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Chen L, Shi Y, Wang M, Li Y, Si Z. Comprehensive epidemiological profiling of poultry-derived Salmonella spp. in Shandong, China, 2019-2022: a longitudinal study of prevalence, antibiotic resistances, virulence factors and molecular characteristics. Front Microbiol 2025; 16:1541084. [PMID: 40109969 PMCID: PMC11920138 DOI: 10.3389/fmicb.2025.1541084] [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: 12/07/2024] [Accepted: 02/19/2025] [Indexed: 03/22/2025] Open
Abstract
Salmonella spp., as a major foodborne pathogen, pose significant threats to public health globally and has been an important zoonotic contamination for poultry industry that should receive increasing attentions. This study aimed to comprehensively investigate the prevalence, antimicrobial resistances, virulence factors, and plasmid types of Salmonella isolates collected from chickens, ducks, and geese across eight cities in Shandong between 2019 and 2022. Out of 300 samples, 53 Salmonella strains (17.67%) were isolated, with varied prevalence from 8.33% to 25.00% in different cities of Shandong. A total of seven serotypes were identified among the 53 Salmonella isolates, wherein the S. Enteritidis (45.28%), S. Pullorum (22.64%) and S. Typhimurium (16.98%) were identified as the most prevalent. Whole-genome sequencing analysis revealed that ST11, ST92, and ST19 were the predominant sequence types for S. Enteritidis, S. Pullorum, and S. Typhimurium, respectively. Phylogenetic analysis indicated that potential clonal spread of S. Enteritidis, S. Pullorum, and S. Typhimurium occurred across different regions, particularly the evidences supported that the S. Typhimurium isolates were dispersed in a cross-species manner. Finally, the phenotypic and genotypic profiling of antibiotic resistance among the isolates revealed that these isolates were multidrug resistant with corresponding antibiotic resistance genes (ARGs) including bla TEM, aac, aph, tet(A), and tet(B) to confer them with resistances to commonly-used veterinary drugs such as β-lactams, quinolones, macrolides. To sum, this study provides valuable insights into the current epidemiology of Salmonella in poultry industry in one of the biggest provinces in China, and shedding the light on the urgent necessity for further approaches to prevent and decontaminate such MDR Salmonella in livestock under One Health concept.
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Affiliation(s)
- Lele Chen
- College of Agriculture and Biology, Liaocheng University, Liaocheng, China
- Phage Research Center, Liaocheng University, Liaocheng, China
| | - Yuxia Shi
- College of Agriculture and Biology, Liaocheng University, Liaocheng, China
- Phage Research Center, Liaocheng University, Liaocheng, China
| | - Minge Wang
- College of Agriculture and Biology, Liaocheng University, Liaocheng, China
- Phage Research Center, Liaocheng University, Liaocheng, China
| | - Yubao Li
- Phage Research Center, Liaocheng University, Liaocheng, China
| | - Zhenshu Si
- College of Agriculture and Biology, Liaocheng University, Liaocheng, China
- Phage Research Center, Liaocheng University, Liaocheng, China
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Kreuze K, Friman VP, Vatanen T. Mobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly? MICROBIOME RESEARCH REPORTS 2024; 4:7. [PMID: 40207272 PMCID: PMC11977359 DOI: 10.20517/mrr.2024.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 10/24/2024] [Accepted: 10/24/2024] [Indexed: 04/11/2025]
Abstract
The gut microbiota is important for healthy infant development. Part of the initial colonizing microbial strains originate from the maternal gut, and undergo a selective event, termed the "colonization bottleneck". While vertical mother-to-infant inheritance and subsequent colonization of bacteria have previously been studied, the role of mobile genetic elements (MGEs) in the infant gut microbiota assembly is unclear. In this perspective article, we discuss how horizontally and vertically transmitted phages and conjugative elements potentially have important roles in infant gut microbiota assembly and colonization through parasitic and mutualistic interactions with their bacterial hosts. While some of these MGEs are likely to be detrimental to their host survival, in other contexts, they may help bacteria colonize new niches, antagonize other bacteria, or protect themselves from other parasitic MGEs in the infant gut. As a result, the horizontal transfer of MGEs likely occurs at high rates in the infant gut, contributing to gene transfer between bacteria and affecting which bacteria can pass the colonization bottleneck. We conclude by highlighting the potential in silico, in vitro, and in vivo methodological approaches that could be employed to study the transmission and colonization dynamics of MGEs and bacteria in the infant gut.
