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Li Y, Yin M, Fang C, Fu Y, Dai X, Zeng W, Zhang L. Genetic analysis of resistance and virulence characteristics of clinical multidrug-resistant Proteus mirabilis isolates. Front Cell Infect Microbiol 2023; 13:1229194. [PMID: 37637463 PMCID: PMC10457174 DOI: 10.3389/fcimb.2023.1229194] [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: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Objective Proteus mirabilis is the one of most important pathogens of catheter-associated urinary tract infections. The emergence of multidrug-resistant (MDR) P. mirabilis severely limits antibiotic treatments, which poses a public health risk. This study aims to investigate the resistance characteristics and virulence potential for a collection of P. mirabilis clinical isolates. Methods and results Antibiotic susceptibility testing revealed fourteen MDR strains, which showed high resistance to most β-lactams and trimethoprim/sulfamethoxazole, and a lesser extent to quinolones. All the MDR strains were sensitive to carbapenems (except imipenem), ceftazidime, and amikacin, and most of them were also sensitive to aminoglycosides. The obtained MDR isolates were sequenced using an Illumina HiSeq. The core genome-based phylogenetic tree reveals the high genetic diversity of these MDR P. mirabilis isolates and highlights the possibility of clonal spread of them across China. Mobile genetic elements SXT/R391 ICEs were commonly (10/14) detected in these MDR P. mirabilis strains, whereas the presence of resistance island PmGRI1 and plasmid was sporadic. All ICEs except for ICEPmiChn31006 carried abundant antimicrobial resistance genes (ARGs) in the HS4 region, including the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-65. ICEPmiChn31006 contained the sole ARG blaCMY-2 and was nearly identical to the global epidemic ICEPmiJpn1. The findings highlight the important roles of ICEs in mediating the spread of ARGs in P. mirabilis strains. Additionally, these MDR P. mirabilis strains have great virulence potential as they exhibited significant virulence-related phenotypes including strong crystalline biofilm, hemolysis, urease production, and robust swarming motility, and harbored abundant virulence genes. Conclusion In conclusion, the prevalence of MDR P. mirabilis with high virulence potential poses an urgent threat to public health. Intensive monitoring is needed to reduce the incidence of infections by MDR P. mirabilis.
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Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Ming Yin
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Yu Fu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Wei Zeng
- Department of Clinical Laboratory, The Hejiang People’s hospital, Luzhou, Sichuan, China
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
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Jiang Y, Zhao L, Li JD, Sun J, Miao R, Shao B, Wu P. The universality of eAREs in animal feces suggesting that eAREs function possibly in horizontal gene transfer. J Adv Vet Anim Res 2023; 10:103-112. [PMID: 37155541 PMCID: PMC10122938 DOI: 10.5455/javar.2023.j658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 05/10/2023] Open
Abstract
Objectives This study aimed to pinpoint the universality of extracellular antimicrobial resistance elements (eAREs) and compare the contents of eAREs with those of intracellular AREs (iAREs) in animal feces, thus laying a foundation for the further analysis of the horizontal transfer of antimicrobial resistance genes (ARGs) in the animal guts. Materials and Methods Extracellular DNAs were isolated from the fecal samples of Pavo cristatus (n = 18), Ursus thibetanus (n = 2), two breeds of broilers (n = 21 and 11, respectively), and from the contents of rabbit intestines (n = 5). eAREs were detected by PCR technology. iAREs in P. cristatus and broiler feces were also detected and compared with the corresponding eAREs. In addition, some gene cassettes of class 1 integrons were sequenced and analyzed. Results The results showed that eAREs exist in animal feces and intestinal contents. In this study, different eAREs were detected from animal feces and intestinal contents, and tetA, tetB, sul1, sul2, class 1 integron, and IncFIB presented the highest detection rates. The detection rates of certain eAREs were significantly higher than those of parallel iAREs. The integral cassettes with intact structures were found in eAREs, and the cassettes carried ARGs. Conclusions The presented study here sheds light on the presence of eAREs in animal feces or guts, and eAREs may play an important role in the horizontal gene transfer of ARGs.
