caused by VIM-4-producing Proteus mirabilis in a Greek tertiary-care hospital. Int J Antimicrob Agents 2020; 56:106060. [PMID: 32574790 DOI: 10.1016/j.ijantimicag.2020.106060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/02/2020] [Accepted: 06/13/2020] [Indexed: 01/19/2023]
Abstract
Carbapenem-resistant Enterobacterales have become a major public-health issue worldwide. Here we report an outbreak caused by a clonal multidrug-resistant Proteus mirabilis strain producing VIM-4 metallo-β-lactamase (MBL) and TEM-2 β-lactamase in a Greek tertiary-care hospital. From July 2015 to February 2016, 27 imipenem-resistant P. mirabilis isolates were recovered from 14 patients hospitalised in two intensive care units (ICUs) and the internal medicine department in AHEPA University Hospital, Thessaloniki. The isolates were either susceptible or resistant to meropenem and were resistant to all remaining β-lactams except aztreonam. Phenotypic and molecular analysis revealed that all of the isolates harboured a blaVIM-4 MBL gene. Resistome analysis of a representative isolate showed the presence of an IncQ1 plasmid harbouring the blaVIM-4 carbapenemase and blaTEM-2 β-lactamase genes among resistance genes coding for resistance to β-lactams, aminoglycosides, trimethoprim, sulfonamides and lincosamides. Genotyping by pulsed-field electrophoresis (PFGE) revealed that the isolates were epidemiologically related. After recovery of the index carbapenemase-producing P. mirabilis clinical isolate, infection control measures were intensified in the affected departments. Rectal sampling for carbapenem-resistant bacteria was initiated on a weekly basis among patients admitted to the general ICU. The outbreak was finally interrupted 6 months later in February 2016. This is the first documentation of the blaVIM-4 MBL gene in P. mirabilis as well as the first hospital outbreak caused by a MBL-producing P. mirabilis strain.
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Affiliation(s)
- Efthymia Protonotariou
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kiriakidi 1, 546 36, Thessaloniki, Greece.
| | - Aggeliki Poulou
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kiriakidi 1, 546 36, Thessaloniki, Greece
| | - Lida Politi
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Georgios Meletis
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kiriakidi 1, 546 36, Thessaloniki, Greece
| | - Fani Chatzopoulou
- Laboratory of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Antigoni Malousi
- Laboratory of Biological Chemistry, Medical School, Aristotle University of Thessaloniki, Greece
| | - Symeon Metallidis
- First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, University of Athens, Athens, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, S. Kiriakidi 1, 546 36, Thessaloniki, Greece
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29
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AbuOun M, O'Connor HM, Stubberfield EJ, Nunez-Garcia J, Sayers E, Crook DW, Smith RP, Anjum MF. Characterizing Antimicrobial Resistant Escherichia coli and Associated Risk Factors in a Cross-Sectional Study of Pig Farms in Great Britain. Front Microbiol 2020; 11:861. [PMID: 32523560 PMCID: PMC7261845 DOI: 10.3389/fmicb.2020.00861] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022] Open
Abstract
Combatting antimicrobial resistant (AMR) using a One-Health approach is essential as various bacteria, including Escherichia coli, a common bacteria, are becoming increasingly resistant and livestock may be a reservoir. The AMR gene content of 492 E. coli, isolated from 56 pig farms across Great Britain in 2014–2015, and purified on antibiotic selective and non-selective plates, was determined using whole genome sequencing (WGS). The E. coli were phylogenetically diverse harboring a variety of AMR profiles with widespread resistance to “old” antibiotics; isolates harbored up to seven plasmid Inc-types. None showed concurrent resistance to third-generation cephalosporins, fluoroquinolones and clinically relevant aminoglycosides, although ∼3% harbored AMR genes to both the former two. Transferable resistance to carbapenem and colistin were absent, and six of 117 E. coli STs belonged to major types associated with human disease. Prevalence of genotypically MDR E. coli, gathered from non-selective media was 35% and that of extended-spectrum-beta-lactamase E. coli was low (∼2% from non-selective). Approximately 72.6% of E. coli from ciprofloxacin plates and only 8.5% from the other plates harbored fluoroquinolone resistance due to topoisomerase mutations; the majority were MDR. In fact, multivariable analysis confirmed E. coli purified from CIP enrichment plates were more likely to be MDR, and suggested MDR isolates were also more probable from farms with high antibiotic usage, specialist finisher farms, and farms emptying their manure pits only after each batch. Additionally, farms from the South East were more likely to have MDR E. coli, whereas farms in Yorkshire and the Humber were less likely. Future investigations will determine whether suggested improvements such as better biosecurity or lower antimicrobial use decreases MDR E. coli on pig farms. Although this study focuses on pig farms, we believe the methodology and findings can be applied more widely to help livestock farmers in the United Kingdom and elsewhere to tackle AMR.
