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For: Arredondo-Alonso S, Rogers MRC, Braat JC, Verschuuren TD, Top J, Corander J, Willems RJL, Schürch AC. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species. Microb Genom 2018;4. [PMID: 30383524 PMCID: PMC6321875 DOI: 10.1099/mgen.0.000224] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
O'Brien B, Yushchenko A, Suh J, Jung D, Cai Z, Nguyen NS, Semret M, Dufour S, Fanning S, Ronholm J. Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation. One Health 2025;20:100970. [PMID: 39898312 PMCID: PMC11787494 DOI: 10.1016/j.onehlt.2025.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 11/15/2024] [Accepted: 01/07/2025] [Indexed: 02/04/2025]  Open
2
Mu C, Wang S, Wang A, Li W. Genomic analysis elucidates characteristics and possible origins of high-risk antimicrobial resistance genes in Enterococcus faecium from a global perspective. One Health 2025;20:101054. [PMID: 40417283 PMCID: PMC12098168 DOI: 10.1016/j.onehlt.2025.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2025] [Revised: 03/22/2025] [Accepted: 04/27/2025] [Indexed: 05/27/2025]  Open
3
Reid CJ, Cummins ML, Djordjevic SP. Major F plasmid clusters are linked with ColV and pUTI89-like marker genes in bloodstream isolates of Escherichia coli. BMC Genomics 2025;26:57. [PMID: 39838323 PMCID: PMC11748317 DOI: 10.1186/s12864-025-11226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 01/08/2025] [Indexed: 01/23/2025]  Open
4
Tsoumtsa Meda L, Lagarde J, Guillier L, Roussel S, Douarre PE. Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits. Methods Mol Biol 2025;2852:223-253. [PMID: 39235748 DOI: 10.1007/978-1-0716-4100-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
5
Mane A, Sanderson H, White AP, Zaheer R, Beiko R, Chauve C. Plaseval: a framework for comparing and evaluating plasmid detection tools. BMC Bioinformatics 2024;25:365. [PMID: 39592962 PMCID: PMC11590284 DOI: 10.1186/s12859-024-05941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 09/19/2024] [Indexed: 11/28/2024]  Open
6
Long J, Chen J, Yuan Y, Yang S, Xie X, Wu X, Liu Y, Guo J, Chen Y, Wang C, Liu X. First Report of Carbapenem-Resistant Klebsiella michiganensis Co-Harboring bla KPC-2 and TmexCD2-ToprJ2 Isolated from Wastewater at a Tertiary Hospital in Beijing. Infect Drug Resist 2024;17:5117-5128. [PMID: 39600323 PMCID: PMC11589776 DOI: 10.2147/idr.s448256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 10/31/2024] [Indexed: 11/29/2024]  Open
7
Irimaso E, Keinprecht H, Szostak MP, Rosel AC, Stessl B, Desvars-Larrive A, Ntakirutimana C, Fischer OW, Wittek T, Müller E, Feßler AT, Braun SD, Schwarz S, Monecke S, Ehricht R, Spergser J, Ruppitsch W, Loncaric I. Survey in ruminants from Rwanda revealed high diversity and prevalence of extended-spectrum cephalosporin-resistant Enterobacterales. BMC Vet Res 2024;20:523. [PMID: 39563382 PMCID: PMC11575003 DOI: 10.1186/s12917-024-04359-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/24/2024] [Indexed: 11/21/2024]  Open
8
Miura T, Miyakawa T, Kusuya Y, Kamino K. Complete genome sequencing of four marine bacteria, Gilvimarinus japonicus NBRC 111987T, Halioxenophilus aromaticivorans JCM 19134T, Maricurvus nonylphenolicus JCM 17778T, and Simiduia litorea JCM 19759T belonging to the family Cellvibrionaceae. Microbiol Resour Announc 2024;13:e0087324. [PMID: 39400139 PMCID: PMC11555993 DOI: 10.1128/mra.00873-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 09/20/2024] [Indexed: 10/15/2024]  Open
9
Li H, Liu X, Li S, Rong J, Xie S, Gao Y, Zhong L, Jiang Q, Jiang G, Ren Y, Sun W, Hong Y, Zhou Z. KleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide. Genome Med 2024;16:130. [PMID: 39529172 PMCID: PMC11556198 DOI: 10.1186/s13073-024-01399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 10/21/2024] [Indexed: 11/16/2024]  Open
10