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Affiliation(s)
- Kim Kreuze
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki FI-00014, Finland
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki FI-00014, Finland
| | - Ville-Petri Friman
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki FI-00014, Finland
| | - Tommi Vatanen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki FI-00014, Finland
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki FI-00014, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki FI-00014, Finland
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Liggins Institute, University of Auckland, Auckland 1142, New Zealand
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Baleivanualala SC, Matanitobua S, Soqo V, Smita S, Limaono J, Sharma SC, Devi SV, Boseiwaqa LV, Vera N, Kumar S, Lalibuli A, Mailulu J, Wilson D, Samisoni Y, Crump JA, Ussher JE. Molecular and clinical epidemiology of carbapenem resistant Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales in Fiji: a multicentre prospective observational study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2024; 47:101095. [PMID: 38867891 PMCID: PMC11166881 DOI: 10.1016/j.lanwpc.2024.101095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/08/2024] [Accepted: 05/06/2024] [Indexed: 06/14/2024]
Abstract
Background Carbapenem resistant organisms (CROs) such as Acinetobacter baumannii (CRAb), Pseudomonas aeruginosa (CRPa), Escherichia coli (CREc), and Klebsiella pneumoniae (CRKp) have been identified by the World Health Organization (WHO) as global priority pathogens. The dissemination of these pathogens and clonal outbreaks within healthcare facilities are of serious concern, particularly in regions with limited resources. In Fiji, where healthcare services are primarily provided by public hospitals, understanding the extent and nature of this problem is essential for the development of effective patient management, prevention interventions and control strategies. Methods CROs isolated from 211 (77.3%) non-sterile (urinary catheters, urine, sputum, wound swab, and endotracheal tube) and 62 (22.7%) normally sterile (blood, cerebrospinal fluid, intravascular catheter, and aspirates) body sites of 272 patients treated at the three major hospitals in Fiji, the Colonial War Memorial Hospital (CWMH), Lautoka Hospital (LTKH), and Labasa Hospital (LBSH), and outer peripheral health centres around Fiji, were analysed. Clinical and demographic patient data such as age, sex, admission diagnosis, admission and discharge dates, patient outcomes, date of death, start and end date of meropenem and colistin treatment were reviewed. These CRO isolates comprised A. baumannii, P. aeruginosa, E. coli, and K. pneumoniae, that were prospectively collected at the microbiology laboratory of CWMH and LBSH from January 2020 through August 2021 and at the LTKH from January 2020 to December 2021. In addition, 10 retrospectively stored CRPa isolates collected from patients at the CWMH from January through December 2019, were also included in the study. All isolates were characterised using mass spectrometry, antimicrobial susceptibility testing, and whole genome sequencing. Phylogenetic relationships among the CROs were assessed through core genome single nucleotide polymorphism (SNP) analysis. The CRAb isolates were also compared to the CRAb isolates from CWMH isolated in 2016/2017 and 2019, along with CRAb isolates obtained from Fijian patients admitted to New Zealand hospitals in 2020 and 2021 from our retrospective study. Findings Of 272 patients, 140 (51.5%) were male, the median (range) age of patients was 45 (<1-89) years, 161 (59.2%) were I-Taukei, 104 (38.2%) Fijians of Indian descent, and 7 (2.6%) were from other ethnic backgrounds. 234 (86.0%) of these 272 patients, had their first positive CRO sample collected ≥72 h following admission and the remaining 38 (14.0%) were isolated within 72 h following admission. Of the 273 CROs, 146 (53.5%) were collected at the CWMH, 66 (24.2%) LTKH, and 61 (22.3%) LBSH, while 62 (22.7%) were isolated from normally sterile sites and 211 (77.3%) from sites that are not sterile. Of 273 isolates, 131 (48.0%) were CRAb, 90 (33.0%) CRPa, 46 (16.8%) CREc, and 6 (2.2%) CRKp. Of 131 CRAb, 108 (82.4%) were ST2, with three distinct clones, all encoding bla OXA-23 and bla OXA - 66, while clone 3 also encoded bla NDM-1; bla OXA-23 was associated with two copies of ISAba1 insertion element, forming the composite transposon Tn2006. The first two CRAb ST2 clones were genetically linked to those isolated at CMWH 2016 through 2019, while the third was genetically linked to isolates from Fijian patients admitted to New Zealand hospitals in 2020 and 2021. Of CRPa, 65 (72.2%) were ST773 and carried β-lactamase genes bla NDM-1, bla OXA-50, and bla OXA-395. Of 10 retrospective CRPa isolates, all belonged to CRPa ST773 and carried bla NDM-1, bla OXA-50, and bla OXA-395. Of 46 CREc, 44 (95.7%) were ST410 and encoded bla NDM-7 on an IncX3 plasmid. Of 6 CRKp, 4 (66.7%) were ST16 and carried bla NDM-5 on an IncX3 plasmid. Other sequence types of CRPa (ST9, ST357, ST654, ST664), CRAb (ST25, ST374, ST499), CREc (ST167), and CRKp (ST45, ST336) were also detected. Of those receiving meropenem treatment in the prospective study, 30 (57.7%) received it inappropriately. Of 272 patients, 65 (23.9%) died within the 30 days after first positive CRO isolation. Interpretation We identified nosocomial transmission of distinct clones of CRAb ST2, CRPa ST773, CREc ST410, and CRKp ST16 within and between the three major hospitals in Fiji. Moreover, community onset infections associated with CRPa, CREc, and CRAb were also detected. Of note, cross-border transmission of CRAb ST2 clone 3 strain between Fiji and New Zealand was also detected. These clones encoded an array of carbapenem resistance genes associated with mobile genetic elements, including plasmids, transposons, and integrative and conjugative elements, signifying their potential for increased mobility, further acquisition of resistance genes, and spread. Inappropriate use of meropenem was common. Of note, the majority of patients who died had acquired CRO during their hospital stay. These findings highlight the need for stringent IPC strategies focusing on catheter and ventilator management, meticulous wound care, rigorous sepsis control, consistent hand hygiene, effective use of disinfectants, and thorough sanitisation of both hospital environments and medical equipment in the three major hospitals in Fiji. Additionally, diligent surveillance of AMR and robust antimicrobial stewardship are crucial for effectively managing nosocomial infections. Funding This project was funded by the Otago Medical School Foundations Trust (Dean's Bequest Fund) and a Fiji National University seed grant. The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report.
