β- Laktamazların Saptanmasında Tüm Genom Dizileme
Özet
Antibiyotik direnci, dünya genelinde hızla artan ve tedavi seçeneklerini kısıtlayan önemli bir halk sağlığı tehdididir. Bu derlemede, direnç mekanizmalarının tanımlanması ve epidemiyolojik analizinde yeni nesil dizileme (NGS) ve tüm genom dizileme (WGS) yaklaşımlarının güncel rolü, ß-laktamazlar özelinde ele alınmıştır. Fenotipik antibiyotik duyarlılık testleri, antibiyotik direncinin tanısında vazgeçilmez olsa da, kültür bağımlılığı ve uzun süren sonuçlanma süresi nedeniyle önemli sınırlılıkları vardır. WGS, ß-laktamazlar da dahil olmak üzere direnç gelişiminden sorumlu genleri güvenilir biçimde tanımlar, kromozomal veya plazmid kaynaklı konumlarını belirler, klonal ilişkileri ve plazmid aracılı yayılımı ortaya koyar. Genotip-fenotip korelasyonu birçok ß-laktam/enzim kombinasyonunda güçlüdür; ancak özellikle AmpC/porin değişiklikleri, heterodirenç ve biyofilm varlığı gibi durumlarda uyumsuzluk gözlenebilir. Yeni varyantların klinik öneminin anlaşılması için WGS bulgularının klonlama ve biyokimyasal analizlerle işlevsel olarak doğrulanması gereklidir. Metagenomik yaklaşımlar, kültür gereksinimini ortadan kaldırarak çevresel ve zoonotik rezistomun haritalanmasını ve Tek Sağlık perspektifinden direnç sürveyansını güçlendirir. WGS, tanı ile epidemiyoloji arasındaki boşluğu dolduran, ß-laktamaz çeşitliliğinin izlenmesi, yeni ß-laktamazların keşfi ve antibiyoitk direnç yönetiminde yüksek potansiyel taşıyan bir araçtır.
Antimicrobial resistance is a rapidly increasing global public health threat that limits available treatment options. This review addresses the current role of next-generation sequencing (NGS) and whole-genome sequencing (WGS) in elucidating resistance mechanisms and their epidemiological characterization, specifically focusing on ß-lactamases. Although phenotypic antimicrobial susceptibility testing is diagnostically indispensable in defining antimicrobial resistance, its dependence on culture and long turnaround times represent significant limitations. WGS reliably detects common genes, including ß-lactamases, responsible for the development af antimicrobial resistance, determines their chromosomal or plasmidic localization, and reveals clonal relationships and plasmid-mediated dissemination. The genotype–phenotype correlation is strong for many ß-lactam/enzyme combinations; however, discrepancies may occur especially in the presence of AmpC or porin alterations, heteroresistance, and biofilm formation. Functional validation of WGS findings through cloning and biochemical analyses is essential to clarify the clinical relevance of newly identified variants. Metagenomic approaches eliminate the need for culture, enabling the mapping of environmental and zoonotic resistomes and strengthening antimicrobial resistance surveillance within the One Health framework. Overall, WGS bridges the gap between diagnostics and epidemiology, providing a powerful tool for monitoring ß-lactamase diversity, enabling the discovery of new ß-lactamases and improving antimicrobial resistance management.
Referanslar
Olsen NS, Riber L. Metagenomics as a transformative tool for antibiotic resistance surveillance: highlighting the impact of mobile genetic elements with a focus on the complex role of phages. Antibiotics. 2025;14(3):296.
Yee R, Simner PJ. Next-generation sequencing approaches to predicting antimicrobial susceptibility testing results. Adv Mol Pathol. 2019;2(1):99-110.
Otto M. Next-generation sequencing to monitor the spread of antimicrobial resistance. Genome Med. 2017;9(1):68.
Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet. 2014;30(9):401-7.
Bush K. Past and present perspectives on β-lactamases. Antimicrob Agents Chemother. 2018;62(10):10.1128/aac. 01076-18.
Ellington M, Ekelund O, Aarestrup FM et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017;23(1):2-22.
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, et al. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotech. 2017;243:16-24.
