The role of whole genome sequencing in characterisation of multi-resistant Gram-negative bacteria

Abstract

U ovom radu se opisuje uloga cjelogenomskog sekvencioniranja u opisivanju multirezistentnih gram-negativnih (MDRGN) bakterija. Unutar ove teme obrađeni su i mehanizmi rezistencije te njihova genetska podloga. Također je opisan princip rada cjelogenomskog sekvencioniranja. Multirezistentne gram-negativne bakterije su bakterije koje imaju rezistenciju na 2 ili više antibiotika. Mehanizmi rezistencije imaju genetsku podlogu te se stoga osim klasičnim fenotipskim metodama mogu određivati i novijim molekularnim metodama. Jedna takva metoda je cjelogenomsko sekvencioniranje. Cjelogenomskim sekvencioniranjem možemo dobiti gotovo čitavu DNA sekvencu nekog organizma. Cjelogenomskim sekvencioniranjem MDRGN bakterija možemo odrediti gene rezistencije, a uz upotrebu strojnog učenja moguće je otkriti nove gene rezistencije. U detekciji gena rezistencije ovom metodom koriste se različiti bioinformatički programi. Takvi programi sadrže mehanizam detekcije gena rezistencije i bazu podataka s poznatim genima rezistencije. Cjelogenomsko sekvencioniranje je moguće koristi za detekciju rezistencije MDRGN bakterija, istraživanje evolucije antibiotske rezistencije MDRGN bakterija, nadziranje epidemija uzrokovanih MDRGN bakterijama te radi uspostava mjera kontrole širenja infekcija u klinci. Cjelogenomsko sekvencioniranje se pokazalo kao vrlo vrijedno sredstvo u karakterizaciji MDRGN bakterija i u borbi protiv antibiotske rezistencije. Donedavno se vrlo rijetko koristilo zbog skupoće i manjka točnih i pouzdanih pristupa. Danas se to mijenja zbog velikog povećanja efikasnosti DNA sekvencioniranja, pada cijena sekvencioniranja i pojave robusnih računalnih alata.The topic of this paper is the role of whole-genome sequencing (WGS) in describing multidrug-resistant gram-negative (MDRGN) bacteria. Within this topic, the mechanisms of resistance and their genetic background are also discussed. The working principle of WGS is also described. Multidrug-resistant gram-negative bacteria are bacteria that are resistant to 2 or more antibiotics. The mechanisms of resistance have a genetic basis and therefore, in addition to classical phenotypic methods, they can also be determined by newer molecular methods. One such method is WGS. By WGS, we can obtain almost the entire DNA sequence of an organism. By WGS of MDRGN bacteria, we can determine resistance genes, and with the use of machine learning, it is possible to detect new resistance genes. Various bioinformatics programs are used in the detection of resistance genes by this method. Such programs contain a gene detection platform and a database with known resistance genes. WGS can be used to detect MDRGN bacterial resistance, investigate the evolution of antibiotic resistance in MDRGN bacteria, monitor epidemics caused by MDRGN bacteria, and to establish measures to control the spread of infections in the clinic. WGS has proven to be a very valuable tool in the characterization of MDRGN bacteria and invaluable in the fight against antibiotic resistance. Until recently, it was very rarely used due to its high cost and lack of accurate and reliable approaches. Today, this is changing due to the large increase in DNA sequencing efficiency, lower sequencing costs, and the emergence of robust computer tools