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Affiliation(s)
- Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
| | - Heather M O'Connor
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Emma J Stubberfield
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Javier Nunez-Garcia
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Ellie Sayers
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Derick W Crook
- National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom.,Modernising Medical Microbiology Consortium, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Richard P Smith
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom.,National Institute for Health Research, Health Protection Research Unit, University of Oxford in Partnership with Public Health England (PHE), Oxford, United Kingdom
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30
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Deciphering the Structural Diversity and Classification of the Mobile Tigecycline Resistance Gene tet(X)-Bearing Plasmidome among Bacteria. mSystems 2020; 5:5/2/e00134-20. [PMID: 32345737 PMCID: PMC7190383 DOI: 10.1128/msystems.00134-20] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally. The emergence of novel plasmid-mediated resistance genes constitutes a great public concern. Recently, mobile tet(X) variants were reported in diverse pathogens from different sources. However, the diversity of tet(X)-bearing plasmids remains largely unknown. In this study, the phenotypes and genotypes of all the tet(X)-positive tigecycline-resistant strains isolated from a slaughterhouse in China were characterized by antimicrobial susceptibility testing, conjugation, pulsed-field gel electrophoresis with S1 nuclease (S1-PFGE), and PCR. The diversity and polymorphism of tet(X)-harboring strains and plasmidomes were investigated by whole-genome sequencing (WGS) and single-plasmid-molecule analysis. Seventy-four tet(X4)-harboring Escherichia coli strains and one tet(X6)-bearing Providencia rettgeri strain were identified. The tet(X4)-bearing elements in 27 strains could be transferred to the recipient strain via plasmids. All tet(X4)-bearing plasmids isolated in this study and 15 tet(X4)-bearing plasmids reported online were analyzed. tet(X4)-bearing plasmids ranged from 9 to 294 kb and were categorized as ColE2-like, IncQ, IncX1, IncA/C2, IncFII, IncFIB, and hybrid plasmids with different replicons. The core tet(X4)-bearing genetic contexts were divided into four major groups: ISCR2-tet(X4)-abh, △ISCR2-abh-tet(X4)-ISCR2, ISCR2-abh-tet(X4)-ISCR2-virD2-floR, and abh-tet(X4)-ISCR2-yheS-cat-zitR-ISCR2-virD2-floR. Tandem repeats of tet(X4) were universally mediated by ISCR2. Different tet(X)-bearing strains existed in the same microbiota. Reorganization of tet(X4)-bearing multidrug resistance plasmids was found to be mediated by IS26 and other homologous regions. Finally, single-plasmid-molecule analysis captured the heterogenous state of tet(X4)-bearing plasmids. These findings significantly expand our knowledge of the tet(X)-bearing plasmidome among microbiotas, which establishes a baseline for investigating the structure and diversity of human, animal, and environmental tigecycline resistomes. Characterization of tet(X) genes among different microbiotas should be performed systematically to understand the evolution and ecology. IMPORTANCE Tigecycline is an expanded-spectrum tetracycline used as a last-resort antimicrobial for treating infections caused by superbugs such as carbapenemase-producing or colistin-resistant pathogens. Emergence of the plasmid-mediated mobile tigecycline resistance gene tet(X4) created a great public health concern. However, the diversity of tet(X4)-bearing plasmids and bacteria remains largely uninvestigated. To cover this knowledge gap, we comprehensively identified and characterized the tet(X)-bearing plasmidome in different sources using advanced sequencing technologies for the first time. The huge diversity of tet(X4)-bearing mobile elements demonstrates the high level of transmissibility of the tet(X4) gene among bacteria. It is crucial to enhance stringent surveillance of tet(X) genes in animal and human pathogens globally.
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Miller EA, Elnekave E, Flores-Figueroa C, Johnson A, Kearney A, Munoz-Aguayo J, Tagg KA, Tschetter L, Weber BP, Nadon CA, Boxrud D, Singer RS, Folster JP, Johnson TJ. Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America. mSphere 2020; 5:e00056-20. [PMID: 32295868 PMCID: PMC7160679 DOI: 10.1128/msphere.00056-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/26/2020] [Indexed: 01/09/2023] Open
Abstract
Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source.IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans.
