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Zou C, Xu C, Yu R, Shan X, Schwarz S, Li D, Du XD. Tandem amplification of a plasmid-borne tet(A) variant gene confers tigecycline resistance in Escherichia coli. J Antimicrob Chemother 2024; 79:1294-1302. [PMID: 38574003 DOI: 10.1093/jac/dkae095] [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: 10/21/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024] Open
Abstract
OBJECTIVES To elucidate the mechanism of tigecycline resistance in Escherichia coli that is mediated by the tet(A) variant gene. METHODS E. coli strain 573 carried a plasmid-borne tet(A) variant gene, tentatively designated tet(A)TIG, that conferred decreased tigecycline susceptibility (MIC 0.5 mg/L). When exposed to increasing concentrations of tigecycline (0.25-8 mg/L), mutants growing at 2, 4 and 8 mg/L were obtained and sequenced. Copies of plasmid and tet(A)TIG relative to the chromosomal DNA in the mutants were determined by WGS and quantitative PCR (qPCR). Expression of tet(A)TIG in the mutants was evaluated by RT-qPCR. The tet(A)TIG-carrying plasmids were visualized by S1-PFGE and Southern blot hybridization. PCR served for the detection of a tet(A)TIG-carrying unconventional circularizable structure (UCS). RESULTS Tigecycline resistance with maximum MICs of 16 mg/L was seen in E. coli mutants selected in the presence of tigecycline. Compared with the parental strain, the relative copy number and transcription level of tet(A)TIG in the mutants increased significantly in the presence of 2, 4 and 8 mg/L tigecycline, respectively. With increasing tigecycline selection pressure, the tet(A)TIG-carrying plasmids in the mutants increased in size, correlating with the number of tandem amplificates of a ΔTnAs1-flanked UCS harbouring tet(A)TIG. These tandem amplificates were not stable in the absence of tigecycline. CONCLUSIONS Tigecycline resistance is due to the tandem amplification of a ΔTnAs1-flanked tet(A)TIG-carrying plasmid-borne segment in E. coli. The gain/loss of the tandem amplificates in the presence/absence of tigecycline represents an economic way for the bacteria to survive in the presence of tigecycline.
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Affiliation(s)
- Chenhui Zou
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Chunyan Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Runhao Yu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xinxin Shan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Stefan Schwarz
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Dexi Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, P. R. China
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Sun L, Zhuang H, Chen M, Chen Y, Chen Y, Shi K, Yu Y. Vancomycin heteroresistance caused by unstable tandem amplifications of the vanM gene cluster on linear conjugative plasmids in a clinical Enterococcus faecium. Antimicrob Agents Chemother 2024; 68:e0115923. [PMID: 38506549 PMCID: PMC11064493 DOI: 10.1128/aac.01159-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/20/2024] [Indexed: 03/21/2024] Open
Abstract
Vancomycin heteroresistance is prone to missed detection and poses a risk of clinical treatment failure. We encountered one clinical Enterococcus faecium strain, SRR12, that carried a complete vanM gene cluster but was determined as susceptible to vancomycin using the broth microdilution method. However, distinct subcolonies appeared within the clear zone of inhibition in the E-test assay, one of which, named SRR12-v1, showed high-level resistance to vancomycin. SRR12 was confirmed as heteroresistant to vancomycin using population analysis profiling and displayed "revive" growth curves with a lengthy lag phase of over 13 hours when exposed to 2-32 mg/L vancomycin. The resistant subcolony SRR12-v1 was found to carry an identical vanM gene cluster to that of SRR12 but a significantly increased vanM copy number in the genome. Long-read whole genome sequencing revealed that a one-copy vanM gene cluster was located on a pELF1-like linear plasmid in SRR12. In comparison, tandem amplification of the vanM gene cluster jointed with IS1216E was seated on a linear plasmid in the genome of SRR12-v1. These amplifications of the vanM gene cluster were demonstrated as unstable and would decrease accompanied by fitness reversion after serial passaging for 50 generations under increasing vancomycin pressure or without antibiotic pressure but were relatively stable under constant vancomycin pressure. Further, vanM resistance in resistant variants was verified to be carried by conjugative plasmids with variable sizes using conjugation assays and S1-pulsed field gel electrophoresis blotting, suggesting the instability/flexibility of vanM cluster amplification in the genome and an increased risk of vanM resistance dissemination.
