The genomic approach of antimicrobial resistance of Salmonella Typhimurium isolates from guinea pigs in Lima, Peru

Research in Microbiology - Tập 174 - Trang 104086 - 2023
Raquel Hurtado1, Debmalya Barh1,2, Luís Cláudio Lima de Jesus1, Marcus Vinicius Canário Viana1, Sandeep Tiwari3,4, Flávia Figueira Aburjaile5, Dennis E. Carhuaricra Huaman6, Bertram Brenig7, Lenin Maturrano Hernández6, Vasco Azevedo1
1Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
2Institute of Integrative Omics and Applied Biotechnology, Nonakuri, Purba Medinipur, West Bengal, 721172, India
3Pós-graduação em Microbiologia, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahía, Brazil
4Programa de Pós-graduação em Imunologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Bahía, Brazil
5Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
6SANIGEN, Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, San Borja, Lima, 15021, Peru
7Institute of Veterinary Medicine, University of Göttingen, Burckhardtweg 2, Göttingen, Germany

Tài liệu tham khảo

Matsuura, 2010, Susceptibilidad a antibacterianos in vitro de Salmonella enterica aislada de cuyes de crianza familiar-comercial en la provincia de Carhuaz, Áncash, Rev Investig Vet Perú, 21, 93 Sánchez-Macías, 2018, Guinea pig for meat production: a systematic review of factors affecting the production, carcass and meat quality, Meat Sci, 143, 165, 10.1016/j.meatsci.2018.05.004 Huamán, 2020, Genetic characterization and antimicrobial resistance patterns of Salmonella enterica subsp. enterica serovar Typhimurium in Guinea pigs under intensive breeding, Rev Investig Vet Peru, 31 Quesada, 2016, Antimicrobial resistance of Salmonella spp isolated animal food for human consumption, Rev Peru Med Exp Salud Pública, 33, 32, 10.17843/rpmesp.2016.331.1899 Wang, 2019, Antibiotic resistance in Salmonella typhimurium isolates recovered from the food chain through national antimicrobial resistance monitoring system between 1996 and 2016, Front Microbiol, 10 2019, Boletin epidemiologico del Peru, Boletin Epidemiol Peru, 28, 1245 Wessels, 2021, Salmonella in chicken meat: consumption, outbreaks, characteristics, current control methods and the potential of bacteriophage use, Foods, 10, 1742, 10.3390/foods10081742 Fournier, 2015, Family outbreaks of nontyphoidal salmonellosis following a meal of Guinea pigs, Case Rep Infect Dis, 2015, 864640 Moya, 2019 Darphorn, 2021, Antibiotic resistance plasmid composition and architecture in Escherichia coli isolates from meat, Sci Rep, 11, 1, 10.1038/s41598-021-81683-w Rampadarath, 2015, Repetitive element palindromic PCR (rep-PCR) as a genetic tool to study interspecific diversity in Euphorbiaceae family, Electron J Biotechnol, 18, 412, 10.1016/j.ejbt.2015.09.003 Hurtado, 2022, WGS-based lineage and antimicrobial resistance pattern of Salmonella typhimurium isolated during 2000–2017 in Peru, Antibiotics, 11, 1170, 10.3390/antibiotics11091170 Pearce, 2018, Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak, Int J Food Microbiol, 274, 1, 10.1016/j.ijfoodmicro.2018.02.023 Guillermo, 2018, Antimicrobial resistance and genotyping of Salmonella Typhimurium strains isolated from Guinea pigs (Cavia porcellus) from intensive production farms of the city of lima, Peru, Rev Investig Vet Peru, 29, 319 Jamshidi, 2010, Isolation and identification of Salmonella Enteritidis and Salmonella typhimurium from the eggs of retail stores in Mashhad, Iran using conventional culture method and Multiplex pcr assay, J Food Saf, 30, 558 Andrews, 2015 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Wick, 2017, Unicycler: resolving bacterial genome assemblies from short and long sequencing reads, PLoS Comput Biol, 10.1371/journal.pcbi.1005595 Galardini, 2011, CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes, Source Code Biol Med, 10.1186/1751-0473-6-11 Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 Zhang, 2019, SeqSero2: rapid and improved Salmonella serotype determination using whole-genome sequencing data, Appl Environ Microbiol, 85, 10.1128/AEM.01746-19 Page, 2015, Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, 31, 3691, 10.1093/bioinformatics/btv421 Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033 Zhou, 