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Affiliation(s)
- Elizabeth A Miller
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ehud Elnekave
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | | | - Abigail Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Ashley Kearney
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Jeannette Munoz-Aguayo
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
| | | | - Lorelee Tschetter
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Bonnie P Weber
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Celine A Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Winnipeg, Canada
| | - Dave Boxrud
- Minnesota Department of Health, Saint Paul, Minnesota, USA
| | - Randall S Singer
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA
- Mid-Central Research and Outreach Center, University of Minnesota, Willmar, Minnesota, USA
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Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol 2020; 18:e3000465. [PMID: 32310938 PMCID: PMC7192512 DOI: 10.1371/journal.pbio.3000465] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 04/30/2020] [Accepted: 04/02/2020] [Indexed: 01/05/2023] Open
Abstract
Countering the rise of antibiotic-resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g., via resource competition) but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonisation by focal E. coli but also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic-resistance evolution of individual species.
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Affiliation(s)
- Michael Baumgartner
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Florian Bayer
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Katia R. Pfrunder-Cardozo
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, United Kingdom
| | - Alex R. Hall
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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Dungan RS, Bjorneberg DL. Antibiotic resistance genes, class 1 integrons, and IncP-1/IncQ-1 plasmids in irrigation return flows. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113568. [PMID: 31733967 DOI: 10.1016/j.envpol.2019.113568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/30/2019] [Accepted: 11/02/2019] [Indexed: 06/10/2023]
Abstract
Surface waters could be a dominant route by which antibiotic resistance genes (ARGs) are disseminated. In the present study we explored the prevalence and abundance of ARGs [blaCTX-M-1, erm(B), sul1, tet(B), tet(M), and tet(X)], class 1 integron-integrase gene (intI1), and IncP-1 and IncQ-1 plasmids in eight irrigation return flows (IRFs) and a background site (Main Line Canal, MLC) in the Upper Snake Rock watershed in southern Idaho. Grab samples were collected on a monthly basis for a calendar year, which were processed to extract microbial DNA, followed by droplet digital PCR to quantify the gene copies on an absolute (per 100 mL) and relative (per 16S rRNA gene copies) basis. The antibiotic resistance and intI1 genes and IncP-1/IncQ-1 plasmids were recovered at all IRF sampling sites with detections ranging from 55 to 81 out of 81 water sampling events. The blaCTX-M-1 gene was detected the least frequently (68%), while the other genes were detected more frequently (88-100%). All of the genes were also detected at MLC from April to Oct when water was present in the canal. The genes from lowest to greatest relative abundance in the IRFs were: blaCTX-M-1 < erm(B) < tet(B) < IncQ-1 < tet(M) < sul1 < intI1 = IncP-1 < tet(X). When compared to the average annual relative gene abundances in MLC water samples, they were found to be at statistically greater levels (P ≤ 0.008) except that of the IncP-1 and IncQ-1 plasmids (P = 0.8 and 0.08, respectively). The fact that most IRFs contained higher levels than found in the canal water, indicates that IRFs can be a point source of ARGs that ultimately discharge into surface waters.
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Affiliation(s)
- Robert S Dungan
- USDA-Agricultural Research Service, Northwest Irrigation & Soils Research Laboratory, 3793 North 3600 East, Kimberly, ID, 83341, USA.
| | - David L Bjorneberg
- USDA-Agricultural Research Service, Northwest Irrigation & Soils Research Laboratory, 3793 North 3600 East, Kimberly, ID, 83341, USA
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Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria. Nat Commun 2019; 10:5809. [PMID: 31863068 PMCID: PMC6925257 DOI: 10.1038/s41467-019-13709-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/21/2019] [Indexed: 01/07/2023] Open
Abstract
Transmissible plasmids spread genes encoding antibiotic resistance and other traits to new bacterial species. Here we report that laboratory populations of Escherichia coli with a newly acquired IncQ plasmid often evolve 'satellite plasmids' with deletions of accessory genes and genes required for plasmid replication. Satellite plasmids are molecular parasites: their presence reduces the copy number of the full-length plasmid on which they rely for their continued replication. Cells with satellite plasmids gain an immediate fitness advantage from reducing burdensome expression of accessory genes. Yet, they maintain copies of these genes and the complete plasmid, which potentially enables them to benefit from and transmit the traits they encode in the future. Evolution of satellite plasmids is transient. Cells that entirely lose accessory gene function or plasmid mobility dominate in the long run. Satellite plasmids also evolve in Snodgrassella alvi colonizing the honey bee gut, suggesting that this mechanism may broadly contribute to the importance of IncQ plasmids as agents of bacterial gene transfer in nature.