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Affiliation(s)
- Lingyan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Hemu Zhuang
- Department of Respiratory and Critical Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengzhen Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yiyi Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
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Sobkowiak A, Scherff N, Schuler F, Bletz S, Mellmann A, Schwierzeck V, van Almsick V. Plasmid-encoded gene duplications of extended-spectrum β-lactamases in clinical bacterial isolates. Front Cell Infect Microbiol 2024; 14:1343858. [PMID: 38469349 PMCID: PMC10925753 DOI: 10.3389/fcimb.2024.1343858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The emergence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae is an urgent and alarming One Health problem. This study aimed to investigate duplications of plasmid-encoded ESBL genes and their impact on antimicrobial resistance (AMR) phenotypes in clinical and screening isolates. Methods Multi-drug-resistant bacteria from hospitalized patients were collected during routine clinical surveillance from January 2022 to June 2023, and their antimicrobial susceptibility patterns were determined. Genotypes were extracted from long-read whole-genome sequencing data. Furthermore, plasmids and other mobile genetic elements associated with ESBL genes were characterized, and the ESBL genes were correlated to ceftazidime minimal inhibitory concentration (MIC). Results In total, we identified four cases of plasmid-encoded ESBL gene duplications that match four genetically similar plasmids during the 18-month surveillance period: five Escherichia coli and three Klebsiella pneumoniae isolates. As the ESBL genes were part of transposable elements, the surrounding sequence regions were duplicated as well. In-depth analysis revealed insertion sequence (IS)-mediated transposition mechanisms. Isolates with duplicated ESBL genes exhibited a higher MIC for ceftazidime in comparison to isolates with a single gene copy (3-256 vs. 1.5-32 mg/L, respectively). Conclusion ESBL gene duplications led to an increased phenotypic resistance against ceftazidime. Our data suggest that ESBL gene duplications by an IS-mediated transposition are a relevant mechanism for how AMR develops in the clinical setting and is part of the microevolution of plasmids.
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Affiliation(s)
- Annika Sobkowiak
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
| | - Natalie Scherff
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Franziska Schuler
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan Bletz
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | | | - Vera Schwierzeck
- Institute of Hygiene, University Hospital Münster, Münster, Germany
| | - Vincent van Almsick
- Institute of Hygiene, University Hospital Münster, Münster, Germany
- Department of Cardiology I – Coronary and Peripheral Vascular Disease, Heart Failure, University Hospital Münster, Münster, Germany
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Han X, Zhou J, Yu L, Shao L, Cai S, Hu H, Shi Q, Wang Z, Hua X, Jiang Y, Yu Y. Genome sequencing unveils blaKPC-2-harboring plasmids as drivers of enhanced resistance and virulence in nosocomial Klebsiella pneumoniae. mSystems 2024; 9:e0092423. [PMID: 38193706 PMCID: PMC10878039 DOI: 10.1128/msystems.00924-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
The threat posed by Klebsiella pneumoniae in healthcare settings has worsened due to the evolutionary advantages conferred by blaKPC-2-harboring plasmids (pKPC-2). However, the specific evolutionary pathway of nosocomial K. pneumoniae carrying pKPC-2 and its transmission between patients and healthcare environments are not yet well understood. Between 1 August and 31 December 2019, 237 ST11 KPC-2-producing-carbapenem-resistant K. pneumoniae (CRKP) (KPC-2-CRKP) were collected from patient or ward environments in an intensive care unit and subjected to Illumina sequencing, of which 32 strains were additionally selected for Nanopore sequencing to obtain complete plasmid sequences. Bioinformatics analysis, conjugation experiments, antimicrobial susceptibility tests, and virulence assays were performed to identify the evolutionary characteristics of pKPC-2. The pKPC-2 plasmids were divided into three subgroups with distinct evolutionary events, including Tn3-mediated plasmid homologous recombination, IS26-mediated horizontal gene transfer, and dynamic duplications of antibiotic resistance genes (ARGs). Surprisingly, the incidence rates of multicopy blaKPC-2, blaSHV-12, and blaCTX-M-65 were quite high (ranging from 27.43% to 67.01%), and strains negative for extended-spectrum β-lactamase tended to develop multicopy blaKPC-2. Notably, the presence of multicopy blaSHV-12 reduced sensitivity to ceftazidime/avibactam (CZA), and the relative expression level of blaSHV-12 in the CZA-resistant group was 6.12 times higher than that in the sensitive group. Furthermore, a novel hybrid pKPC-2 was identified, presenting enhanced virulence levels and decreased susceptibility to CZA. This study emphasizes the notable prevalence of multicopy ARGs and provides a comprehensive insight into the intricate and diverse evolutionary pathways of resistant plasmids that disseminate among patients and healthcare environments.IMPORTANCEThis study is based on a CRKP screening program between patients and ward environments in an intensive care unit, describing the pKPC-2 (blaKPC-2-harboring plasmids) population structure and evolutionary characteristics in clinical settings. Long-read sequencing was performed in genetically closely related strains, enabling the high-resolution analysis of evolution pathway between or within pKPC-2 subgroups. We revealed the extremely high rates of multicopy antibiotic resistance genes (ARGs) in clinical settings and its effect on resistance profile toward novel β-lactam/β-lactamase inhibitor combinations, which belongs to the last line treatment choices toward CRKP infection. A novel hybrid pKPC-2 carrying CRKP with enhanced resistance and virulence level was captured during its clonal spread between patients and ward environment. These evidences highlight the threat of pKPC-2 to CRKP treatment and control. Thus, surveillance and timely disinfection in clinical settings should be practiced to prevent transmission of CRKP carrying threatful pKPC-2. And rational use of antibiotics should be called for to prevent inducing of pKPC-2 evolution, especially the multicopy ARGs.
