Jossue Ortiz Álvarez, Corazón Barrientos Flores, Claudia Adriana Colín Castro, Melissa Hernández Durán, María Guadalupe Martínez Zavaleta, Braulio Josué Méndez Sotelo, Cindy Fabiola Hernández Pérez, Christian Sohlenkamp, Rafael Franco Cendejas, Luis Esaú López Jácome
{"title":"揭示耐药性：来自墨西哥城一家转诊医院的两种新型头孢地考耐药窄养单胞菌的比较基因组分析。","authors":"Jossue Ortiz Álvarez, Corazón Barrientos Flores, Claudia Adriana Colín Castro, Melissa Hernández Durán, María Guadalupe Martínez Zavaleta, Braulio Josué Méndez Sotelo, Cindy Fabiola Hernández Pérez, Christian Sohlenkamp, Rafael Franco Cendejas, Luis Esaú López Jácome","doi":"10.1093/jambio/lxaf048","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Stenotrophomonas maltophilia is the species most frequently identified by clinical microbiology laboratories due to its presence in the main identification systems databases. Phenotypic identification methods are widely used in laboratories, and the misidentification of Stenotrophomonas spp. is highly probable due to the presence of cryptic species. Our aim was to confirm the identity of five cefiderocol-resistant Stenotrophomonas species, initially identified as S. maltophilia, using genome analysis tools, performing comparative and functional analyses of these clinical strains associated with infectious processes.</p><p><strong>Methods: </strong>Identifications were performed using average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization. Virulence factors, resistance mechanisms, prophages, CRISPR elements, and metabolism elements were identified and annotated.</p><p><strong>Results: </strong>We confirmed the identity of the strains C960 and C2866 as Stenotrophomonas geniculata, and of strain C1657 as Stenotrophomonas indicatrix. The species designation parameters obtained indicated that the strains C4297 and C2852 are novel species. In comparison with the hypothetical proteome of the S. maltophilia complex species analyzed, elements associated with amino acid metabolism, DNA/RNA processing and repair, envelope biogenesis, and intracellular transport are predominant. Elements probably associated with antibiotic resistance, such as efflux pumps, aminoglycoside transferases, and phosphoethanolamine transferases, were identified, and the presence of genes related to capsule formation, iron acquisition, and intracellular survival probably contributes to virulence.</p><p><strong>Conclusions: </strong>This is the first report of S. geniculata and S. indicatrix as human pathogens. Besides, we proposed two novel species members of Smc: Stenotrophomonas veracruzanensis sp. nov. and Stenotrophomonas mexicanensis sp. nov.</p>","PeriodicalId":15036,"journal":{"name":"Journal of Applied Microbiology","volume":" ","pages":""},"PeriodicalIF":3.2000,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Unveiling the resistance: comparative genomic analysis of two novel cefiderocol-resistant Stenotrophomonas species from a referral hospital in Mexico City.\",\"authors\":\"Jossue Ortiz Álvarez, Corazón Barrientos Flores, Claudia Adriana Colín Castro, Melissa Hernández Durán, María Guadalupe Martínez Zavaleta, Braulio Josué Méndez Sotelo, Cindy Fabiola Hernández Pérez, Christian Sohlenkamp, Rafael Franco Cendejas, Luis Esaú López Jácome\",\"doi\":\"10.1093/jambio/lxaf048\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Stenotrophomonas maltophilia is the species most frequently identified by clinical microbiology laboratories due to its presence in the main identification systems databases. Phenotypic identification methods are widely used in laboratories, and the misidentification of Stenotrophomonas spp. is highly probable due to the presence of cryptic species. Our aim was to confirm the identity of five cefiderocol-resistant Stenotrophomonas species, initially identified as S. maltophilia, using genome analysis tools, performing comparative and functional analyses of these clinical strains associated with infectious processes.</p><p><strong>Methods: </strong>Identifications were performed using average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization. Virulence factors, resistance mechanisms, prophages, CRISPR elements, and metabolism elements were identified and annotated.</p><p><strong>Results: </strong>We confirmed the identity of the strains C960 and C2866 as Stenotrophomonas geniculata, and of strain C1657 as Stenotrophomonas indicatrix. The species designation parameters obtained indicated that the strains C4297 and C2852 are novel species. In comparison with the hypothetical proteome of the S. maltophilia complex species analyzed, elements associated with amino acid metabolism, DNA/RNA processing and repair, envelope biogenesis, and intracellular transport are predominant. Elements probably associated with antibiotic resistance, such as efflux pumps, aminoglycoside transferases, and phosphoethanolamine transferases, were identified, and the presence of genes related to capsule formation, iron acquisition, and intracellular survival probably contributes to virulence.</p><p><strong>Conclusions: </strong>This is the first report of S. geniculata and S. indicatrix as human pathogens. Besides, we proposed two novel species members of Smc: Stenotrophomonas veracruzanensis sp. nov. and Stenotrophomonas mexicanensis sp. nov.</p>\",\"PeriodicalId\":15036,\"journal\":{\"name\":\"Journal of Applied Microbiology\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":3.2000,\"publicationDate\":\"2025-03-03\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Applied Microbiology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/jambio/lxaf048\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Applied Microbiology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/jambio/lxaf048","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
Unveiling the resistance: comparative genomic analysis of two novel cefiderocol-resistant Stenotrophomonas species from a referral hospital in Mexico City.
Background: Stenotrophomonas maltophilia is the species most frequently identified by clinical microbiology laboratories due to its presence in the main identification systems databases. Phenotypic identification methods are widely used in laboratories, and the misidentification of Stenotrophomonas spp. is highly probable due to the presence of cryptic species. Our aim was to confirm the identity of five cefiderocol-resistant Stenotrophomonas species, initially identified as S. maltophilia, using genome analysis tools, performing comparative and functional analyses of these clinical strains associated with infectious processes.
Methods: Identifications were performed using average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization. Virulence factors, resistance mechanisms, prophages, CRISPR elements, and metabolism elements were identified and annotated.
Results: We confirmed the identity of the strains C960 and C2866 as Stenotrophomonas geniculata, and of strain C1657 as Stenotrophomonas indicatrix. The species designation parameters obtained indicated that the strains C4297 and C2852 are novel species. In comparison with the hypothetical proteome of the S. maltophilia complex species analyzed, elements associated with amino acid metabolism, DNA/RNA processing and repair, envelope biogenesis, and intracellular transport are predominant. Elements probably associated with antibiotic resistance, such as efflux pumps, aminoglycoside transferases, and phosphoethanolamine transferases, were identified, and the presence of genes related to capsule formation, iron acquisition, and intracellular survival probably contributes to virulence.
Conclusions: This is the first report of S. geniculata and S. indicatrix as human pathogens. Besides, we proposed two novel species members of Smc: Stenotrophomonas veracruzanensis sp. nov. and Stenotrophomonas mexicanensis sp. nov.
期刊介绍：
Journal of & Letters in Applied Microbiology are two of the flagship research journals of the Society for Applied Microbiology (SfAM). For more than 75 years they have been publishing top quality research and reviews in the broad field of applied microbiology. The journals are provided to all SfAM members as well as having a global online readership totalling more than 500,000 downloads per year in more than 200 countries. Submitting authors can expect fast decision and publication times, averaging 33 days to first decision and 34 days from acceptance to online publication. There are no page charges.
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