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Affiliation(s)
- Sakiusa C. Baleivanualala
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- College of Medicine, Nursing and Health Science, Fiji National University, Suva, Fiji
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 92019, New Zealand
| | | | | | | | | | | | - Swastika V. Devi
- College of Medicine, Nursing and Health Science, Fiji National University, Suva, Fiji
| | | | - Numa Vera
- College of Medicine, Nursing and Health Science, Fiji National University, Suva, Fiji
| | | | | | | | - Donald Wilson
- College of Medicine, Nursing and Health Science, Fiji National University, Suva, Fiji
| | | | - John A. Crump
- Division of Health Sciences, Centre for International Health, University of Otago, Dunedin, New Zealand
- Otago Global Health Institute, University of Otago, Dunedin 9054, New Zealand
| | - James E. Ussher
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 92019, New Zealand
- Otago Global Health Institute, University of Otago, Dunedin 9054, New Zealand
- Awanui Labs, Dunedin Hospital, Dunedin, New Zealand
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Farrell ML, Chueiri A, Maguire M, Kovářová A, Miliotis G, O'Connor L, McDonagh F, Duane S, Cormican M, Devane G, Tuohy A, DeLappe N, De Bock F, Burke LP, Morris D. Longitudinal carriage of antimicrobial resistant Enterobacterales in healthy individuals in Ireland - Assessing the impact of recreational water use on duration of carriage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167100. [PMID: 37717747 DOI: 10.1016/j.scitotenv.2023.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
The increasing prevalence of extended-spectrum beta-lactamase (ESBL) producing Enterobacterales (ESBL-PE) and carbapenemase-producing Enterobacterales (CPE) is a major public health concern worldwide. Despite the associated risk of infection from gut colonisation with a resistant Enterobacterales, the incidence and duration of carriage in healthy individuals is poorly studied. This "persistence study" is the first in Ireland to assess the longitudinal carriage of ESBL-PE and CPE in healthy individuals. A cohort of 45 participants, 22 of whom were colonised with ESBL-PE, was recruited from a recently completed point prevalence study that investigated colonisation in recreational water users (WU) versus controls. Six bi-monthly faecal samples per participant were analysed for CPE and ESBL-PE over one year and the relationship between persistent colonisation and exposure to natural waters was investigated. For 11 of 45 participants (24.4 %) ESBL-E. coli (ESBL-EC) was detected in at least one sample. Genomic analysis revealed that six participants harboured the same ESBL-EC strains as identified in the preceding study. ESBL-EC persisted in the gut for a median duration of 10.3 months (range 4-23 months), consistent with previous research. Five participants (11.1 %) carried ESBL-EC for the entire study year. The carbapenemase gene blaIMI-2 was detected once. Colonisation was higher in water users during the non-bathing season (n = 10, November 2021-April 2022), than during the bathing season (n = 5, May 2022-September 2022) [relative risk 1.99 (95 % CI 0.34-11.71)]. However, overall WU were less likely to be colonised with ESBL-EC than controls (19 % vs 25 % respectively, RR 0.76, CI 0.24-2.34). Further research is warranted to better understand the factors influencing the persistence of gut colonisation with ESBL-EC and CPE and to what extent bathing water quality impacts colonisation for those regularly exposed.
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Affiliation(s)
- Maeve Louise Farrell
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland.