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35
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Campos PA, Fuga B, Cerdeira LT, Ferreira ML, Dias VL, Machado LG, Rossi I, Lincopan N, Gontijo-Filho PP, Ribas RM. Early Dissemination of IncQ1 Plasmids in KPC-2-Producing Klebsiella pneumoniae CG258. Microb Drug Resist 2019; 25:1257-1259. [DOI: 10.1089/mdr.2019.0123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Paola A. Campos
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Bruna Fuga
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Louise T. Cerdeira
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Melina L. Ferreira
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Vinícius L. Dias
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Luiz G. Machado
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Iara Rossi
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Paulo P. Gontijo-Filho
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
| | - Rosineide M. Ribas
- Institute of Biomedical Sciences, Laboratory of Molecular Microbiology, Federal University of Uberlandia, Uberlandia, Brazil
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Sun J, Chen C, Cui CY, Zhang Y, Liu X, Cui ZH, Ma XY, Feng Y, Fang LX, Lian XL, Zhang RM, Tang YZ, Zhang KX, Liu HM, Zhuang ZH, Zhou SD, Lv JN, Du H, Huang B, Yu FY, Mathema B, Kreiswirth BN, Liao XP, Chen L, Liu YH. Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli. Nat Microbiol 2019; 4:1457-1464. [PMID: 31235960 PMCID: PMC6707864 DOI: 10.1038/s41564-019-0496-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/22/2019] [Indexed: 02/03/2023]
Abstract
Tigecycline is one of the last-resort antibiotics to treat complicated infections caused by both multidrug-resistant Gram-negative and Gram-positive bacteria1. Tigecycline resistance has sporadically occurred in recent years, primarily due to chromosome-encoding mechanisms, such as overexpression of efflux pumps and ribosome protection2,3. Here, we report the emergence of the plasmid-mediated mobile tigecycline resistance mechanism Tet(X4) in Escherichia coli isolates from China, which is capable of degrading all tetracyclines, including tigecycline and the US FDA newly approved eravacycline. The tet(X4)-harbouring IncQ1 plasmid is highly transferable, and can be successfully mobilized and stabilized in recipient clinical and laboratory strains of Enterobacteriaceae bacteria. It is noteworthy that tet(X4)-positive E. coli strains, including isolates co-harbouring mcr-1, have been widely detected in pigs, chickens, soil and dust samples in China. In vivo murine models demonstrated that the presence of Tet(X4) led to tigecycline treatment failure. Consequently, the emergence of plasmid-mediated Tet(X4) challenges the clinical efficacy of the entire family of tetracycline antibiotics. Importantly, our study raises concern that the plasmid-mediated tigecycline resistance may further spread into various ecological niches and into clinical high-risk pathogens. Collective efforts are in urgent need to preserve the potency of these essential antibiotics.
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Affiliation(s)
- Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chong Chen
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Chao-Yue Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yan Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ze-Hua Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiao-Yu Ma
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Youjun Feng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xin-Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Rong-Min Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - You-Zhi Tang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Kou-Xing Zhang
- Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Han-Mian Liu
- Intensive Care Unit, Huizhou Municipal Central Hospital, Huizhou, China
| | - Zhi-Hui Zhuang
- Intensive Care Unit, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shi-Dan Zhou
- Intensive Care Unit, Huizhou Municipal Central Hospital, Huizhou, China
| | - Jing-Nan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Bin Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Fang-You Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barry N Kreiswirth
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
| | - Liang Chen
- Hackensack-Meridian Health Center for Discovery and Innovation, Nutley, NJ, USA.
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.
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37
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Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B, Guerra B, Mevius DJ, Hordijk J. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2019; 73:1121-1137. [PMID: 29370371 DOI: 10.1093/jac/dkx488] [Citation(s) in RCA: 507] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Bacterial antimicrobial resistance (AMR) is constantly evolving and horizontal gene transfer through plasmids plays a major role. The identification of plasmid characteristics and their association with different bacterial hosts provides crucial knowledge that is essential to understand the contribution of plasmids to the transmission of AMR determinants. Molecular identification of plasmid and strain genotypes elicits a distinction between spread of AMR genes by plasmids and dissemination of these genes by spread of bacterial clones. For this reason several methods are used to type the plasmids, e.g. PCR-based replicon typing (PBRT) or relaxase typing. Currently, there are 28 known plasmid types in Enterobacteriaceae distinguished by PBRT. Frequently reported plasmids [IncF, IncI, IncA/C, IncL (previously designated IncL/M), IncN and IncH] are the ones that bear the greatest variety of resistance genes. The purpose of this review is to provide an overview of all known AMR-related plasmid families in Enterobacteriaceae, the resistance genes they carry and their geographical distribution.
