Cipher: 1116
Nomenclature: Methods of molecular diagnostics in the detection of multi-resistant bacteria
Study programme: Molecular biosciences
Module: elective course (methodological)
Case holder:

Izv.prof.dr.sc. Domagoj Drenjancevic
Institution of the case holder:

J. J. Strossmayer University of Osijek, Faculty of Medicine Osijek
Contributors - Contractors:

the doc.dr.sc. Mirjana Suver Stević, zn. Associate
Dr.sc. Maja Bogdan, zn. Associate
Subject status: Electoral College
The year in which the case is submitted: Year I
The semester in which the case is submitted: Semester I
Subject objective:

Understand the latest molecular diagnostic methods in the research and detection of multi-resistant bacteria, methods of molecular epidemiology and genotyping of bacteria, and understand the application of molecular detection methods in clinical diagnostic practice.
Case contents:

The evolution of resistance and the importance of multi-resistant bacteria in the emergence of a global threat. The role of timely detection and control over the spread of resistant determinants among the bacterial population. Genetic grounds for the onset of antimicrobial resistance. Gentotyping of bacteria: gel-electrophoresis in pulsed field (pulsed-field gel electrophoresis, PFGE), multi-gene sequence analysis (multilocus sequence typing, MLST) and analysis of loci containing a different number of consecutive repetitions (multiple locus variable number of tandem repeat analysis, MLVA) . Laboratory diagnosis of multi-resistant bacteria. Phenotypic vs. genotypic methods in the detection of multi-resistant causative agents - benefits and disadvantages. Presentation of molecular methods in the detection of resistant bacteria: amplification methods based on polymerase chain reaction (PCR) - "conventional" PCR, real-time PCR and commemorative RT-PCR whales, multiplex PCR, polymorphism of the length of restrictive fragments (restriction fragment of length polymorphism RFLP), DNA probe-based hybridization essays, combined essays (DNA probe-based + PCR, PCR+ELISA). Genome sequencing in bacterial resistance detection and a new generation of high-throughput sequencing. Microarray technology in the detection of multi-resistant bacteria. New methods in rapid detection and identification of multi-resistant bacteria: Pyrosequencing® technology, Liquid array and matrix-associated laser desorption ionization-time of flight (MALDI-TOF) – application possibilities and future directions.
Learning outcomes: competences, knowledge, skills that the subject develops:

1. Analyze the methods of genotyping and molecular diagnostics of multi-resistant bacteria.
2. Review the application and importance of genotyping methods and molecular diagnostics of multi-resistant bacteria in monitoring the spread of bacterial resistance.
3. Propose the application of genotyping methods and molecular diagnostics in biomedical research in the field of microbiology and infectious diseases.
ECTS Credits 4
Lectures 15
Seminars (IS) 10
Exercises (E) 0
Altogether 25
The way of teaching and acquiring knowledge:

Attendance and active participation in seminars.
Ways of teaching and acquiring knowledge: (notes)
Monitoring and evaluating students (mark in fat printing only relevant categories) Teaching activities, Mandatory seminar work
Rating method: Oral exam, Essay/Seminar, Continuous examination of knowledge in the course of teaching
Mandatory literature:

1. Diagnostic Bacteriology Protocols 2nd edition, L. O'Connor (Ed.) Series: Methods in Molecular Biology, Vol. 345. Humana Press; New Jersey: 2006.
2. Sundsfjord A, Simonsen GS, Haldorsen BC, Haaheim H, Hjelmevoll SO, Littauer P et al. Genetic methods for detection of antimicrobial resistance. APMIS 2004;112:815-37.
3. Espy MJ, Uhl JR, Sloan LM, Buckwalter SP, Jones MF, Vetter EA et al. Real-time PCR in clinical microbiology: applications for routine laboratory testing. Clin Microbiol Rev 2006;19:165-256.
4. Fluit AC, Visser MR, Schmitz FJ. Molecular detection of antimicrobial resistance. Clin Microbiol Rev 2001;14:836-71.
5. Lecuit M, Eloit M. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front Cell Infect Microbiol 2014 6;4:25.
6. Tuite N, Reddington K, Barry T, Zumla A, Enne V. Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? J Antimicrob Chemother 2014;69:1729-33.
7. Osei Sekyere J, Govinden U, Essack SY. Review of established and innovative detection methods for carbapenemase-producing Gram-negative bacteria. J Appl Microbiol 2015;119:1219-33.
8. Hrabák J1, Chudácková E, Walková R.Matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry for detection of antibiotic resistance mechanisms: from research to routine diagnosis. Clin Microbiol Rev. 2013;26:103-14.
9. Card RM, Warburton PJ, MacLaren N, Mullany P, Allan E, Anjum MF. Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans. PLoS One. 2014 22,9(1):e86428.
Supplementary (recommended) literature:

1. Singh A, Goering RV, Simjee S, Foley SL, Zervos MJ. Application of molecular techniques to the study of hospital infection. Clin Microbiol Rev. 2006;19:512-30.
2. Antibiotic Resistance, Methods and Protocols. Stephen H. Gillespie, editor. Series: Methods in Molecular Biology, Vol. 48. Humana Press; New Jersey: 2001.
How to monitor the quality and performance performance (evaluation):

The success of the course will be evaluated annually by the joint expert committee of the Rudjer Boskovic Institute, the University of Dubrovnik and the University of Osijek, and the leaders will receive information from the participants about the adequacy of the program and performance by the leadership through the survey.