2020, The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity, Genome Res, 30, 138, 10.1101/gr.251678.119 Robertson, 2018, MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies, Microb Genom, 10.1099/mgen.0.000206 Li, 2018, oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements, Nucleic Acids Res, 46, W229, 10.1093/nar/gky352 Xie, 2017, ISEScan: automated identification of insertion sequence elements in prokaryotic genomes, Bioinforma Oxf Engl, 33, 3340, 10.1093/bioinformatics/btx433 Alikhan, 2011, BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons, BMC Genomics, 12, 402, 10.1186/1471-2164-12-402 Jia, 2017, CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database, Nucleic Acids Res, 10.1093/nar/gkw1004 Chen, 2004, VFDB: a reference database for bacterial virulence factors, Nucleic Acids Res, 33, D325, 10.1093/nar/gki008 Zankari, 2017, PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens, J Antimicrob Chemother, 72, 2764, 10.1093/jac/dkx217 Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res, 33, 511, 10.1093/nar/gki198 Page, 2016, SNP-sites: rapid efficient extraction of SNPs from multi- FASTA alignments, Microb Genom, 10.1099/mgen.0.000056 Rodrigues, 2021, DynaMut2: assessing changes in stability and flexibility upon single and multiple point missense mutations, Protein Sci Publ Protein Soc, 30, 60, 10.1002/pro.3942 Carhuaricra Huaman, 2022, Genomic characterization of Salmonella typhimurium isolated from Guinea pigs with salmonellosis in Lima, Peru, Microorganisms, 10, 1726, 10.3390/microorganisms10091726 Fu, 2017, Comparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles, Sci Rep, 7, 1, 10.1038/s41598-017-06079-1 Id, 2020 Sun, 2020, The epidemiology of monophasic Salmonella typhimurium, Foodborne Pathog Dis, 17, 87, 10.1089/fpd.2019.2676 Ingle, 2021, Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia, Nat Commun, 12, 4786, 10.1038/s41467-021-25073-w Branchu, 2018, Genome variation and molecular epidemiology of Salmonella enterica serovar Typhimurium pathovariants, Infect Immun, 10.1128/IAI.00079-18 Van Puyvelde, 2019, An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation, Nat Commun, 10.1038/s41467-019-11844-z Kombade, 2021 Wahl, 2019, Prophages in Salmonella enterica: a driving force in reshaping the genome and physiology of their bacterial host?, Mol Microbiol, 111, 303, 10.1111/mmi.14167 Lee, 2015, A novel bacteriophage targeting Cronobacter sakazakii is a potential biocontrol agent in foods, Appl Environ Microbiol, 82, 192, 10.1128/AEM.01827-15 Razavi, 2020, The association between insertion sequences and antibiotic resistance genes, mSphere, 5, 10.1128/mSphere.00418-20 Sun, 2014, Resistance to β-lactam antibiotics conferred by point mutations in penicillin-binding proteins PBP3, PBP4 and PBP6 in Salmonella enterica, PLoS ONE, 9 Li, 2009, Efflux-mediated drug resistance in bacteria: an update, Drugs, 69, 1555, 10.2165/11317030-000000000-00000 Jones, 2020, The nature and extent of plasmid variation in Chlamydia trachomatis, Microorganisms, 8, E373, 10.3390/microorganisms8030373 Javier, 2016, Efecto de la suplementación con una mezcla probiótica sobre el comportamiento productivo de cuyes (Cavia Porcellus) durante la fase de crecimiento y acabado, Rev investig vet Perú., 27, 51, 10.15381/rivep.v27i1.11458 McMillan, 2019, Antimicrobial resistance genes, cassettes, and plasmids present in Salmonella enterica associated with United States food animals, Front Microbiol, 10.3389/fmicb.2019.00832 Neuert, 2018, Prediction of phenotypic antimicrobial resistance profiles from whole genome sequences of non-typhoidal Salmonella enterica, Front Microbiol, 10.3389/fmicb.2018.00592 Irrgang, 2021, Characterization of E. coli isolates producing extended spectrum beta-lactamase SHV-variants from the food chain in Germany, Microorganisms, 9, 1926, 10.3390/microorganisms9091926 Zhang, 2019, Replicon-based typing of IncI-complex plasmids, and comparative genomics analysis of IncIγ/K1 plasmids, Front Microbiol, 10, 48, 10.3389/fmicb.2019.00048 Tate, 2021, A national antimicrobial resistance monitoring system survey of antimicrobial-resistant foodborne bacteria isolated from retail veal in the United States, J Food Protect, 84, 1749, 10.4315/JFP-21-005