Mendes RE, Jones RN, Woosley LN, Cattoir V, Castanheira M, editors. Application of next-generation sequencing for characterization of surveillance and clinical trial isolates: analysis of the distribution of β-lactamase resistance genes and lineage background in the United States. Open forum infectious diseases; 2019: Oxford University Press US.
Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 2018;6(1):23.
Sabença C, Rivière R, Costa E et al. Whole-Genome Sequencing of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from Human Bloodstream Infections. Pathogens. 2025;14(3):205.
Jamal AJ, Mataseje LF, Williams V et al. Genomic Epidemiology of carbapenemase-producing enterobacterales at a hospital system in Toronto, Ontario, Canada, 2007 to 2018. Antimicrob Agents Chemother. 2021;65(8):10.1128/aac. 00360-21.
Wang L-J, Chen E-Z, Yang L, Feng D-H, Xu Z, Chen D-Q. Emergence of clinical Pseudomonas aeruginosa isolate Guangzhou-PaeC79 carrying crpP, bla GES-5, and bla KPC-2 in Guangzhou of China. Microb Drug Resist. 2021;27(7):965-70.
Wang W, Weng J, Wei J et al. Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne bla OXA-23. Microbiol Spect. 2024;12(9):e00501-24.
Bush K, Bradford PA. Epidemiology of β-lactamase-producing pathogens. Clin Microbiol Rev. 2020;33(2):10.1128/cmr. 00047-19.
Yong D, Toleman MA, Giske CG et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009;53(12):5046-54.
Al-Marzooq F, Ghazawi A, Allam M, Collyns T, Saleem A. Novel Variant of New Delhi Metallo-Β-Lactamase (bla NDM-60) Discovered in a Clinical Strain of Escherichia coli from the United Arab Emirates: An Emerging Challenge in Antimicrobial Resistance. Antibiotics. 2024;13(12):1158.
Frenk S, Rakovitsky N, Kon H et al. OXA-900, a novel OXA sub-family carbapenemase identified in Citrobacter freundii, evades detection by commercial molecular diagnostics tests. Microorganisms. 2021;9(9):1898.
Xu M, Zhao J, Xu L et al. Emergence of transferable ceftazidime–avibactam resistance in KPC-producing Klebsiella pneumoniae due to a novel CMY AmpC β-lactamase in China. Clin Microbiol Infect. 2022;28(1):136. e1-. e6.
Cavallini S, Unali I, Bertoncelli A, Cecchetto R, Mazzariol A. Ceftazidime/avibactam resistance is associated with different mechanisms in KPC-producing Klebsiella pneumoniae strains. Acta Microbiol Immunol Hung. 2021;68(4):235-9.
Zhang X, Xie Y, Zhang Y et al. Evolution of ceftazidime–avibactam resistance driven by mutations in double-copy bla KPC-2 to bla KPC-189 during treatment of ST11 carbapenem-resistant Klebsiella pneumoniae. Msystems. 2024;9(10):e00722-24.
Martino F, De Belder D, Rapoport M et al. GES-66: Characterization of a New β-Lactamase Gene Variant Detected in Klebsiella pneumoniae. J Infect Dis. 2025:jiaf302.
Martínez-Álvarez SA, Asencio-Egea MÁ, Huertas-Vaquero M et al. Genomic epidemiology of ESBL-and Carbapenemase-producing Enterobacterales in a Spanish hospital: Exploring the clinical–environmental interface. Microorganisms. 2025;13(8):1854.
Al Mana H, Sundararaju S, Tsui CK et al. Whole-genome sequencing for molecular characterization of carbapenem-resistant Enterobacteriaceae causing lower urinary tract infection among pediatric patients. Antibiotics. 2021;10(8):972.
Becerra-Aparicio F, Gómez-Zorrilla S, Hernández-García M, Xanthopoulou K, Gijón D, Siverio A, et al., editors. Whole Genome Sequencing Analysis of Klebsiella pneumoniae Isolates from Health Care–Associated Bacteremia of Urinary Origin in Spain: Findings from the Multicenter ITUBRAS-2 Cohort Study. Open Forum Infectious Diseases; 2025: Oxford University Press US.
Zhu Y, Jia X, Jia P, Li X, Yang Q. Genetic and phenotypic characterization of the novel metallo-β-lactamase NDM-29 from Escherichia coli. Front Microbiol. 2021;12:743981.