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Mark Maguire
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Aneta Kovářová
- Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Sinead Duane
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland; J.E. Cairnes School of Business and Economics, University of Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland; National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Genevieve Devane
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Alma Tuohy
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Niall DeLappe
- National Carbapenemase-producing Enterobacterales Reference Laboratory Service, Ireland
| | - Florence De Bock
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Liam P Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Ireland; Centre for One Health, Ryan Institute, University of Galway, Ireland
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Shao J, Dai H, Xu L, Zhu S, Zhu J, Fu H, Ge M, He X. Genomic Characteristics of Extended Spectrum β-Lactamase Producing Escherichia coli Isolates Recovered from a District Hospital in China. Infect Drug Resist 2023; 16:3589-3600. [PMID: 37309377 PMCID: PMC10257927 DOI: 10.2147/idr.s415373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/02/2023] [Indexed: 06/14/2023] Open
Abstract
Purpose The isolation rate of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is increasing, posing a challenge to clinical anti-infective therapy. This study aims to provide new insight into the genomic characteristics and antimicrobial resistance mechanisms of extended spectrum β-lactamase producing E. coli isolates recovered from a district hospital in China. Methods A total of 36 ESBL-producing E. coli isolates were collected from body fluid samples from a Chinese district hospital. All isolates were subjected to whole genome sequencing to identify their antimicrobial resistance genes, virulence genes, serotypes, sequence types, and phylogenetic relationships by BacWGSTdb 2.0 webserver. Results Among these isolates, all were resistant to cefazolin, cefotaxime, ceftriaxone, ampicillin, 24 (66.7%) were resistant to aztreonam, 16 (44.4%) were resistant to cefepime, and 15 were resistant (41.7%) to ceftazidime. The blaCTX-M gene was detected in all ESBL-producing E. coli isolates. Two isolates carrying two different types of blaCTX-M genes simultaneously. The carbapenem resistance gene blaKPC-2 was detected in one (2.8%) isolate. A total of 17 sequence types (STs) were found, with ST131 accounting for the majority (n =13; 36.1%). The most common serotype was O16:H5 associated with seven ST131 strains, followed by O25:H4/ST131 (n = 5) and O75:H5/ST1193 (n = 5). Evaluation of clonal relatedness revealed that all blaCTX-M gene-carrying E. coli had a difference of SNPs range from 7 to 79,198, which could be divided into four clusters. Only 7 SNPs could be found between EC266 and EC622, indicating that they are variants of the same clonal lineage. Conclusion This study investigated the genomic characteristics of ESBL-producing E. coli isolates recovered from a district hospital in China. Continuous surveillance of ESBL-producing E. coli infections is imperative to create efficient strategies for controlling the transmission of these multi-drug resistant bacteria in clinical and community settings.
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Affiliation(s)
- Jiayu Shao
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Hangdong Dai
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Liwei Xu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Shuilong Zhu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Jufang Zhu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Hangyu Fu
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Minxia Ge
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
| | - Xianhong He
- Department of Clinical Laboratory, the Third People’s Hospital of Xiaoshan, Hangzhou, People’s Republic of China
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Tang B, Wang C, Sun D, Lin H, Ma J, Guo H, Yang H, Li X. In Silico Characterization of blaNDM-Harboring Conjugative Plasmids in Acinetobacter Species. Microbiol Spectr 2022; 10:e0210222. [PMID: 36301090 PMCID: PMC9769834 DOI: 10.1128/spectrum.02102-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
New Delhi metallo-β-lactamase (NDM)-producing clinical strains in Acinetobacter spp. have been recently reported in many countries and have received considerable attention. The vast majority of blaNDM cases occur on conjugative plasmids, which play a vital role in disseminating blaNDM. To characterize the conjugative plasmids bearing blaNDM genes in Acinetobacter spp., we analyzed the variants of blaNDM, conjugative transfer regions, genetic contexts of blaNDM, and the phylogenetic pattern of the 62 predicted blaNDM-positive plasmids, which were selected from 1,191 plasmids of Acinetobacter species from GenBank. We identified 30 conjugative plasmids from the 62 blaNDM-harboring plasmids in Acinetobacter species, with the oriT sites similar to plasmid pNDM-YR7 in our study, genes coding for relaxases of the MOBQ family, genes encoding type IV coupling proteins (T4CPs) of the TrwB/TraD subfamily, and VirB-like type IV secretion system (T4SS) gene clusters. The genome sizes of all 30 pNDM-YR7-like plasmids ranged from 39.36 kb to 49.65 kb, with a median size of 44.56 kb. The most common species of Acinetobacter containing the blaNDM-positive conjugative plasmids was A. baumannii, followed by Acinetobacter lwoffii and Acinetobacter indicus. Notably, pNDM-YR7 is the first report on a blaNDM-positive conjugative plasmid in Acinetobacter junii. Moreover, all 30 blaNDM-positive conjugative plasmids in Acinetobacter species were found to contain genetic contexts with the structure ISAba14-aph(3')-VI-ISAba125-blaNDM-ble. Our findings provide