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Affiliation(s)
- M Rozwandowicz
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - M S M Brouwer
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Fischer
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - J A Wagenaar
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - B Gonzalez-Zorn
- Department of Animal Health and VISAVET, Complutense University of Madrid, Madrid, Spain
| | - B Guerra
- Department of Biological Safety, Federal Institute for Risk Assessment, BfR, Berlin, Germany
| | - D J Mevius
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - J Hordijk
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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Bonardi S, Pitino R. Carbapenemase-producing bacteria in food-producing animals, wildlife and environment: A challenge for human health. Ital J Food Saf 2019; 8:7956. [PMID: 31316921 PMCID: PMC6603432 DOI: 10.4081/ijfs.2019.7956] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/09/2019] [Indexed: 01/11/2023] Open
Abstract
Antimicrobial resistance is an increasing global health problem and one of the major concerns for economic impacts worldwide. Recently, resistance against carbapenems (doripenem, ertapenem, imipenem, meropenem), which are critically important antimicrobials for human cares, poses a great risk all over the world. Carbapenemases are β-lactamases belonging to different Ambler classes (A, B, D) and encoded by both chromosomal and plasmidic genes. They hydrolyze a broad variety of β-lactams, including carbapenems, cephalosporins, penicillins and aztreonam. Despite several studies in human patients and hospital settings have been performed in European countries, the role of livestock animals, wild animals and the terrestrial and aquatic environment in the maintenance and transmission of carbapenemase- producing bacteria has been poorly investigated. The present review focuses on the carbapenemase-producing bacteria detected in pigs, cattle, poultry, fish, mollusks, wild birds and wild mammals in Europe as well as in non-European countries, investigating the genetic mechanisms for their transmission among food-producing animals and wildlife. To shed light on the important role of the environment in the maintenance and genetic exchange of resistance determinants between environmental and pathogenic bacteria, studies on aquatic sources (rivers, lakes, as well as wastewater treatment plants) are described.
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Affiliation(s)
- Silvia Bonardi
- Department of Veterinary Science, University of Parma, Italy
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McMillan EA, Gupta SK, Williams LE, Jové T, Hiott LM, Woodley TA, Barrett JB, Jackson CR, Wasilenko JL, Simmons M, Tillman GE, McClelland M, Frye JG. Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. Front Microbiol 2019; 10:832. [PMID: 31057528 PMCID: PMC6479191 DOI: 10.3389/fmicb.2019.00832] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/01/2019] [Indexed: 11/13/2022] Open
Abstract
The ability of antimicrobial resistance (AR) to transfer, on mobile genetic elements (MGEs) between bacteria, can cause the rapid establishment of multidrug resistance (MDR) in bacteria from animals, thus creating a foodborne risk to human health. To investigate MDR and its association with plasmids in Salmonella enterica, whole genome sequence (WGS) analysis was performed on 193 S. enterica isolated from sources associated with United States food animals between 1998 and 2011; 119 were resistant to at least one antibiotic tested. Isolates represented 86 serotypes and variants, as well as diverse phenotypic resistance profiles. A total of 923 AR genes and 212 plasmids were identified among the 193 strains. Every isolate contained at least one AR gene. At least one plasmid was detected in 157 isolates. Genes were identified for resistance to aminoglycosides (n = 472), β-lactams (n = 84), tetracyclines (n = 171), sulfonamides (n = 91), phenicols (n = 42), trimethoprim (n = 8), macrolides (n = 5), fosfomycin (n = 48), and rifampicin (n = 2). Plasmid replicon types detected in the isolates were A/C (n = 32), ColE (n = 76), F (n = 43), HI1 (n = 4), HI2 (n = 20), I1 (n = 62), N (n = 4), Q (n = 7), and X (n = 35). Phenotypic resistance correlated with the AR genes identified in 95.4% of cases. Most AR genes were located on plasmids, with many plasmids harboring multiple AR genes. Six antibiotic resistance cassette structures (ARCs) and one pseudo-cassette were identified. ARCs contained between one and five resistance genes (ARC1: sul2, strAB, tetAR; ARC2: aac3-iid; ARC3: aph, sph; ARC4: cmy-2; ARC5: floR; ARC6: tetB; pseudo-ARC: aadA, aac3-VIa, sul1). These ARCs were present in multiple isolates and on plasmids of multiple replicon types. To determine the current distribution and frequency of these ARCs, the public NCBI database was analyzed, including WGS data on isolates collected by the USDA Food Safety and Inspection Service (FSIS) from 2014 to 2018. ARC1, ARC4, and ARC5 were significantly associated with cattle isolates, while ARC6 was significantly associated with chicken isolates. This study revealed that a diverse group of plasmids, carrying AR genes, are responsible for the phenotypic resistance seen in Salmonella isolated from United States food animals. It was also determined that many plasmids carry similar ARCs.