Al-Mustapha AI, Tiwari A, Laukkanen-Ninios R et al. Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli. Sci Rep. 2025;15(1):7400.
Berglund F, Marathe NP, Österlund T et al. Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome. 2017;5(1):134.
Hendriksen RS, Munk P, Njage P et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun. 2019;10(1):1124.
Peker N, Rossen JW, Deurenberg RH et al. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli using amplicon-based next-generation sequencing and automated analysis. Microorganisms. 2018;6(1):6.
Schweizer C, Bischoff P, Bender J et al. Plasmid-mediated transmission of KPC-2 carbapenemase in Enterobacteriaceae in critically ill patients. Front Microbiol. 2019;10:276.
David S, Reuter S, Harris SR et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol. 2019;4(11):1919-29.
Wyres KL, Lam MM, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol. 2020;18(6):344-59.
Snitkin ES, Zelazny AM, Thomas et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012;4(148):148ra16-ra16.
Zhou K, Lokate M, Deurenberg RH, et al. Characterization of a CTX-M-15 producing Klebsiella pneumoniae outbreak strain assigned to a novel sequence type (1427). Front Microbiol. 2015;6:1250.
Zhou K, Lokate M, Deurenberg RH et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016;6(1):20840.
Doyle RM, O'sullivan DM, Aller SD et al. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom. 2020;6(2):e000335.
Referanslar
Olsen NS, Riber L. Metagenomics as a transformative tool for antibiotic resistance surveillance: highlighting the impact of mobile genetic elements with a focus on the complex role of phages. Antibiotics. 2025;14(3):296.
Yee R, Simner PJ. Next-generation sequencing approaches to predicting antimicrobial susceptibility testing results. Adv Mol Pathol. 2019;2(1):99-110.
Otto M. Next-generation sequencing to monitor the spread of antimicrobial resistance. Genome Med. 2017;9(1):68.
Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet. 2014;30(9):401-7.
Bush K. Past and present perspectives on β-lactamases. Antimicrob Agents Chemother. 2018;62(10):10.1128/aac. 01076-18.
Ellington M, Ekelund O, Aarestrup FM et al. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect. 2017;23(1):2-22.
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, et al. Application of next generation sequencing in clinical microbiology and infection prevention. J Biotech. 2017;243:16-24.
Mendes RE, Jones RN, Woosley LN, Cattoir V, Castanheira M, editors. Application of next-generation sequencing for characterization of surveillance and clinical trial isolates: analysis of the distribution of β-lactamase resistance genes and lineage background in the United States. Open forum infectious diseases; 2019: Oxford University Press US.
Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 2018;6(1):23.
Sabença C, Rivière R, Costa E et al. Whole-Genome Sequencing of Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Isolated from Human Bloodstream Infections. Pathogens. 2025;14(3):205.
Jamal AJ, Mataseje LF, Williams V et al. Genomic Epidemiology of carbapenemase-producing enterobacterales at a hospital system in Toronto, Ontario, Canada, 2007 to 2018. Antimicrob Agents Chemother. 2021;65(8):10.1128/aac. 00360-21.
Wang L-J, Chen E-Z, Yang L, Feng D-H, Xu Z, Chen D-Q. Emergence of clinical Pseudomonas aeruginosa isolate Guangzhou-PaeC79 carrying crpP, bla GES-5, and bla KPC-2 in Guangzhou of China. Microb Drug Resist. 2021;27(7):965-70.
Wang W, Weng J, Wei J et al. Whole genome sequencing insight into carbapenem-resistant and multidrug-resistant Acinetobacter baumannii harboring chromosome-borne bla OXA-23. Microbiol Spect. 2024;12(9):e00501-24.
Bush K, Bradford PA. Epidemiology of β-lactamase-producing pathogens. Clin Microbiol Rev. 2020;33(2):10.1128/cmr. 00047-19.
Yong D, Toleman MA, Giske CG et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother. 2009;53(12):5046-54.
Al-Marzooq F, Ghazawi A, Allam M, Collyns T, Saleem A. Novel Variant of New Delhi Metallo-Β-Lactamase (bla NDM-60) Discovered in a Clinical Strain of Escherichia coli from the United Arab Emirates: An Emerging Challenge in Antimicrobial Resistance. Antibiotics. 2024;13(12):1158.
