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Hu J, Li J, Liu C, Zhang Y, Xie H, Li C, Shen H, Cao X. Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis. BMC Microbiol 2022; 22:255. [PMID: 36266616 DOI: 10.1186/s12866-022-02667-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/10/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE To analyze the characteristics of global β-lactamase-producing Enterobacter cloacae including the distribution of β-lactamase, sequence types (STs) as well as plasmid replicons. METHODS All the genomes of the E. cloacae were downloaded from GenBank. The distribution of β-lactamase encoding genes were investigated by genome annotation after the genome quality was checked. The STs of these strains were analyzed by multi-locus sequence typing (MLST). The distribution of plasmid replicons was further explored by submitting these genomes to the genome epidemiology center. The isolation information of these strains was extracted by Per program from GenBank. RESULTS A total of 272 out of 276 strains were found to carry β-lactamase encoding genes. Among them, 23 varieties of β-lactamase were identified, blaCMH (n = 130, 47.8%) and blaACT (n = 126, 46.3%) were the most predominant ones, 9 genotypes of carbapenem-hydrolyzing β-lactamase (CHβLs) were identified with blaVIM (n = 29, 10.7%) and blaKPC (n = 24, 8.9%) being the most dominant ones. In addition, 115 distinct STs for the 272 ß-lactamase-carrying E. cloacae and 48 different STs for 106 CHβLs-producing E. cloacae were detected. ST873 (n = 27, 9.9%) was the most common ST. Furthermore, 25 different plasmid replicons were identified, IncHI2 (n = 65, 23.9%), IncHI2A (n = 64, 23.5%) and IncFII (n = 62, 22.8%) were the most common ones. Notably, the distribution of plasmid replicons IncHI2 and IncHI2A among CHβLs-producing strains were significantly higher than theat among non-CHβLs-producing strains (p < 0.05). CONCLUSION Almost all the E. cloacae contained β-lactamase encoding gene. Among the global E. cloacae, blaCMH and blaACT were main blaAmpC genes. BlaTEM and blaCTX-M were the predominant ESBLs. BlaKPC, blaVIM and blaNDM were the major CHβLs. Additionally, diversely distinct STs and different replicons were identified.
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Affiliation(s)
- Jincao Hu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Jia Li
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Chang Liu
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Yan Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Hui Xie
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China
| | - Chuchu Li
- Department of Acute Infectious Disease Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Han Shen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China.
| | - Xiaoli Cao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, GulouJiangsu Province, Nanjing, People's Republic of China.
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Jabeen R, Iqbal A, Deeba F, Zulfiqar F, Mustafa G, Nawaz H, Habiba U, Nafees M, Zaid A, Siddique KHM. Isolation and characterization of peroxidase P7-like gene and Rab-GDI like gene from potential medicinal plants: A step toward understanding cell defense signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:975852. [PMID: 36119597 PMCID: PMC9478186 DOI: 10.3389/fpls.2022.975852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/10/2022] [Indexed: 05/17/2023]
Abstract
Defensin genes form part of a plant's defense system and are activated when exposed to biotic or abiotic stress. They play a vital role in controlling many signaling pathways involved in various plant defense mechanisms. This research aimed to isolate and characterize novel defensin genes from selected medicinally important plants to explore their signaling mechanisms and defense associated roles for breeding. The DNA of Albizia lebbeck and Moringa oleifera was subjected to PCR amplification using gene-specific primers of defensin genes. Two novel defensin genes were isolated in each species, with sequence lengths of 300 bp in A. lebbeck and 150 bp in M. oleifera. In-silico analysis undertaken to retrieve and align their orthologous sequences revealed 100% similarity of the A. lebbeck gene with the Musa acuminate peroxidase P7-like gene and 85% similarity of the M. oleifera gene with the Manihot esculenta GDP dissociation inhibitor gene. The reliability, stability and physiochemical properties of homology models of these sequences was confirmed through online computational studies. This preliminary study confirmed the presence of novel genes with peroxidase P7 and Rab GDP dissociation inhibitor gene-like activity in A. lebbeck and M. oleifera, respectively, and their potential defense role in plants. Thus, the defensin genes of both species could be used in the synthesis of transgenic self-defensive plants with increased disease resistance and as potential candidates for improved crop production and thraputic formulation in the future.