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Affiliation(s)
| | - Sushim K Gupta
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Laura E Williams
- Department of Biology, Providence College, Providence, RI, United States
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Lari M Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Tiffanie A Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - John B Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Charlene R Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
| | - Jamie L Wasilenko
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Mustafa Simmons
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Glenn E Tillman
- Eastern Lab, United States Department of Agriculture, Food Safety and Inspection Service, Athens, GA, United States
| | - Michael McClelland
- Department of Microbiology & Molecular Genetics, University of California, Irvine, Irvine, CA, United States
| | - Jonathan G Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Athens, GA, United States
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40
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Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn 4401 Elements (NTE KPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258. Antimicrob Agents Chemother 2019; 63:AAC.02140-18. [PMID: 30602517 DOI: 10.1128/aac.02140-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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41
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Characterization of the First OXA-10 Natural Variant with Increased Carbapenemase Activity. Antimicrob Agents Chemother 2018; 63:AAC.01817-18. [PMID: 30397053 DOI: 10.1128/aac.01817-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/26/2018] [Indexed: 12/25/2022] Open
Abstract
While carbapenem resistance in Gram-negative bacteria is mainly due to the production of efficient carbapenemases, β-lactamases with a narrower spectrum may also contribute to resistance when combined with additional mechanisms. OXA-10-type class D β-lactamases, previously shown to be weak carbapenemases, could represent such a case. In this study, two novel OXA-10 variants were identified as the sole carbapenem-hydrolyzing enzymes in meropenem-resistant enterobacteria isolated from hospital wastewater and found by next-generation sequencing to express additional β-lactam resistance mechanisms. The new variants, OXA-655 and OXA-656, were carried by two related IncQ1 broad-host-range plasmids. Compared to the sequence of OXA-10, they both harbored a Thr26Met substitution, with OXA-655 also bearing a leucine instead of a valine in position 117 of the SAV catalytic motif. Susceptibility profiling of laboratory strains replicating the natural bla OXA plasmids and of recombinant clones expressing OXA-10 and the novel variants in an isogenic background indicated that OXA-655 is a more efficient carbapenemase. The carbapenemase activity of OXA-655 is due to the Val117Leu substitution, as shown by steady-state kinetic experiments, where the k cat of meropenem hydrolysis was increased 4-fold. In contrast, OXA-655 had no activity toward oxyimino-β-lactams, while its catalytic efficiency against oxacillin was significantly reduced. Moreover, the Val117Leu variant was more efficient against temocillin and cefoxitin. Molecular dynamics indicated that Val117Leu affects the position 117-Leu155 interaction, leading to structural shifts in the active site that may alter carbapenem alignment. The evolutionary potential of OXA-10 enzymes toward carbapenem hydrolysis combined with their spread by promiscuous plasmids indicates that they may pose a future clinical threat.
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Jeannot K, Danassie M, Triponney P, Bour M, Gueudet T, Beyrouthy R, Bonnet R, Plésiat P. A novel IncQ plasmid carrying geneblaCTX-M-3 inPseudomonas aeruginosa. J Antimicrob Chemother 2018; 74:823-825. [DOI: 10.1093/jac/dky454] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Katy Jeannot
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
- UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France
| | - Marion Danassie
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Pauline Triponney
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Maxime Bour
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - Racha Beyrouthy
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Richard Bonnet
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
- CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France
- Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Patrick Plésiat
- Centre National de Référence de la Résistance aux Antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
- UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France
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Transposase-Mediated Chromosomal Integration of Exogenous Genes in Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2018; 84:AEM.01381-18. [PMID: 30143507 DOI: 10.1128/aem.01381-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
The development of Acidithiobacillus ferrooxidans as a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used to identify the insertion sites of the KDC gene in several mutants, leading to the identification of a region on the chromosome that may be suitable for future genetic insertions. These results demonstrate that functional exogenous metabolic genes have been chromosomally integrated into A. ferrooxidans, and this advance will facilitate the future development of these cells for new biotechnology applications.IMPORTANCE Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph and is a key member of the microbial consortia used in industrial biomining applications. There is interest in exploiting these cells for other metal recovery applications as well as in developing them as unique nonmodel microbial cell factories. Plasmid-driven expression of exogenous genes has been reported, and homologous recombination has been used to knock out some gene expression. Here, new selection protocols facilitated the development of a transposition method for chromosomal integration of exogenous genes into A. ferrooxidans This greatly expands the available genetic toolbox, which will open the door to greater metabolic engineering efforts for these cells.