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Affiliation(s)
- Yusha Jiang
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Lang Zhao
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Jia Danyang Li
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Jialiang Sun
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Rui Miao
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Bo Shao
- College of Life Sciences, Southwest Forestry University, Kunming, China
| | - Peifu Wu
- College of Life Sciences, Southwest Forestry University, Kunming, China
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Zhang F, Wu S, Dai J, Huang J, Zhang J, Zhao M, Rong D, Li Y, Wang J, Chen M, Xue L, Ding Y, Wu Q. The emergence of novel macrolide resistance island in Macrococcus caseolyticus and Staphylococcus aureus of food origin. Int J Food Microbiol 2023; 386:110020. [PMID: 36427466 DOI: 10.1016/j.ijfoodmicro.2022.110020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/11/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
Abstract
Food-derived Staphylococcaceae species with severe antimicrobial resistance, especially Staphylococcus aureus, is a major threat to public health. Macrococcus caseolyticus (M. caseolyticus) is a member of the Staphylococcaceae family which plays a vital role in fermented products and disease causation in animals. In our previous study, several Staphylococcus aureus antibiotic-resistant island msr (SaRImsr) were found in multidrug-resistant S. aureus. In this study, novel SaRImsr, SaRImsr-III emerged from S. aureus. Another novel SaRImsr-like further emerged in M. caseolyticus from food. These isolates' prevalence and genetic environment were investigated and characterized to understand the distribution and transmission of these novel SaRImsr strains. All SaRImsr-positive S. aureus isolates exhibited a multidrug resistance (MDR) phenotype, within which a series of antimicrobial resistance genes (ARGs) and virulence factor genes (VFs) were identified. In addition, three SaRImsr types, SaRImsr-I (15.1 kb), SaRImsr-II (16-17 kb), and SaRImsr-III (18 kb) carrying mef(D)-msr(F), were identified in these isolates' chromosomes. SaRImsr-(I-III) contains a site-specific integrase gene int and operon mef(D)-msr(F). SaRImsr-III has an additional orf3-orf4-IS30 arrangement downstream of mef(D) and msr(F). Moreover, the SaRImsr-like and macrolide-resistant transposon Tn6776 forming a novel mosaic structure coexisted in one M. caseolyticus isolate. Within this mosaic structure, the macrolide-resistant genes mef(D)-msr(F) were absent in SaRImsr-like, whereas an operon, mef(F)-msr(G), was identified in Tn6776. The SaRImsr-(I-III) and SaRImsr-like structure were inserted into the rpsI gene encoding the 30S ribosomal protein S9 in the chromosome. Excision and cyclisation of SaRImsr-III, SaRImsr-like, operon mef(D)-msr(F), and orf3-orf4-IS30 arrangements were confirmed using two-step PCR. This study is the first to report MDR S. aureus harbouring novel SaRImsr-III and M. caseolyticus containing novel mosaic structures isolated from retail foods. Similar SaRImsr-type resistant islands' occurrence and propagation in Staphylococcaceae species require continuous monitoring and investigation.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Shi Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jingsha Dai
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jiahui Huang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Jumei Zhang
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Miao Zhao
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Dongli Rong
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Yuanyu Li
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Juan Wang
- College of Food Science, South China Agricultural University, Guangzhou 510432, China
| | - Moutong Chen
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Liang Xue
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China
| | - Yu Ding
- Department of Food Science & Technology, Jinan University, Guangzhou 510632, China.
| | - Qingping Wu
- Key Laboratory of Agricultural Microbiomics and Precision Application, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, 510070, China.
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Liu M, Li D, Jia W, Ma J, Zhao X. Study of the molecular characteristics and homology of carbapenem-resistant Proteus mirabilis by whole genome sequencing. J Med Microbiol 2023; 72. [PMID: 36748625 DOI: 10.1099/jmm.0.001648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Introduction. Proteus mirabilis is part of the family Enterobacteriaceae, and is naturally resistant to various antimicrobial drugs. In recent years, outbreaks of severe nosocomial infections caused by carbapenem-resistant P. mirabilis (CR-PMI) have been frequently reported. Few studies exist on the whole-genome molecular characteristics of this bacterium in China and elsewhere, which stimulated the implementation of this study.Hypothesis. CR-PMI strains contained the multiple drug resistance genes and exhibited a high resistance rate to commonly used antimicrobial drugs.Aim. Our goals here were to identify resistance mechanisms and homology of CR-PMI strains and provide a theoretical basis for clinical treatment and controlling nosocomial infections.Methodology. Bacterial species identification was carried out using matrix-assisted laser desorption/ionization time of flight MS (MALDI-TOF-MS). Antimicrobial susceptibility was determined using the VITEK 2 system and Kirby-Bauer (K-B) disc-diffusion method. Whole-genome sequencing (WGS) was conducted by the Illumina platform NovaSeq sequencer. Antibiotic resistance genes (ARGs) were identified using the NCBI database with Abricate. Plasmid replicon types were identified using PlasmidFinder, available at the Center for Genomic Epidemiology.Results. Five CR-PMI strains collected in our hospital from July 2019 to September 2021 were resistant to almost all antimicrobial agents except aztreonam (ATM), amikacin (AMK) and cefotetan (CTT). All CR-PMI strains contained the carbapenem resistance gene New Delhi metallo-β-lactamase 1 (bla NDM-1), and two strains harboured extended-spectrum β-lactamase (ESBL) genes bla PER-4 and bla CTX-M-65. The five CR-PMI strains contained 27, 18, 30, 25 and 24 drug-resistance genes, respectively. Most antimicrobial resistance genes were detected for aminoglycosides (n=14), followed by cephalosporins (n=7). The phylogenetic tree was divided into five evolutionary groups, and the five CR-PMI strains were in the four evolutionary groups B-E.Conclusion Overall, CR-PMI strains exhibited a high resistance rate to commonly used antimicrobial drugs, and contained the carbapenem resistance gene bla NDM-1. The CR-PMI strains showed a polyclonal trend in different wards at different times. Most importantly, all strains identified contained important antimicrobial resistance genes, which may lead to severe drug resistance transmission and fatal multiple resistant bacterial infections.