Abdelsalam NA, ElBanna SA, Mouftah SF, Cobo-Díaz JF, Shata AH, Shawky SM, Atteya R, Elhadidy M. Genomic dynamics of high-risk carbapenem-resistant klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings. BMC Infect Dis 2024;24:1193. [PMID: 39438795 PMCID: PMC11515790 DOI: 10.1186/s12879-024-10056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2024] [Accepted: 10/03/2024] [Indexed: 10/25/2024]  Open
11
Olatunji I, Bardaji DKR, Miranda RR, Savka MA, Hudson AO. Artificial intelligence tools for the identification of antibiotic resistance genes. Front Microbiol 2024;15:1437602. [PMID: 39070267 PMCID: PMC11272472 DOI: 10.3389/fmicb.2024.1437602] [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: 05/24/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024]  Open
12
Mogoi NN, Sifuna AW, Okoth PK, Reva O, Malaba R, Negesa R, Nyongesa KP, Osoro KE, Welch M. Staphylococcus aureus associated with surgical site infections in Western Kenya reveals genomic hotspots for pathogen evolution. Access Microbiol 2024;6:000734.v4. [PMID: 39045253 PMCID: PMC11261728 DOI: 10.1099/acmi.0.000734.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 07/25/2024]  Open
13
Timková I, Maliničová L, Nosáľová L, Kolesárová M, Lorková Z, Petrová N, Pristaš P, Kisková J. Genomic insights into the adaptation of Acinetobacter johnsonii RB2-047 to the heavy metal-contaminated subsurface mine environment. Biometals 2024;37:371-387. [PMID: 37973678 PMCID: PMC11006771 DOI: 10.1007/s10534-023-00555-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/21/2023] [Indexed: 11/19/2023]
14
Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Application of phylodynamics to identify spread of antimicrobial-resistant Escherichia coli between humans and canines in an urban environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;916:170139. [PMID: 38242459 DOI: 10.1016/j.scitotenv.2024.170139] [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: 08/29/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
15
Lipworth S, Matlock W, Shaw L, Vihta KD, Rodger G, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto T, Crook D, Walker AS, Stoesser N. The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies. Nat Commun 2024;15:1612. [PMID: 38383544 PMCID: PMC10881496 DOI: 10.1038/s41467-024-45761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 02/01/2024] [Indexed: 02/23/2024]  Open
16
Hamed SM, Mohamed HO, Ashour HM, Fahmy LI. Comparative genomic analysis of strong biofilm-forming Klebsiella pneumoniae isolates uncovers novel ISEcp1-mediated chromosomal integration of a full plasmid-like sequence. Infect Dis (Lond) 2024;56:91-109. [PMID: 37897710 DOI: 10.1080/23744235.2023.2272624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023]  Open
17
Paganini JA, Kerkvliet JJ, Vader L, Plantinga NL, Meneses R, Corander J, Willems RJL, Arredondo-Alonso S, Schürch AC. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microb Genom 2024;10:001193. [PMID: 38376388 PMCID: PMC10926690 DOI: 10.1099/mgen.0.001193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]  Open
18
Dinda V, Kimang’a AN, Kariuki D, Sifuna AW, O’Brien TJ, Welch M, Reva ON. Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya. Access Microbiol 2024;6:000667.v4. [PMID: 38361654 PMCID: PMC10866029 DOI: 10.1099/acmi.0.000667.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024]  Open
19
McInnes RS, Snaith AE, Dunn SJ, Papangeli M, Hardy KJ, Hussain A, van Schaik W. Integration of vanHAX downstream of a ribosomal RNA operon restores vancomycin resistance in a susceptible Enterococcus faecium strain. NPJ ANTIMICROBIALS AND RESISTANCE 2024;2:2. [PMID: 39843953 PMCID: PMC11702846 DOI: 10.1038/s44259-023-00017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/27/2023] [Indexed: 01/24/2025]
20
Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Genomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023;30:114678-114684. [PMID: 37845596 DOI: 10.1007/s11356-023-30374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
21
Sielemann J, Sielemann K, Brejová B, Vinař T, Chauve C. plASgraph2: using graph neural networks to detect plasmid contigs from an assembly graph. Front Microbiol 2023;14:1267695. [PMID: 37869681 PMCID: PMC10587606 DOI: 10.3389/fmicb.2023.1267695] [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: 07/26/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]  Open
22
Lopes R, Furlan JPR, Ramos MS, Santos LDRD, Rosa RDS, Stehling EG. Klebsiella quasipneumoniae subsp. similipneumoniae ST1859 O5:KL35 from Soil: First Report of qnrE1 in the Environment. Microb Drug Resist 2023;29:492-496. [PMID: 37428613 DOI: 10.1089/mdr.2023.0075] [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: 07/12/2023]  Open
23
Jati AP, Sola-Campoy PJ, Bosch T, Schouls LM, Hendrickx APA, Bautista V, Lara N, Raangs E, Aracil B, Rossen JWA, Friedrich AW, Navarro Riaza AM, Cañada-García JE, Ramírez de Arellano E, Oteo-Iglesias J, Pérez-Vázquez M, García-Cobos S, The Dutch and Spanish Collaborative Working Groups on Surveillance on Carbapenemase-Producing Enterobacterales. Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICEKp) among Nonoutbreak OXA-48-Producing Klebsiella pneumoniae Clinical Isolates from Spain and the Netherlands. Microbiol Spectr 2023;11:e0471622. [PMID: 37310221 PMCID: PMC10434048 DOI: 10.1128/spectrum.04716-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/22/2023] [Indexed: 06/14/2023]  Open
24
Mane A, Faizrahnemoon M, Vinař T, Brejová B, Chauve C. PlasBin-flow: a flow-based MILP algorithm for plasmid contigs binning. Bioinformatics 2023;39:i288-i296. [PMID: 37387134 DOI: 10.1093/bioinformatics/btad250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
25
Zhu Q, Gao S, Xiao B, He Z, Hu S. Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features. Microbiol Spectr 2023;11:e0464522. [PMID: 37191574 PMCID: PMC10269668 DOI: 10.1128/spectrum.04645-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/26/2023] [Indexed: 05/17/2023]  Open
26
Walas N, Müller NF, Parker E, Henderson A, Capone D, Brown J, Barker T, Graham JP. Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543064. [PMID: 37398411 PMCID: PMC10312604 DOI: 10.1101/2023.06.01.543064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
27
Walas N, Slown S, Amato HK, Lloyd T, Bender M, Varghese V, Pandori M, Graham JP. The role of plasmids in carbapenem resistant E. coli in Alameda County, California. BMC Microbiol 2023;23:147. [PMID: 37217873 DOI: 10.1186/s12866-023-02900-2] [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: 02/10/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]  Open
28
Sartori L, Sellera FP, Fuga B, Sano E, Monte DFM, Cardoso B, Côrtes LDA, Lincopan N. Phylogenomic Analysis of CTX-M-15-Positive Escherichia coli from Companion Animal Reveals Intercontinental Dissemination of ST90 Within a One Health Framework. Microb Drug Resist 2023. [PMID: 37155698 DOI: 10.1089/mdr.2022.0249] [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: 05/10/2023]  Open
29
Sun Z, Yang F, Ji J, Cao W, Liu C, Ding B, Xu X. Dissecting the genotypic features of a fluoroquinolone-resistant Pseudomonas aeruginosa ST316 sublineage causing ear infections in Shanghai, China. Microb Genom 2023;9:mgen000989. [PMID: 37079456 PMCID: PMC10210959 DOI: 10.1099/mgen.0.000989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/20/2023] [Indexed: 04/21/2023]  Open
30
Berbers B, Vanneste K, Roosens NHCJ, Marchal K, Ceyssens PJ, De Keersmaecker SCJ. Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium. Microb Genom 2023;9:mgen000925. [PMID: 36748573 PMCID: PMC9973847 DOI: 10.1099/mgen.0.000925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/03/2022] [Indexed: 01/25/2023]  Open
31