important insights into the phylogeny and evolution of blaNDM-positive plasmids of Acinetobacter species and further address their role in acquiring and spreading blaNDM genes in Acinetobacter species. IMPORTANCE Conjugative plasmids harboring the blaNDM gene play a vital role in disseminating carbapenem resistance. In this study, we first report a conjugative plasmid, pNDM-YR7, in Acinetobacter junii. Based on the genomic characteristics of the blaNDM-positive pNDM-YR7, we performed in silico typing and comparative analysis of blaNDM-positive plasmids using the 1,191 plasmids of Acinetobacter species available in the NCBI RefSeq database. We analyzed the characteristics of blaNDM-positive plasmids, including the variants of blaNDM, genetic features associated with blaNDM, conjugative transfer regions, and the phylogenetic pattern of the blaNDM-positive plasmids. All 30 blaNDM-positive conjugative plasmids were found to contain an ISAba14-aph(3')-VI-ISAba125-blaNDM-ble region. This study provides novel insights into the phylogeny and evolution of blaNDM-harboring conjugative plasmids and contributes to the repertoire of knowledge surrounding blaNDM-positive plasmids in the genus Acinetobacter.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chenyu Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Hengzhao Guo
- Department of Radiation Oncology, Zhuhai People’s Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, Guangdong, China
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Li W, Guo H, Gao Y, Yang X, Li R, Li S, Sun C, Du W, Chen S, Xu P, Huang W, Shi J, Yi X, Li X. Comparative genomic analysis of plasmids harboring bla OXA-48-like genes in Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:1082813. [PMID: 36605127 PMCID: PMC9807924 DOI: 10.3389/fcimb.2022.1082813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The emergence and spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious medical problem worldwide. Acquired OXA-48-like carbapenemases encoded by plasmids are important causes of carbapenem resistance in K. pneumoniae. To explore the links between plasmids and bla OXA-48-like genes in K. pneumoniae, we systematically analyzed the variants of bla OXA-48-like plasmid replicon types, phylogenetic patterns, geographic distribution, conjugative transfer regions, and the genetic environments surrounding bla OXA-48-like of 191 bla OXA-48-like-harboring plasmids, which were identified from 4451 plasmids of K. pneumoniae downloaded from GenBank. Our results showed that seven different variants of bla OXA-48-like genes were identified from the 191 bla OXA-48-like-harboring plasmids in K. pneumoniae, with bla OXA-48, bla OXA-232, and bla OXA-181 being highly prevalent. In K. pneumoniae, bla OXA-48 was mainly carried by the composite transposon Tn1999.2 located on IncL/M-type conjugative plasmids, which were mainly geographically distributed in Switzerland, Germany, and China. In K. pneumoniae, the blaOXA-232 gene was mainly carried by 6.1-kb ColKP3-type mobilizable plasmids, which were mainly isolated in India. In K. pneumoniae, bla OXA-181 was mainly carried by a group of 50-kb ColKP3-IncX3 hybrid conjugative plasmids and a group of small ColKP3-type mobilizable plasmids with lengths of 5.9-9.3 kb, the former was sporadically discovered in China, South Korea, India, and Czech Republic, while the latter was almost all isolated in India. In addition, five bla OXA-245-harboring 65.9-kb IncL plasmids of K. pneumoniae isolated in Spain were found to have the genetic context of bla OXA-245 more complicated than that of bla OXA-48-harboring IncL/M-type plasmids, with two copies of IS1R inserted both upstream and downstream of bla OXA-245-lysR. These findings enhance our understanding of the genetic diversity of bla OXA-48-like-harboring plasmids in K. pneumoniae.
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Affiliation(s)
- Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Hengzhao Guo
- Department of Radiation Oncology, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China
| | - Yi Gao
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xiaofan Yang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Ruirui Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Shuangyu Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Chunlong Sun
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Wen Du
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Shaopeng Chen
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Pengpeng Xu
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Wenwen Huang
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China,Binzhou Key Laboratory of Chemical Drug R&D and Quality Control (preparation), Binzhou, China
| | - Jia Shi
- Department of Stomatology, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
| | - Xinfeng Yi
- Department of Neurosurgery, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital (Zhuhai hospital affiliated with Jinan University), Zhuhai, China,*Correspondence: Xiaobin Li, ; Xinfeng Yi, ; Jia Shi,
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8
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Malavez Y, Loperena-Gonzalez PN, Nieves-Miranda SM, Vazquez-Rodriguez E, Centeno-Velez CN, Xiaoli L, Dudley EG. Virulence Potential of Escherichia coli Isolates from a Beef Farm in Puerto Rico. Microbiol Resour Announc 2022; 11:e0044322. [PMID: 36286991 PMCID: PMC9670937 DOI: 10.1128/mra.00443-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/02/2022] [Indexed: 11/07/2022] Open
Abstract
Sixteen Escherichia coli isolates were obtained from fecal matter from a beef farm in Puerto Rico. Isolates were whole-genome sequenced for in silico characterization, including pathotype characterization, virulence, and plasmid identification. The results of the draft genomes identified potential pathogenic E. coli strains from beef cattle in Puerto Rico.