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Affiliation(s)
- Mi Liu
- Department of Clinical Laboratory, Weifang People's Hospital, 151 Guangwen Street, Weifang Shandong Province, 261041, PR China
| | - Dan Li
- Department of Clinical Laboratory, Weifang People's Hospital, 151 Guangwen Street, Weifang Shandong Province, 261041, PR China
| | - Wei Jia
- Department of Clinical Laboratory, Weifang People's Hospital, 151 Guangwen Street, Weifang Shandong Province, 261041, PR China
| | - Jie Ma
- Department of Clinical Laboratory, Weifang People's Hospital, 151 Guangwen Street, Weifang Shandong Province, 261041, PR China
| | - Xue Zhao
- Department of Clinical Laboratory, Weifang People's Hospital, 151 Guangwen Street, Weifang Shandong Province, 261041, PR China
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Li Y, Liu Q, Qiu Y, Fang C, Zhou Y, She J, Chen H, Dai X, Zhang L. Genomic characteristics of clinical multidrug-resistant Proteus isolates from a tertiary care hospital in southwest China. Front Microbiol 2022; 13:977356. [PMID: 36090113 PMCID: PMC9449695 DOI: 10.3389/fmicb.2022.977356] [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: 06/24/2022] [Accepted: 08/05/2022] [Indexed: 11/22/2022] Open
Abstract
Multidrug-resistant (MDR) Proteus, especially those strains producing extended-spectrum β-lactamases (ESBL) and carbapenemases, represents a major public health concern. In the present work, we characterized 27 MDR Proteus clinical isolates, including 23 Proteus mirabilis, three Proteus terrae, and one Proteus faecis, by whole-genome analysis. Among the 27 isolates analyzed, SXT/R391 ICEs were detected in 14 strains, and the complete sequences of nine ICEs were obtained. These ICEs share a common backbone structure but also have different gene contents in hotspots and variable regions. Among them, ICEPmiChn2826, ICEPmiChn2833, ICEPmiChn3105, and ICEPmiChn3725 contain abundant antibiotic resistance genes, including the ESBL gene blaCTX-M-65. The core gene phylogenetic analysis of ICEs showed their genetic diversity, and revealed the cryptic dissemination of them in Proteus strains from food animals and humans on a China-wide scale. One of the isolates, FZP3105, acquired an NDM-1-producing MDR plasmid, designated pNDM_FZP3105, which is a self-transmissible type 1/2 hybrid IncC plasmid. Analysis of the genetic organization showed that pNDM_FZP3105 has two novel antibiotic resistance islands bearing abundant antibiotic resistance genes, among which blaNDM-1 is located in a 9.0 kb ΔTn125 bracketed by two copies of IS26 in the same direction. In isolates FZP2936 and FZP3115, blaKPC-2 was detected on an IncN plasmid, which is identical to the previously reported pT211 in Zhejiang province of China. Besides, a MDR genomic island PmGRI1, a variant of PmGRI1-YN9 from chicken in China, was identified on their chromosome. In conclusion, this study demonstrates abundant genetic diversity of mobile genetic elements carrying antibiotic resistance genes, especially ESBL and carbapenemase genes, in clinical Proteus isolates, and highlights that the continuous monitoring on their transmission and further evolution is needed.
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Affiliation(s)
- Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Qian Liu
- Department of Clinical Laboratory, The Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Yichuan Qiu
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Chengju Fang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Yungang Zhou
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Junping She
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Huan Chen
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Xiaoyi Dai
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
- Xiaoyi Dai,
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
- *Correspondence: Luhua Zhang,
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Research Updates of Plasmid-Mediated Aminoglycoside Resistance 16S rRNA Methyltransferase. Antibiotics (Basel) 2022; 11:antibiotics11070906. [PMID: 35884160 PMCID: PMC9311965 DOI: 10.3390/antibiotics11070906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 01/27/2023] Open
Abstract
With the wide spread of multidrug-resistant bacteria, a variety of aminoglycosides have been used in clinical practice as one of the effective options for antimicrobial combinations. However, in recent years, the emergence of high-level resistance against pan-aminoglycosides has worsened the status of antimicrobial resistance, so the production of 16S rRNA methyltransferase (16S-RMTase) should not be ignored as one of the most important resistance mechanisms. What is more, on account of transferable plasmids, the horizontal transfer of resistance genes between pathogens becomes easier and more widespread, which brings challenges to the treatment of infectious diseases and infection control of drug-resistant bacteria. In this review, we will make a presentation on the prevalence and genetic environment of 16S-RMTase encoding genes that lead to high-level resistance to aminoglycosides.
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