Zou X, Nguyen M, Overbeek J, Cao B, Davis JJ. Classification of bacterial plasmid and chromosome derived sequences using machine learning. PLoS One 2022;17:e0279280. [PMID: 36525447 PMCID: PMC9757591 DOI: 10.1371/journal.pone.0279280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]  Open
32
Zamudio R, Boerlin P, Beyrouthy R, Madec JY, Schwarz S, Mulvey MR, Zhanel GG, Cormier A, Chalmers G, Bonnet R, Haenni M, Eichhorn I, Kaspar H, Garcia-Fierro R, Wood JLN, Mather AE. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nat Commun 2022;13:7490. [PMID: 36509735 PMCID: PMC9744880 DOI: 10.1038/s41467-022-34970-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022]  Open
33
Ewers C, Göpel L, Prenger-Berninghoff E, Semmler T, Kerner K, Bauerfeind R. Occurrence of mcr-1 and mcr-2 colistin resistance genes in porcine Escherichia coli isolates (2010-2020) and genomic characterization of mcr-2-positive E. coli. Front Microbiol 2022;13:1076315. [PMID: 36569100 PMCID: PMC9780603 DOI: 10.3389/fmicb.2022.1076315] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022]  Open
34
Li Z, Pang B, Lu X, Kan B, Kan B, School of Public Health, Shandong University, Jinan City, China. The Establishment and Application of a Kraken Classifier for Salmonella Plasmid Sequence Prediction. China CDC Wkly 2022;4:1110-1116. [PMID: 36751662 PMCID: PMC9889229 DOI: 10.46234/ccdcw2022.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]  Open
35
Lobato A, Souza CO, Martins WMBS, Barata RR, Camargo DS, Dutra LMG, Carneiro ICRS, Costa CJS, Brasiliense DM. Genomic characterization of BKC-1-producing Klebsiella pneumoniae strain belonging to high-risk clone sequence type 11 isolated from a river in Brazil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022;850:157917. [PMID: 35952879 DOI: 10.1016/j.scitotenv.2022.157917] [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: 04/28/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
36
Afolayan AO, Aboderin AO, Oaikhena AO, Odih EE, Ogunleye VO, Adeyemo AT, Adeyemo AT, Bejide OS, Underwood A, Argimón S, Abrudan M, Egwuenu A, Ihekweazu C, Aanensen DM, Okeke IN. An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals. Microb Genom 2022;8:mgen000863. [PMID: 36748556 PMCID: PMC9837563 DOI: 10.1099/mgen.0.000863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/15/2022] [Indexed: 12/23/2022]  Open
37
Levent G, Schlochtermeier A, Vinasco J, Jennings J, Richeson J, Ives SE, Norman KN, Lawhon SD, Loneragan GH, Scott HM. Long-Term Effects of Single-Dose Cephalosporin or Macrolide Use on the Prevalence of AmpC and Extended-Spectrum β-Lactamase Producing Escherichia coli in the Feces of Beef Cattle. Microorganisms 2022;10:microorganisms10102071. [PMID: 36296347 PMCID: PMC9610231 DOI: 10.3390/microorganisms10102071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022]  Open
38
Raethong N, Santivarangkna C, Visessanguan W, Santiyanont P, Mhuantong W, Chokesajjawatee N. Whole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3, a gamma-aminobutyric acid (GABA)-producing strain isolated from Thai pickled weed. Front Microbiol 2022;13:969548. [PMID: 36212812 PMCID: PMC9539741 DOI: 10.3389/fmicb.2022.969548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022]  Open
39
Huang Y, Yu Z, Liu L, Che Y, Zhang T. Acesulfame Anoxic Biodegradation Coupled to Nitrate Reduction by Enriched Consortia and Isolated Shinella spp. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022;56:13096-13106. [PMID: 36040144 DOI: 10.1021/acs.est.2c03656] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
40
Al Mana H, Johar AA, Kassem II, Eltai NO. Transmissibility and Persistence of the Plasmid-Borne Mobile Colistin Resistance Gene, mcr-1, Harbored in Poultry-Associated E. coli. Antibiotics (Basel) 2022;11:774. [PMID: 35740180 PMCID: PMC9220209 DOI: 10.3390/antibiotics11060774] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]  Open
41