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Affiliation(s)
- Yadira Malavez
- Department of Natural Sciences, University of Puerto Rico, Aguadilla, Puerto Rico
| | | | | | | | | | - Lingzi Xiaoli
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Edward G. Dudley
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania, USA
- E. coli Reference Center, The Pennsylvania State University, University Park, Pennsylvania, USA
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9
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Yu Z, Zhang Z, Shi L, Hua S, Luan T, Lin Q, Zheng Z, Feng X, Liu M, Li X. In silico characterization of IncX3 plasmids carrying blaOXA-181 in Enterobacterales. Front Cell Infect Microbiol 2022; 12:988236. [PMID: 36159637 PMCID: PMC9492964 DOI: 10.3389/fcimb.2022.988236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/23/2022] [Indexed: 12/03/2022] Open
Abstract
Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring blaOXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of blaOXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring blaOXA-181 in Enterobacterales, we identified 81 blaOXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored blaOXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of blaOXA-181 among the 66 blaOXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring blaOXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring blaOXA-181 were human origin. Almost all the blaOXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both blaOXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of blaOXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading blaOXA-181 genes in Enterobacterales.
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Affiliation(s)
- Zhijian Yu
- Department of Otolaryngology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Zhengrong Zhang
- Department of Urology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Lile Shi
- Department of Cardiology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Shengni Hua
- Department of Radiation Oncology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Ting Luan
- Community Health Service Center of Xinkou Town, Tianjin, China
| | - Qiuping Lin
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Zhixiong Zheng
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Xiaosan Feng
- Department of Neonatology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
| | - Mubiao Liu
- Department of Obstetrics and Gynecology, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
- *Correspondence: Xiaobin Li, ; Mubiao Liu, ; Xiaosan Feng,
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10
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Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana. Sci Rep 2022; 12:1843. [PMID: 35115628 PMCID: PMC8813988 DOI: 10.1038/s41598-022-05869-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 01/17/2022] [Indexed: 12/18/2022] Open
Abstract
Recently, the emergence and rapid dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria, particularly of the family Enterobacteriaceae, has posed serious healthcare challenges. Here, we determined the antimicrobial susceptibility and genetic characteristics of 164 Escherichia coli strains isolated from infected patients in two hospitals in Ghana. In total, 102 cefotaxime-resistant isolates (62.2%) were identified as ESBL-producers. Multilocus sequence typing of the ESBL-producers identified 20 different sequence types (STs) with ST131 (n = 25, 24.5%) as the dominant group. Other detected STs included ST410 (n = 21, 20.6%) and ST617 (n = 19, 18.6%). All identified ESBL-producers harbored blaCTX-M-14, blaCTX-M-15, or blaCTX-M-27, with blaCTX-M-15 (n = 96, 94.1%) being the most predominant ESBL allele. Further analysis showed that the immediate genetic environment around blaCTX-M-15 is conserved within blaCTX-M-15 containing strains. Five of the 25 ST131 isolates were clustered with clade A, one with sub-clade C1, and 19 with the dominant sub-clade C2. The results show that fluoroquinolone-resistant, blaCTX-M-14- and blaCTX- M-15-producing ESBL E. coli ST131 strains belonging to clade A and sub-clades C1 and C2 are disseminating in Ghanaian hospitals. To the best of our knowledge, this is the first report of the ST131 phylogeny in Ghana.
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11
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Zhang Z, Guo H, Li X, Li W, Yang G, Ni W, Zhan M, Lu L, Zhang Z, Li X, Zhou Z. Genetic Diversity and Characteristics of bla NDM-Positive Plasmids in Escherichia coli. Front Microbiol 2021; 12:729952. [PMID: 34867846 PMCID: PMC8636099 DOI: 10.3389/fmicb.2021.729952] [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: 06/24/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022] Open
Abstract
New Delhi metallo-β-lactamases (NDMs), including at least 28 variants, are a rapidly emerging family of β-lactamases worldwide, with a variety of infections caused by NDM-positive strains usually associated with very poor prognosis and high mortality. NDMs are the most prevalent carbapenemases in Escherichia coli (E. coli) worldwide, especially in China. The vast majority of blaNDM cases occur on plasmids, which play a vital role in the dissemination of blaNDM. To systematically explore the relationships between plasmids and blaNDM genes in E. coli and obtain an overall picture of the conjugative and mobilizable blaNDM-positive plasmids, we analyzed the variants of blaNDM, replicon types, phylogenetic patterns, conjugative transfer modules, host STs, and geographical distributions of 114 blaNDM-positive plasmids, which were selected from 3786 plasmids from 1346 complete whole genomes of E. coli from the GenBank database. We also established links among the characteristics of blaNDM-positive plasmids in E. coli. Eight variants of blaNDM were found among the 114 blaNDM-positive plasmids, with blaNDM–5 (74 blaNDM–5 genes in 73 plasmids), and blaNDM–1 (31 blaNDM–1 genes in 28 plasmids) being the most dominant. The variant blaNDM–5 was mainly carried by the IncX3 plasmids and IncF plasmids in E. coli, the former were mainly geographically distributed in East Asia (especially in China) and the United States, and the latter were widely distributed worldwide. IncC plasmids were observed to be the predominant carriers of blaNDM–1 genes in E. coli, which were mainly geographically distributed in the United States and China. Other blaNDM–1-carrying plasmids also included IncM2, IncN2, and IncHI1. Moreover, the overall picture of the conjugative and mobilizable blaNDM-positive plasmids in E. coli was described in our study. Our findings enhance our understanding of the genetic diversity and characteristics of blaNDM-positive plasmids in in E. coli.