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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: 1156] [Impact Index Per Article: 192.7] [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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Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E. Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins. Microb Genom 2018; 4. [PMID: 30080134 PMCID: PMC6202452 DOI: 10.1099/mgen.0.000203] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To understand the evolutionary dynamics of extended-spectrum β-lactamase (ESBL)-encoding genes in Escherichia coli, we undertook a comparative genomic analysis of 116 whole plasmid sequences of human or animal origin isolated over a period spanning before and after the use of third-generation cephalosporins (3GCs) using a gene-sharing network approach. The plasmids included 82 conjugative, 22 mobilizable and 9 non-transferable plasmids and 3 P-like bacteriophages. ESBL-encoding genes were found on 64 conjugative, 6 mobilizable, 2 non-transferable plasmids and 2 P1-like bacteriophages, indicating that these last three types of mobile elements also play a role, albeit modest, in the diffusion of the ESBLs. The network analysis showed that the plasmids clustered according to their genome backbone type, but not by origin or period of isolation or by antibiotic-resistance type, including type of ESBL-encoding gene. There was no association between the type of plasmid and the phylogenetic history of the parental strains. Finer scale analysis of the more abundant clusters IncF and IncI1 showed that ESBL-encoding plasmids and plasmids isolated before the use of 3GCs had the same diversity and phylogenetic history, and that acquisition of ESBL-encoding genes had occurred during multiple independent events. Moreover, the blaCTX-M-15 gene, unlike other CTX-M genes, was inserted at a hot spot in a blaTEM-1-Tn2 transposon. These findings showed that ESBL-encoding genes have arrived on wide range of pre-existing plasmids and that the successful spread of blaCTX-M-15 seems to be favoured by the presence of well-adapted IncF plasmids that carry a Tn2-blaTEM-1 transposon.
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Affiliation(s)
- Catherine Branger
- 1IAME, UMR1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, UFR de Medecine, 16 Rue Henri Huchard, Paris 75018, France
| | - Alice Ledda
- 2Department of Infectious Disease Epidemiology, Imperial College, London, W2 1PG, UK
| | | | - Benoît Doublet
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Stéphanie Fouteau
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - Valérie Barbe
- 5Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA, Genoscope, Institut de Biologie François-Jacob, 9100, Evry, France
| | - David Roche
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Stéphane Cruveiller
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Claudine Médigue
- 6UMR8030, CNRS, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, CEA, Institut de Génomique - Genoscope, Université Évry-Val-d'Essonne, 91000, Evry, France
| | - Miguel Castellanos
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Dominique Decré
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Laurence Drieux-Rouze
- 9APHP, Hôpital de la Pitié-Salpêtrière Service de Bactériologie-Hygiène, 75015, Paris, France
| | - Olivier Clermont
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Jérémy Glodt
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Olivier Tenaillon
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
| | - Axel Cloeckaert
- 4ISP, INRA, Université François Rabelais de Tours, UMR 1282, 37380 Nouzilly, France
| | - Guillaume Arlet
- 8CIMI, UMR 1135, INSERM, Université Pierre et Marie Curie Sorbonne Université, 75013, Paris, France
| | - Erick Denamur
- 7IAME, UMR 1137, INSERM, Université Paris Diderot, Université Paris13, Sorbonne Paris Cité, 75018, Paris, France
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Mastrorilli E, Pietrucci D, Barco L, Ammendola S, Petrin S, Longo A, Mantovani C, Battistoni A, Ricci A, Desideri A, Losasso C. A Comparative Genomic Analysis Provides Novel Insights Into the Ecological Success of the Monophasic Salmonella Serovar 4,[5],12:i:. Front Microbiol 2018; 9:715. [PMID: 29719530 PMCID: PMC5913373 DOI: 10.3389/fmicb.2018.00715] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Over the past decades, Salmonella 4,[5],12:i:- has rapidly emerged and it is isolated with high frequency in the swine food chain. Although many studies have documented the epidemiological success of this serovar, few investigations have tried to explain this phenomenon from a genetic perspective. Here a comparative whole-genome analysis of 50 epidemiologically unrelated S. 4,[5],12:i:-, isolated in Italy from 2010 to 2016 was performed, characterizing them in terms of genetic elements potentially conferring resistance, tolerance and persistence characteristics. Phylogenetic analyses indicated interesting distinctions among the investigated isolates. The most striking genetic trait characterizing the analyzed isolates is the widespread presence of heavy metals tolerance gene cassettes: most of the strains possess genes expected to confer resistance to copper and silver, whereas about half of the isolates also contain the mercury tolerance gene merA. A functional assay showed that these genes might be useful for preventing the toxic effects of metals, thus supporting the hypothesis that they can contribute to the success of S. 4,[5],12:i:- in farming environments. In addition, the analysis of the distribution of type II toxin-antitoxin families indicated that these elements are abundant in this serovar, suggesting that this is another factor that might favor its successful spread.