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Affiliation(s)
- Xinhong Han
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junxin Zhou
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lifei Yu
- Department of Infectious Diseases, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lina Shao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shiqi Cai
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huangdu Hu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiucheng Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhengan Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, Son HI, You L. Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria. Nat Commun 2024; 15:1449. [PMID: 38365845 PMCID: PMC10873360 DOI: 10.1038/s41467-024-45638-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 01/29/2024] [Indexed: 02/18/2024] Open
Abstract
Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities.
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Affiliation(s)
- Rohan Maddamsetti
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Yi Yao
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Teng Wang
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Junheng Gao
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Vincent T Huang
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Grayson S Hamrick
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC, USA
| | - Hye-In Son
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lingchong You
- Center for Quantitative Biodesign, Duke University, Durham, NC, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Biomolecular and Tissue Engineering, Duke University, Durham, NC, USA.
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
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Wang Y, He J, Sun L, Jiang Y, Hu L, Leptihn S, Zhu P, Fu X, Yu Y, Hua X. IS26 mediated bla CTX-M-65 amplification in Escherichia coli increase the antibiotic resistance to cephalosporin in vivo. J Glob Antimicrob Resist 2023; 35:202-209. [PMID: 37802302 DOI: 10.1016/j.jgar.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/08/2023] Open
Abstract
OBJECTIVES To characterize two Escherichia coli strains isolated from a patient pre- and post-treatment, using β-lactams and β-lactam/β-lactamase inhibitor combinations (BLBLIs). METHODS A combination of antibiotic susceptibility testing (AST) with whole genome sequencing using Illumina and Oxford Nanopore platforms. Long-read sequencing and reverse transcription-quantitative PCR were performed to determine the copy numbers and expression levels of antibiotic resistance genes (ARGs), respectively. Effect on fitness costs were assessed by growth rate determination. RESULTS The strain obtained from the patient after the antibiotic treatment (XH989) exhibited higher resistance to cefepime, BLBLIs and quinolones compared with the pre-treatment strain (XH987). Sequencing revealed IS26-mediated duplications of a IS26-fosA3-blaCTX-M-65 plasmid-embedded element in strain XH989. Long-read sequencing (7.4 G data volume) indicated a variation in copy numbers of blaCTX-M-65 within one single culture of strain XH989. Increased copy numbers of the IS26-fosA3-blaCTX-M-65 element were correlated with higher CTX-M-65 expression level and did not impose fitness costs, while facilitating faster growth under high antibiotic concentrations. CONCLUSION Our study is an example from the clinic how BLBLIs and β-lactams exposure in vivo possibly promoted the amplification of an IS26-multiple drug resistance (MDR) region. The observation of a copy number variation seen with the blaCTX-M-65 gene in the plasmid of the post-treatment strain expands our knowledge of insertion sequence dynamics and evolution during treatment.
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Affiliation(s)
- Yinping Wang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jintao He
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Long Sun
- Department of Clinical Laboratory, Hangzhou Women's Hospital, Hangzhou Maternity and Child Health Care Hospital, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lihua Hu
- Department of Critical Care Medicine, Hangzhou General Hospital of Chinese People's Armed Police, Hangzhou, People's Republic of China
| | - Sebastian Leptihn
- Department of Vaccines and Infection Models, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; University of Edinburgh Medical School, Biomedical Sciences, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Pengfei Zhu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; Qingdao Single-Cell Biotech Co. Ltd., Qingdao, Shandong, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China; Qingdao Single-Cell Biotech Co. Ltd., Qingdao, Shandong, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, China.