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Affiliation(s)
- Zhiren Zhang
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Hengzhao Guo
- Department of Radiation Oncology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Xiaodong Li
- Department of Spine and Osteology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Wenting Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Guang Yang
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Wenjun Ni
- Department of Urology, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Meixiao Zhan
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Zhuhai Interventional Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Ligong Lu
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China.,Zhuhai Interventional Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Zhenlin Zhang
- Department of Clinical Laboratory, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Xiaobin Li
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
| | - Zhiling Zhou
- Department of Pharmacy, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, China
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12
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Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls. Microorganisms 2021; 9:microorganisms9030567. [PMID: 33801844 PMCID: PMC7999438 DOI: 10.3390/microorganisms9030567] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli ST216, including those that carry blaKPC-2, blaFOX-5, blaCTX-M-15 and mcr-1, have been linked to wild and urban-adapted birds and the colonisation of hospital environments causing recalcitrant, carbapenem-resistant human infections. Here we sequenced 22 multiple-drug resistant ST216 isolates from Australian silver gull chicks sampled from Five Islands, of which 21 carried nine or more antibiotic resistance genes including blaIMP-4 (n = 21), blaTEM-1b (n = 21), aac(3)-IId (n = 20), mph(A) (n = 20), catB3 (n = 20), sul1 (n = 20), aph(3”)-Ib (n = 18) and aph(6)-Id (n = 18) on FIB(K) (n = 20), HI2-ST1 (n = 11) and HI2-ST3 (n = 10) plasmids. We show that (i) all HI2 plasmids harbour blaIMP-4 in resistance regions containing In809 flanked by IS26 (HI2-ST1) or IS15DI (HI2-ST3) and diverse metal resistance genes; (ii) HI2-ST1 plasmids are highly related to plasmids reported in diverse Enterobacteriaceae sourced from humans, companion animals and wildlife; (iii) HI2 were a feature of the Australian gull isolates and were not observed in international ST216 isolates. Phylogenetic analyses identified close relationships between ST216 from Australian gull and clinical isolates from overseas. E. coli ST216 from Australian gulls harbour HI2 plasmids encoding resistance to clinically important antibiotics and metals. Our studies underscore the importance of adopting a one health approach to AMR and pathogen surveillance.
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13
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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14
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Taylor WS, Pearson J, Miller A, Schmeier S, Frizelle FA, Purcell RV. MinION Sequencing of colorectal cancer tumour microbiomes-A comparison with amplicon-based and RNA-Sequencing. PLoS One 2020; 15:e0233170. [PMID: 32433701 PMCID: PMC7239435 DOI: 10.1371/journal.pone.0233170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/29/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Recent evidence suggests a role for the gut microbiome in the development and progression of many diseases and many studies have been carried out to analyse the microbiome using a variety of methods. In this study, we compare MinION sequencing with meta-transcriptomics and amplicon-based sequencing for microbiome analysis of colorectal tumour tissue samples. METHODS DNA and RNA were extracted from 11 colorectal tumour samples. 16S rRNA amplicon sequencing and MinION sequencing was carried out using genomic DNA, and RNA-Sequencing for meta-transcriptomic analysis. Non-human MinION and RNA-Sequencing reads, and 16S rRNA amplicon sequencing reads were taxonomically classified using a database built from available RefSeq bacterial and archaeal genomes and a k-mer based algorithm in Kraken2. Concordance between the three platforms at different taxonomic levels was tested on a per-sample basis using Spearman's rank correlation. RESULTS The average number of reads per sample using RNA-Sequencing was greater than 129 times that generated using MinION sequencing. However, the average read length of MinION sequences was more than 13 times that of RNA or 16S rRNA amplicon sequencing. Taxonomic assignment using 16S sequencing was less reliable beyond the genus level, and both RNA-Sequencing and MinION sequencing could detect greater numbers of phyla and genera in the same samples, compared to 16S sequencing. Bacterial species associated with colorectal cancer, Fusobacterium nucleatum, Parvimonas micra, Bacteroides fragilis and Porphyromonas gingivalis, were detectable using MinION, RNA-Sequencing and 16S rRNA amplicon sequencing data. CONCLUSIONS Long-read sequences generated using MinION sequencing can compensate for low numbers of reads for bacterial classification. MinION sequencing can discriminate between bacterial strains and plasmids and shows potential as a cost-effective tool for rapid microbiome sequencing in a clinical setting.