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Affiliation(s)
- Eleonora Mastrorilli
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Lisa Barco
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Serena Ammendola
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Sara Petrin
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alessandra Longo
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Claudio Mantovani
- Science Communication Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Antonia Ricci
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | | | - Carmen Losasso
- Department of Food Safety, National Reference Center for Salmonella, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Marathe NP, Janzon A, Kotsakis SD, Flach CF, Razavi M, Berglund F, Kristiansson E, Larsson DGJ. Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste. ENVIRONMENT INTERNATIONAL 2018; 112:279-286. [PMID: 29316517 DOI: 10.1016/j.envint.2017.12.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 05/28/2023]
Abstract
Evolution has provided environmental bacteria with a plethora of genes that give resistance to antibiotic compounds. Under anthropogenic selection pressures, some of these genes are believed to be recruited over time into pathogens by horizontal gene transfer. River sediment polluted with fluoroquinolones and other drugs discharged from bulk drug production in India constitute an environment with unprecedented, long-term antibiotic selection pressures. It is therefore plausible that previously unknown resistance genes have evolved and/or are promoted here. In order to search for novel resistance genes, we therefore analyzed such river sediments by a functional metagenomics approach. DNA fragments providing resistance to different antibiotics in E. coli were sequenced using Sanger and PacBio RSII platforms. We recaptured the majority of known antibiotic resistance genes previously identified by open shot-gun metagenomics sequencing of the same samples. In addition, seven novel resistance gene candidates (six beta-lactamases and one amikacin resistance gene) were identified. Two class A beta-lactamases, blaRSA1 and blaRSA2, were phylogenetically close to clinically important ESBLs like blaGES, blaBEL and blaL2, and were further characterized for their substrate spectra. The blaRSA1 protein, encoded as an integron gene cassette, efficiently hydrolysed penicillins, first generation cephalosporins and cefotaxime, while blaRSA2 was an inducible class A beta-lactamase, capable of hydrolyzing carbapenems albeit with limited efficiency, similar to the L2 beta-lactamase from Stenotrophomonas maltophilia. All detected novel genes were associated with plasmid mobilization proteins, integrons, and/or other resistance genes, suggesting a potential for mobility. This study provides insight into a resistome shaped by an exceptionally strong and long-term antibiotic selection pressure. An improved knowledge of mobilized resistance factors in the external environment may make us better prepared for the resistance challenges that we may face in clinics in the future.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Anders Janzon
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Stathis D Kotsakis
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-413 46 Gothenburg, Sweden.
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A novel plasmid, pSAA0430-08, from Streptococcus anginosus subsp. anginosus strain 0430-08. Plasmid 2018; 95:16-27. [DOI: 10.1016/j.plasmid.2018.01.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/02/2018] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
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Genetic Characterization of Broad-Host-Range IncQ Plasmids Harboring blaVEB-18 in Vibrio Species. Antimicrob Agents Chemother 2017; 61:AAC.00708-17. [PMID: 28507104 DOI: 10.1128/aac.00708-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Carbapenemase-Producing Enterobacteriaceae Recovered from the Environment of a Swine Farrow-to-Finish Operation in the United States. Antimicrob Agents Chemother 2017; 61:AAC.01298-16. [PMID: 27919894 DOI: 10.1128/aac.01298-16] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) present an urgent threat to public health. While use of carbapenem antimicrobials is restricted for food-producing animals, other β-lactams, such as ceftiofur, are used in livestock. This use may provide selection pressure favoring the amplification of carbapenem resistance, but this relationship has not been established. Previously unreported among U.S. livestock, plasmid-mediated CRE have been reported from livestock in Europe and Asia. In this study, environmental and fecal samples were collected from a 1,500-sow, U.S. farrow-to-finish operation during 4 visits over a 5-month period in 2015. Samples were screened using selective media for the presence of CRE, and the resulting carbapenemase-producing isolates were further characterized. Of 30 environmental samples collected from a nursery room on our initial visit, 2 (7%) samples yielded 3 isolates, 2 sequence type 218 (ST 218) Escherichia coli and 1 Proteus mirabilis, carrying the metallo-β-lactamase gene blaIMP-27 on IncQ1 plasmids. We recovered on our third visit 15 IMP-27-bearing isolates of multiple Enterobacteriaceae species from 11 of 24 (46%) environmental samples from 2 farrowing rooms. These isolates each also carried blaIMP-27 on IncQ1 plasmids. No CRE isolates were recovered from fecal swabs or samples in this study. As is common in U.S. swine production, piglets on this farm receive ceftiofur at birth, with males receiving a second dose at castration (≈day 6). This selection pressure may favor the dissemination of blaIMP-27-bearing Enterobacteriaceae in this farrowing barn. The absence of this selection pressure in the nursery and finisher barns likely resulted in the loss of the ecological niche needed for maintenance of this carbapenem resistance gene.
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