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Molecular identification, typing and adaptation of Achromobacter spp. during the course of chronic infection
Učíková, Barbora ; Dřevínek, Pavel (advisor) ; Nemec, Alexandr (referee)
Achromobacter spp. is an emerging pathogen, especially in chronic respiratory infections in patients with cystic fibrosis. MALDI-TOF mass spectrometry provides reliable identification only at the genus level. The nrdA gene sequence is used for species identification of representatives. Clonality studies using multilocus sequence typing can determine whether a patient is still infected with the same clone or whether reinfection with a new strain occurs over time. Time-collected isolates of Achromobacter spp. from patients with cystic fibrosis were included in our study. Patients were divided into three groups according to the time interval between collections. In the first group, the external interval between collections was approximately 10 years, in the second group 7 to 12 months, and the remaining group consisted of single isolates. In the course of chronic infection, Achromobacter spp. adapt to the exposed antibiotics and to the host. Isolates sampled at an interval of 10 years showed a higher number of mutations than isolates with a sampling interval of up to one year. During chronic infection, loss of motility occurs, which we demonstrated phenotypically at the level of motility, reduction in flagella number and changes in flagellar genes. Increased resistance was observed in some isolates by...
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Molecular epidemiology and characteristics of bacterial pathogens on lung infection in patients with cystic fibrosis
Vošahlíková, Šárka ; Nemec, Alexandr (advisor) ; Melter, Oto (referee) ; Osička, Radim (referee)
Cystic fibrosis is the most abundant inherited autosomal recessive disease in Caucasian population. Cystic fibrosis is caused by a dysfunction of a transport channel which is responsible for the transport of chloride ions on the apical side of the plasma membrane. Despite the fact that the dysfunction of the transport channel is present in several organs, the most severely affected one is the respiratory system. Because of the ion imbalance, thick sticky mucus is produced on the surface of the airways which then prevents the removal of dust particles and bacteria. The main complications of cystic fibrosis are the bacterial infections of the respiratory system which become chronic during the patient's life and thus are the most common causes of the respiratory failure and premature death. The most important agents causing these infections are Pseudomonas aeruginosa and Burkholderia cepacia (Bcc). Infections caused by those bacteria are practically untreatable and serious complications arise from the existence of epidemic strains which can be transfered from patient to patient. Precise and fast diagnostics of pathogenic strains is a critical step to avoid spreading bacterial infections as well as strictly followed anti- epidemic strategies mainly based on isolation of cystic fibrosis patients according to...
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Extensively resistant Acinetobacter baumannii in the Czech Republic: population genetic structure and mechanisms of resistance to carbapenems and aminoglycosides
Švandová, Ladislava ; Nemec, Alexandr (advisor) ; Melter, Oto (referee)
This study focuses on the question of the epidemiology of resistance to antibiotics in Acinetobacter baumannii, which is nowadays one of the most problematic bacterial patho- gens associated with failing antimicrobial therapy. Its aim was to define population-genetic properties, epidemiology and the nature of multidrug resistance for a sample of the current population of A. baumannii from Czechia. A total of 55 isolates were collected in eight medi- cal facilities in central Bohemia from October 2016 to May 2018. The isolates were assessed for their identity at the species, clonal and strain levels as well as resistance phenotype and genotype; they were classified into five clonal groups, each of which encompassed isolates that were likely to be epidemiologically related. The 55 isolates studied belonged, nearly exclusively, to global clone ECII, with 53 % of them forming a genetically relatively homoge- neous group characterized by extensive resistance to antibiotics (susceptible only to col- istin), the presence of genes encoding ArmA a OXA-23 (resistance to all aminoglycosides and carbapenems) and spread in all locations. The in-depth epidemiological analysis of isolates from the city of Příbram and its vicinity indicated the regional spread of two strains, one of which belonged to the...