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Affiliation(s)
- William S. Taylor
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Allison Miller
- Gene Structure and Function Laboratory, University of Otago, Christchurch, New Zealand
| | - Sebastian Schmeier
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Frank A. Frizelle
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Rachel V. Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand
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15
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Naha S, Sands K, Mukherjee S, Roy C, Rameez MJ, Saha B, Dutta S, Walsh TR, Basu S. KPC-2-producing Klebsiella pneumoniae ST147 in a neonatal unit: Clonal isolates with differences in colistin susceptibility attributed to AcrAB-TolC pump. Int J Antimicrob Agents 2020; 55:105903. [PMID: 31954832 DOI: 10.1016/j.ijantimicag.2020.105903] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/08/2020] [Accepted: 01/11/2020] [Indexed: 01/21/2023]
Abstract
This study characterizes four KPC-2-producing Klebsiella pneumoniae isolates from neonates belonging to a single sequence type 147 (ST147) in relation to carbapenem resistance and explores probable mechanisms of differential colistin resistance among the clonal cluster. Whole genome sequencing (WGS) revealed that the isolates were nearly 100% identical and harbored resistance genes (blaKPC-2,OXA-9,CTX-M-15,SHV-11,OXA-1,TEM-1B, oqxA, oqxB, qnrB1, fosA, arr-2, sul1, aacA4, aac(6')Ib-cr, aac(6')Ib), and several virulence genes. blaKPC-2 was the only carbapenem-resistant gene found, bracketed between ISKpn7 and ISKpn6 of Tn4401b on a non-conjugative IncFII plasmid. Remarkably, one of the clonal isolates was resistant to colistin, the mechanistic basis of which was not apparent from comparative genomics. The transmissible colistin resistance gene, mcr, was absent. Efflux pump inhibitor, carbonyl cyanide 3-chlorophenylhydrazone (CCCP) rendered a 32-fold decrease in the minimum inhibitory concentration (MIC) of colistin in the resistant isolate only. acrB, tolC, ramA, and soxS genes of the AcrAB-TolC pump system overexpressed exclusively in the colistin-resistant isolate, although the corresponding homologs of the AcrAB-TolC pump, regulators and promoters were mutually identical. No change was observed in the expression of other efflux genes (kpnE/F and kpnG/H) or two-component system (TCS) genes (phoP/phoQ, pmrA/pmrB). Colistin resistance in one of the clonal KPC-2-producing isolates is postulated to be due to overexpression of the AcrAB-TolC pump. This study is probably the first to report clinical clonal K. pneumoniae isolates with differences in colistin susceptibility. The presence of carbapenem-resistant isolates with differential behavior in the expression of a genomically identical pump system indicates the nuances of the resistance mechanisms and the difficulty of treatment thereof.
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Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Kirsty Sands
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Subhankar Mukherjee
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Chayan Roy
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Moidu Jameela Rameez
- Department of Microbiology, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Bijan Saha
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata-700020, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
| | - Timothy R Walsh
- Department of Medical Microbiology and Infectious Disease, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33, CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India.
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16
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Das L, Virmani R, Sharma V, Rawat D, Singh Y. Human Milk Microbiota: Transferring the Antibiotic Resistome to Infants. Indian J Microbiol 2019; 59:410-416. [PMID: 31762502 DOI: 10.1007/s12088-019-00824-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022] Open
Abstract
Commensal bacterial population is believed to be a reservoir for antibiotic resistance genes (ARGs). The infant gut microbiota has relatively higher abundance of ARGs than the adults. These genes can get transferred from commensals to pathogens by horizontal gene transfer, which magnifies the spectrum of antibiotic resistance in the environment. The presence of ARGs in neo-nates and infants, with no prior antibiotic exposure, questions their origin in the naïve commensal population. Breast milk microbiota that is responsible for the initial seeding of infant gut microbiota has also been found to harbour a vast array of ARGs. This review discusses the recent findings that indicate the potential of breast milk microbiota to act as a vehicle for transmission of ARGs to infants.
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Affiliation(s)
- Lahari Das
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Richa Virmani
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vishal Sharma
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Deepti Rawat
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
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