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Affiliation(s)
- Raheela Jabeen
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
- *Correspondence: Raheela Jabeen,
| | - Atia Iqbal
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Farah Deeba
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Punjab, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Faisal Zulfiqar,
| | - Ghulam Mustafa
- Department of Biochemsitry, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Haq Nawaz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Punjab, Pakistan
| | - Ume Habiba
- Department of Microbiology and Molecular Genetics, The Women University Multan, Multan, Punjab, Pakistan
| | - Muhammad Nafees
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Abbu Zaid
- Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Re-examining the association of AmpC variants with Enterobacter species in the context of updated taxonomy. Antimicrob Agents Chemother 2021; 65:e0159621. [PMID: 34516244 DOI: 10.1128/aac.01596-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We performed whole genome sequencing for 17 Enterobacter clinical strains and analyzed all available Enterobacter genomes and its closely-related genera (n=3,389) from NCBI. The exact origin of plasmid-borne blaCMH and blaMIR genes is Enterobacter cloacae and Enterobacter roggenkampii, respectively, while plasmid-borne blaACT genes originated from multiple other Enterobacter species including Enterobacter xiangfangensis, Enterobacter hoffmannii, and Enterobacter asburiae, Enterobacter ludwigii, and Enterobacter kobei. The genus of Enterobacter represents a large reservoir of plasmid-borne AmpC β-lactamase.
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Ingti B, Upadhyay S, Hazarika M, Khyriem AB, Paul D, Bhattacharya P, Joshi SR, Bora D, Dhar D, Bhattacharjee A. Distribution of carbapenem resistant Acinetobacter baumannii with bla ADC-30 and induction of ADC-30 in response to beta-lactam antibiotics. Res Microbiol 2020; 171:128-133. [PMID: 31988011 DOI: 10.1016/j.resmic.2020.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 11/09/2019] [Accepted: 01/14/2020] [Indexed: 10/25/2022]
Abstract
A wide range of intrinsic Acinetobacter-derived cephalosporinases (ADC) along with other carbapenemases has now been detected in Acinetobacter baumannii leaving clinicians with few treatment options. The present study reports the spread of ADC-30 co-producing KPC-2 along with other β-lactamases among carbapenem resistant A. baumannii strains obtained from ICU patients in two Indian hospitals. Primer extension analysis revealed higher transcript level of the ADC gene when induced with cefoxitin at 8 μg/ml (170 fold), ceftriaxone at 8 μg/ml (136 fold), ceftazidime at 4 μg/ml (65 fold), cefepime at 8 μg/ml (77 fold) and aztreonam at 8 μg/ml (21 fold) when compared with the basal level without antibiotic pressure. Slight increase in expression of blaADC-30 when induced with imipenem and meropenem at 0.25 μg/ml (3 and 6 fold) was observed and may help in conferring resistance to carbapenem. MLST analysis revealed the circulation of A. baumannii sequence types ST188, ST386, ST583 and ST390 in these hospitals.
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Affiliation(s)
- Birson Ingti
- Department of Microbiology, Assam University, Silchar, 788011, India; Department of Microbiology, Royal Global University, Guwahati, 781035, India
| | - Supriya Upadhyay
- Department of Biotechnology & Bioinformatics, North Eastern Hill University, Shillong, 793022, Meghalaya, India
| | | | - Annie Bakorlin Khyriem
- Department of Microbiology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya, India
| | - Deepjyoti Paul
- Department of Microbiology, Assam University, Silchar, 788011, India
| | - Prithwis Bhattacharya
- Department of Anesthesiology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya, India
| | - S R Joshi
- Department of Biotechnology & Bioinformatics, North Eastern Hill University, Shillong, 793022, Meghalaya, India.
| | - Debajyoti Bora
- Department of Statistics, Dibrugarh University, Dibrugarh, India
| | - Debadatta Dhar
- Department of Microbiology, Silchar Medical College and Hospital, Silchar, India
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López-Hernández I, García Barrionuevo A, Díaz de Alba P, Clavijo E, Pascual A. Characterization of NDM-1- and CMH-3-producing Enterobacter cloacae complex ST932 in a patient transferred from Ukraine to Spain. Enferm Infecc Microbiol Clin 2019; 38:327-330. [PMID: 31813643 DOI: 10.1016/j.eimc.2019.10.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 10/25/2022]
Abstract
INTRODUCTION To characterize a carbapenem-resistant Enterobacter cloacae complex isolate recovered from a patient from Ukraine. METHODS The isolate was sent to a regional reference laboratory for molecular characterization by whole genome sequencing. Susceptibility assays, carbapenemase identification, imipenem hydrolysis and clonality were performed. RESULTS The isolate showed resistance or reduced susceptibility to all β-lactam agents tested. Genome analysis led to the identification of an NDM-1-producing E. cloacae complex strain that was assigned to a new multilocus sequence type, ST932. The blaNDM-1 enzyme was located in a conjugative IncX3 plasmid of ca. 50kb. In addition, blaCMH-3, a recently described AmpC β-lactamase sequence, which has not previously been reported in Europe, was also detected and its genetic environment was studied. CONCLUSION To our knowledge, this is the first reported case in Europe of an E. cloacae complex strain that produces both blaNDM-1 and blaCMH-3.