Frenk S, Rakovitsky N, Kon H et al. OXA-900, a novel OXA sub-family carbapenemase identified in Citrobacter freundii, evades detection by commercial molecular diagnostics tests. Microorganisms. 2021;9(9):1898.
Xu M, Zhao J, Xu L et al. Emergence of transferable ceftazidime–avibactam resistance in KPC-producing Klebsiella pneumoniae due to a novel CMY AmpC β-lactamase in China. Clin Microbiol Infect. 2022;28(1):136. e1-. e6.
Cavallini S, Unali I, Bertoncelli A, Cecchetto R, Mazzariol A. Ceftazidime/avibactam resistance is associated with different mechanisms in KPC-producing Klebsiella pneumoniae strains. Acta Microbiol Immunol Hung. 2021;68(4):235-9.
Zhang X, Xie Y, Zhang Y et al. Evolution of ceftazidime–avibactam resistance driven by mutations in double-copy bla KPC-2 to bla KPC-189 during treatment of ST11 carbapenem-resistant Klebsiella pneumoniae. Msystems. 2024;9(10):e00722-24.
Martino F, De Belder D, Rapoport M et al. GES-66: Characterization of a New β-Lactamase Gene Variant Detected in Klebsiella pneumoniae. J Infect Dis. 2025:jiaf302.
Martínez-Álvarez SA, Asencio-Egea MÁ, Huertas-Vaquero M et al. Genomic epidemiology of ESBL-and Carbapenemase-producing Enterobacterales in a Spanish hospital: Exploring the clinical–environmental interface. Microorganisms. 2025;13(8):1854.
Al Mana H, Sundararaju S, Tsui CK et al. Whole-genome sequencing for molecular characterization of carbapenem-resistant Enterobacteriaceae causing lower urinary tract infection among pediatric patients. Antibiotics. 2021;10(8):972.
Becerra-Aparicio F, Gómez-Zorrilla S, Hernández-García M, Xanthopoulou K, Gijón D, Siverio A, et al., editors. Whole Genome Sequencing Analysis of Klebsiella pneumoniae Isolates from Health Care–Associated Bacteremia of Urinary Origin in Spain: Findings from the Multicenter ITUBRAS-2 Cohort Study. Open Forum Infectious Diseases; 2025: Oxford University Press US.
Zhu Y, Jia X, Jia P, Li X, Yang Q. Genetic and phenotypic characterization of the novel metallo-β-lactamase NDM-29 from Escherichia coli. Front Microbiol. 2021;12:743981.
Al-Mustapha AI, Tiwari A, Laukkanen-Ninios R et al. Wastewater based genomic surveillance key to population level monitoring of AmpC/ESBL producing Escherichia coli. Sci Rep. 2025;15(1):7400.
Berglund F, Marathe NP, Österlund T et al. Identification of 76 novel B1 metallo-β-lactamases through large-scale screening of genomic and metagenomic data. Microbiome. 2017;5(1):134.
Hendriksen RS, Munk P, Njage P et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun. 2019;10(1):1124.
Peker N, Rossen JW, Deurenberg RH et al. Evaluation of an Accelerated Workflow for Surveillance of ESBL (CTX-M)-Producing Escherichia coli using amplicon-based next-generation sequencing and automated analysis. Microorganisms. 2018;6(1):6.
Schweizer C, Bischoff P, Bender J et al. Plasmid-mediated transmission of KPC-2 carbapenemase in Enterobacteriaceae in critically ill patients. Front Microbiol. 2019;10:276.
David S, Reuter S, Harris SR et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol. 2019;4(11):1919-29.
Wyres KL, Lam MM, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol. 2020;18(6):344-59.
Snitkin ES, Zelazny AM, Thomas et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med. 2012;4(148):148ra16-ra16.
Zhou K, Lokate M, Deurenberg RH, et al. Characterization of a CTX-M-15 producing Klebsiella pneumoniae outbreak strain assigned to a novel sequence type (1427). Front Microbiol. 2015;6:1250.
Zhou K, Lokate M, Deurenberg RH et al. Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci Rep. 2016;6(1):20840.
Doyle RM, O'sullivan DM, Aller SD et al. Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study. Microb Genom. 2020;6(2):e000335.