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Yao H, Xing H, Wang N, Zhang L, Schwarz S, Li C, Cai C, Xu C, Du XD. IS257-mediated amplification of tet(L) variant as a novel mechanism of enhanced tigecycline resistance in Staphylococcus cohnii. Res Microbiol 2023; 174:104114. [PMID: 37572822 DOI: 10.1016/j.resmic.2023.104114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The mechanism of enhanced tigecycline MIC in Staphylococcus cohnii after in vitro tigecycline exposure was investigated. S. cohnii 11-B-312 was exposed to incremental concentrations of tigecycline (2-32 mg/L) and the mutants growing at 8, 16 and 32 mg/L were determined by AST and WGS. Copy number and relative transcription level of the tet(L) gene were determined by quantitative PCR. The fitness cost was evaluated by growth kinetics and competition assays. The results revealed that enhanced tigecycline MIC was identified in S. cohnii mutants. Copy number and relative transcription level of tet(L) in the mutants increased 8-, 20-, and 23-fold and 20-, 34-, and 39-fold in the presence of 8, 16, and 32 mg/L tigecycline, respectively. The read-mapping depth ratio analysis indicated that a multidrug resistance region carrying the tet(L) variant has a gradually increased copy number, correlating with the tigecycline selection pressure. S. cohnii strain 11-B-312_32 had a fitness cost, and enhanced tigecycline MIC can revert to the initial level in the absence of tigecycline. In summary, enhanced tigecycline MIC develops with extensive amplification of an IS257-flanked tet(L)-carrying segment in S. cohnii. IS257 seems to play a vital role in the gain and loss of the amplification product.
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Affiliation(s)
- Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Hongjie Xing
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Nannan Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Likuan Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany; Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Chenglong Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China
| | - Chang Cai
- College of Arts, Business, Law and Social Sciences, Murdoch University, Murdoch, WA, Australia
| | - Chunyan Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China.
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, PR China.
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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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Neumann B, Lippmann N, Wendt S, Karlas T, Lübbert C, Werner G, Pfeifer Y, Schuster CF. Recurrent bacteremia with a hypermucoviscous Escherichia coli isolated from a patient with perihilar cholangiocarcinoma: insights from a comprehensive genome-based analysis. Ann Clin Microbiol Antimicrob 2022; 21:28. [PMID: 35751078 PMCID: PMC9233328 DOI: 10.1186/s12941-022-00521-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 02/07/2023] Open
Abstract
Background Escherichia coli (E. coli) is a common human pathogen, responsible for a broad spectrum of infections. Sites of infection can vary, but the hepato-biliary system is of particular concern due to the infection-associated formation of gallstones and the spread of pathogens from the bile ducts into the bloodstream. Case presentation The presented case is striking, as the detected isolate showed a positive string test. This hypermucoviscous phenotype is atypical for E. coli and a particular feature of hypervirulent Klebsiella pneumoniae (K. pneumoniae) variants. Objectives To provide new insights into the genomic background of an E. coli strain with an unusual hypermucoviscous phenotype using hybrid short- and long-read sequencing approaches. Results Complete hybrid assemblies of the E. coli genome and plasmids were done and used for genome based typing. Isolate 537–20 was assigned to the multilocus sequence type ST88 and serotype O8:H4. The strain showed a close relationship to avian pathogenic strains. Analysis of the chromosome and plasmids revealed the presence of several virulence factors, such as the Conserved Virulence Plasmidic (CVP) region on plasmid 537-20_1, including several iron acquisition genes (sitABCD, iroABCDEN, iucABCD, hbd) and the iutA gene encoding the receptor of the siderophore aerobactin. The hypermucoviscous phenotype could be caused by encapsulation of putative K. pneumoniae origin. Conclusions Hybrid sequencing enabled detailed genomic characterization of the hypermucoviscous E. coli strain, revealing virulence factors that have their putative origin in K. pneumoniae. Supplementary Information The online version contains supplementary material available at 10.1186/s12941-022-00521-7.
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Affiliation(s)
- Bernd Neumann
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Institute for Hospital Hygiene, Medical Microbiology and Clinical Infectiology, Paracelsus Medical University, Nuremberg General Hospital, 90419, Nuremberg, Germany.
| | - Norman Lippmann
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Sebastian Wendt
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Thomas Karlas
- Division of Gastroenterology, Department of Medicine II, Leipzig University Medical Center, 04103, Leipzig, Germany
| | - Christoph Lübbert
- Interdisciplinary Centre for Infectious Diseases, Leipzig University Hospital, 04103, Leipzig, Germany.,Division of Infectious Diseases and Tropical Medicine, Department of Medicine II, Leipzig University Hospital, 04103, Leipzig, Germany
| | - Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany
| | - Christopher F Schuster
- Division Nosocomial Pathogens and Antibiotic Resistance, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, 38855, Wernigerode, Germany. .,Current Address: Center for Pandemic Vaccines and Therapeutics (ZEPAI), Paul-Ehrlich-Institute, 63225, Langen, Germany.