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Genetic basis of multidrug resistance in Acinetobacter baumannii
Křížová, Lenka ; Nemec, Alexandr (advisor) ; Higgins, Paul (referee) ; Šmajs, David (referee)
Charles University in Prague, Faculty of Science Department of Genetics and Microbiology Ph.D. study program: Molecular and Cellular Biology, Genetics and Virology Genetic basis of multidrug resistance in Acinetobacter baumannii Lenka Křížová Supervisor: Doc. RNDr. Alexandr Nemec, Ph.D. Supervisor-consultant: RNDr. Lubomír Janda, Ph.D. Prague 2014 SUMMARY Acinetobacter baumannii has emerged as a significant bacterial pathogen pre-eminently associated with hospital-acquired infections. Strains of this species may currently exhibit resistance to nearly all or even all clinically relevant drugs. The vast majority of epidemic and multidrug-resistant A. baumannii strains belong to a few globally spread lineages, in particular to the so-called European (EU) clones I, II, and III. Complex resistance patterns displayed by these strains result from their marked capacity to develop, acquire, and combine secondary resistance mechanisms against originally effective agents. The aim of this thesis was to broaden our knowledge on the genetic basis and epidemiology of multidrug resistance in A. baumannii. The obtained results have been published in the form of six studies which are part of this thesis. In the first study, we analysed the epidemiology of carbapenem resistance among hospital strains of Acinetobacter in the...
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The role of the AdeABC efflux system in resistance of Acinetobacter baumannii to aminoglycosides
Kladivová, Lucie ; Nemec, Alexandr (advisor) ; Nunvář, Jaroslav (referee)
Acinetobacter baumannii is an important nosocomial pathogen characterized by the ability to acquire and develop complex resistance to antimicrobial agents. This capability is caused by eflux systems removing molecules of antibiotics from bacterial intracellular space. AdeABC is an RND-type chromosomal eflux system specific for A. baumannii which has a broad substrate spectrum. In this work, we focused on functional analysis of AdeABC to define its role in the resistance development to aminoglycosides in genetically different strains. We studied a set of 15 epidemiologically and genotypically well characterized strains of A. baumannii which were fully susceptible to aminoglycosides and other antibiotics primarily effective against this species. We determined genotyp of AdeABC for these strains and performed a selection for resistant variants in the presence of netilmicin. Using real-time qRT-PCR we compared the expression of the transporter gene adeB in originally sensitive strains and selected variants. The obtained results confirmed that the increased expression of AdeABC significantly reduces susceptibility to aminoglycosides and other antibiotics. The results also suggest that the efflux system provides a significant selective advantage for nosocomial strains of A. baumannii.
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Molecular epidemiology and characteristics of bacterial pathogens on lung infection in patients with cystic fibrosis
Vošahlíková, Šárka ; Nemec, Alexandr (advisor) ; Melter, Oto (referee) ; Osička, Radim (referee)
Cystic fibrosis is the most abundant inherited autosomal recessive disease in Caucasian population. Cystic fibrosis is caused by a dysfunction of a transport channel which is responsible for the transport of chloride ions on the apical side of the plasma membrane. Despite the fact that the dysfunction of the transport channel is present in several organs, the most severely affected one is the respiratory system. Because of the ion imbalance, thick sticky mucus is produced on the surface of the airways which then prevents the removal of dust particles and bacteria. The main complications of cystic fibrosis are the bacterial infections of the respiratory system which become chronic during the patient's life and thus are the most common causes of the respiratory failure and premature death. The most important agents causing these infections are Pseudomonas aeruginosa and Burkholderia cepacia (Bcc). Infections caused by those bacteria are practically untreatable and serious complications arise from the existence of epidemic strains which can be transfered from patient to patient. Precise and fast diagnostics of pathogenic strains is a critical step to avoid spreading bacterial infections as well as strictly followed anti- epidemic strategies mainly based on isolation of cystic fibrosis patients according to...
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Morphogenesis of bacterial colonies
Čepl, Jaroslav ; Markoš, Anton (advisor) ; Konopásek, Ivo (referee) ; Nemec, Alexandr (referee)
The topic of this thesis has been built on previous work of our group, especially Rieger et al. 2008 and Čepl et al. 2010. We examined and described the regularity of morphogenesis of S. marcescens, morphotype F colonies (from "the fountain", because of a shape it resembles). Typical colony consists of elevated red navel, low non-pigmented ring and again elevated red rim. Structured profile of the colony together with changes in pigmentation of structures during development without need of artificial dying, provides considerable advantage in observation of the morphogenesis. Aims of this thesis were (i) to find other factors that affect the morphogenesis, (ii) to characterize interactions of S. marcescens colonies with other bacterial strains (S. rubidaea and E .coli) and finally (iii) to study the phenomenon of induced resistance to the antibiotics described in (Heal and Parsons, 2002; Lu 2004; Bernier et al. 2011) in our model organisms. (i) Mutual interactions of colonies on the plate indicates that morphogenesis is affected by autocrine signals, which diffuse into the medium and the atmosphere and affect the development of surrounding colonies. We have detected changes of pH of the medium during the development of colonies in their vicinity. At ...
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