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Affiliation(s)
- Inmaculada López-Hernández
- Laboratorio PIRASOA, Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain.
| | | | - Paula Díaz de Alba
- Laboratorio PIRASOA, Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | | | - Alvaro Pascual
- Laboratorio PIRASOA, Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain; Instituto de Biomedicina de Sevilla (IBiS), Seville, Spain; Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
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Ku YH, Lee MF, Chuang YC, Yu WL. Detection of Plasmid-Mediated β-Lactamase Genes and Emergence of a Novel AmpC (CMH-1) in Enterobacter cloacae at a Medical Center in Southern Taiwan. J Clin Med 2018; 8:jcm8010008. [PMID: 30577544 PMCID: PMC6352282 DOI: 10.3390/jcm8010008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/03/2022] Open
Abstract
The plasmid-mediated extended-spectrum β-lactamases (ESBLs) and AmpC β-lactamases in Enterobacter spp. have increasingly been reported. In this study, we investigated the prevalence of the plasmid-mediated β-lactamases in Enterobacter cloacae from bloodstream isolates at a medical center in southern Taiwan. ESBL and ampC genes were detected by PCRs and DNA sequencing. Conjugation experiments were conducted to confirm the transferability of the genetic resistance trait. Among 41 non-repetitive blood isolates of cefuroxime-resistant E. cloacae, eight isolates exhibited ESBL phenotype confirmed by double-disk synergistic tests. Nearly all the strains were susceptible to carbapenems. The prevalence rate of the plasmid-mediated blaampC genes was 73% (30/41), including one blaDHA-1, one blaMIR-6, two novel blaCMH-1 genes and other blaACT-like genes. Coexistence of plasmid-mediated blaACT and ESBL genes (10 with blaSHV-12 and one with blaCTX-M-3) was observed. Successful transmissions of the blaACT and blaCMH-1 were demonstrated in some transconjugants. The inducible or derepressed CMH-1 had expanded activity of isolates versus ceftazidime. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis and pulsotype showed distinct patterns suggesting non-clonal relationship. In conclusion, plasmid-mediated blaACT-likeampC genes in E. cloacae isolates have been highly prevalent in southern Taiwan and may continue genetic evolution, contributing to the complexities in antibiotic-resistant mechanisms.
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Affiliation(s)
- Yee-Huang Ku
- Division of Infectious Disease, Department of Internal Medicine, Chi Mei Medical Center-Liouying, Tainan 710, Taiwan.
| | - Mei-Feng Lee
- Laboratory of Environmental Health, Research Center of Humanities and Technology, National University of Kaohsiung, Kaohsiung 811, Taiwan.
| | - Yin-Ching Chuang
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan.
| | - Wen-Liang Yu
- Department of Intensive Care Medicine, Chi Mei Medical Center, Tainan 710, Taiwan.
- Department of Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan.
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Coertze RD, Bezuidenhout CC. The prevalence and diversity of AmpC β-lactamase genes in plasmids from aquatic systems. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2018; 2017:603-611. [PMID: 29851413 DOI: 10.2166/wst.2018.188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study aimed to investigate the presence and diversity of AmpC β-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC β-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0.0 to 29.38 copies per picogram of DNA). Some samples in which ampC was not detected, intI1 was present. Amplicons of ampC genes were subjected to restriction digest using HindIII. Samples where the restriction markers were absent were purified by cloning followed by plasmid extraction, PCR amplification, and sequencing of individual AmpC gene fragments. Phylogenetic analysis identified all positive AmpC genes as Class C β-lactamases, comprising of ampC, CMY- and ACT-families. Detecting AmpC and intl1 genes on plasmids suggests a high risk of horizontal gene transfer and potential dissemination of these and other antibiotic resistance genes surrounding immediate aquatic environments. Consequences of β-lactamase diversity in aquatic ecosystems are relatively unexplored in South African aquatic ecosystems.
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Affiliation(s)
- Roelof Dirk Coertze
- Unit for Environmental Science and Management: Microbiology, North-West University: Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa E-mail:
| | - Cornelius Carlos Bezuidenhout
- Unit for Environmental Science and Management: Microbiology, North-West University: Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa E-mail:
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