Complete Genome Sequence of a Listeria monocytogenes Strain Isolated from Sprouts and Carrying an Antimicrobial Resistance Gene. Microbiol Resour Announc 2022;11:e0020022. [PMID: 35658560 PMCID: PMC9302147 DOI: 10.1128/mra.00200-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
42
Complete Genome Sequence of a Listeria monocytogenes Strain with Antimicrobial Resistance Genes Isolated from Lettuce in Canada. Microbiol Resour Announc 2022;11:e0029822. [PMID: 35658536 PMCID: PMC9302076 DOI: 10.1128/mra.00298-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
43
Gaeta NC, de Carvalho DU, Fontana H, Sano E, Moura Q, Fuga B, Munoz PM, Gregory L, Lincopan N. Genomic features of a multidrug-resistant and mercury-tolerant environmental Escherichia coli recovered after a mining dam disaster in South America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022;823:153590. [PMID: 35122850 PMCID: PMC8994849 DOI: 10.1016/j.scitotenv.2022.153590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/21/2022] [Accepted: 01/28/2022] [Indexed: 05/03/2023]
44
Cufaoglu G, Cengiz G, Onaran Acar B, Yesilkaya B, Ayaz ND, Levent G, Goncuoglu M. Antibiotic, heavy metal, and disinfectant resistance in chicken, cattle, and sheep origin E. coli and whole‐genome sequencing analysis of a multidrug‐resistant E. coli O100:H25 strain. J Food Saf 2022. [DOI: 10.1111/jfs.12995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
45
Bacterial Community and Genomic Analysis of Carbapenem-Resistant Acinetobacter baumannii Isolates from the Environment of a Health Care Facility in the Western Region of Saudi Arabia. Pharmaceuticals (Basel) 2022;15:ph15050611. [PMID: 35631436 PMCID: PMC9145440 DOI: 10.3390/ph15050611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/10/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022]  Open
46
Bloomfield S, Duong VT, Tuyen HT, Campbell JI, Thomson NR, Parkhill J, Le Phuc H, Chau TTH, Maskell DJ, Perron GG, Ngoc NM, Vi LL, Adriaenssens EM, Baker S, Mather AE. Mobility of antimicrobial resistance across serovars and disease presentations in non-typhoidal Salmonella from animals and humans in Vietnam. Microb Genom 2022;8. [PMID: 35511231 PMCID: PMC9465066 DOI: 10.1099/mgen.0.000798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
47
Darrington M, Leftwich PT, Holmes NA, Friend LA, Clarke NVE, Worsley SF, Margaritopolous JT, Hogenhout SA, Hutchings MI, Chapman T. Characterisation of the symbionts in the Mediterranean fruit fly gut. Microb Genom 2022;8. [PMID: 35446250 PMCID: PMC9453069 DOI: 10.1099/mgen.0.000801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
48
Jozefíková A, Valček A, Šoltys K, Nováková E, Bujdáková H. Persistence and multi-ward dissemination of vancomycin resistant Enterococcus faecium ST17 clone in hospital settings in Slovakia from 2017 to 2020. Int J Antimicrob Agents 2022;59:106561. [PMID: 35271995 DOI: 10.1016/j.ijantimicag.2022.106561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 02/19/2022] [Accepted: 02/27/2022] [Indexed: 11/16/2022]
49
Yang L, Shen Y, Jiang J, Wang X, Shao D, Lam MMC, Holt KE, Shao B, Wu C, Shen J, Walsh TR, Schwarz S, Wang Y, Shen Z. Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. NATURE FOOD 2022;3:197-205. [PMID: 37117646 DOI: 10.1038/s43016-022-00470-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 02/03/2022] [Indexed: 04/30/2023]
50
Zhang H, Xiang Y, Huang Y, Liang B, Xu X, Xie J, Du X, Yang C, Liu H, Liu H, Wang H, Yang M, Wang L, Hu X, Jin L, Li J, Jiang Y, Qiu S, Song H. Genetic Characterization of mcr-1-Positive Multidrug-Resistant Salmonella enterica Serotype Typhimurium Isolated From Intestinal Infection in Children and Pork Offal in China. Front Microbiol 2022;12:774797. [PMID: 35082765 PMCID: PMC8784875 DOI: 10.3389/fmicb.2021.774797] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022]  Open
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