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Kresken M, Pfeifer Y, Wagenlehner F, Werner G, Wohlfarth E. Resistance to Mecillinam and Nine Other Antibiotics for Oral Use in Escherichia coli Isolated from Urine Specimens of Primary Care Patients in Germany, 2019/20. Antibiotics (Basel) 2022; 11:antibiotics11060751. [PMID: 35740157 PMCID: PMC9220249 DOI: 10.3390/antibiotics11060751] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 01/24/2023] Open
Abstract
Urinary tract infections (UTIs) are among the most common bacterial infections in humans. Escherichia coli is by far the leading cause of community-acquired UTIs. Pivmecillinam, the oral prodrug of the penicillin derivative mecillinam (amdinocillin), was re-introduced in Germany in March 2016 for first-line treatment of acute uncomplicated cystitis. This study aimed to evaluate the prevalence of resistance to mecillinam in comparison to nine other antibiotics used for oral treatment in E. coli urine isolates after the re-introduction of pivmecillinam. A total of 460 isolates were collected at 23 laboratories of clinical microbiology between October 2019 and March 2020. Forty-six isolates (10.0%) produced an extended-spectrum β-lactamase (ESBL) of the CTX-M family. Resistance to amoxicillin (43.3%) was most widespread, followed by resistance to trimethoprim-sulfamethoxazole (27.0%), amoxicillin-clavulanic acid (18.0%), cefuroxime (11.3%), and ciprofloxacin (11.1%). Twenty-four E. coli isolates (5.2%) were resistant to mecillinam. The concentrations of mecillinam needed to inhibit 50/90% of the ESBL-producing isolates and the remaining isolates were 1/4 mg/L and 0.5/4 mg/L, respectively. The findings support the recommendation to regard pivmecillinam as a first-line option for the treatment of uncomplicated lower UTIs.
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Affiliation(s)
- Michael Kresken
- Antiinfectives Intelligence GmbH, c/o Rechtsrheinisches Technologie- und Gründerzentrum, Gottfried-Hagen-Straße 60-62, 51105 Cologne, Germany;
- Rheinische Fachhochschule gGmbH, Schaevenstraße 1a-b, 50676 Cologne, Germany
- Correspondence: ; Tel.: +49-211-5609-1758
| | - Yvonne Pfeifer
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (Y.P.); (G.W.)
| | - Florian Wagenlehner
- Clinic for Urology, Pediatric Urology and Andrology, Justus-Liebig-University Gießen, Rudolf-Buchheim-Straße 7, 35392 Giessen, Germany;
| | - Guido Werner
- Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, 38855 Wernigerode, Germany; (Y.P.); (G.W.)
| | - Esther Wohlfarth
- Antiinfectives Intelligence GmbH, c/o Rechtsrheinisches Technologie- und Gründerzentrum, Gottfried-Hagen-Straße 60-62, 51105 Cologne, Germany;
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The Use of Long-Read Sequencing Technologies in Infection Control: Horizontal Transfer of a blaCTX-M-27 Containing lncFII Plasmid in a Patient Screening Sample. Microorganisms 2022; 10:microorganisms10030491. [PMID: 35336067 PMCID: PMC8949098 DOI: 10.3390/microorganisms10030491] [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: 02/08/2022] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 01/03/2023] Open
Abstract
Plasmid transfer is one important mechanism how antimicrobial resistance can spread between different species, contributing to the rise of multidrug resistant bacteria (MDRB) worldwide. Here were present whole genome sequencing (WGS) data of two MDRB isolates, an Escherichia coli and a Klebsiella quasipneumoniae, which were isolated from a single patient. Detailed analysis of long-read sequencing data identified an identical F2:A-:B- lncFII plasmid containing blaCTX-M-27 in both isolates, suggesting horizontal plasmid exchange between the two species. As the plasmid of the E. coli strain carried multiple copies of the resistance cassette, the genomic data correlated with the increased antimicrobial resistance (AMR) detected for this isolate. Our case report demonstrates how long-read sequencing data of MDRB can be used to investigate the role of plasmid mediate resistance in the healthcare setting and explain resistance phenotypes.
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