[IGRA methods in the routine operation - QuantiFERON®-TB Gold or T-SPOT.TB?] / IGRA metody v rutinním provozu - QuantiFERON®-TB Gold nebo T-SPOT®.TB?

For indirect diagnosis of tuberculosis, two commercial IGRA (Interferon Gamma Release Assay) assays are available - primal QuantiFERON®-TB Gold test, new version QuantiFERON®-TB Gold Plus test (four tube, differentiation in activity CD4+ a CD8+) and T-SPOT®.TB test. Both methods are based on the same principle, but their workflows are different. In this article, both assays are compared on the collection of 284 patients. Inter-rate agreement measure showed 81.3% consistency and Cohens kappa index was calculated as 0.72. In case of discrepancy between IGRA and other methods (clinical aspects, X-ray diagnostic, etc.), results should be confirmed by second IGRA assay for correct interpretation.

Complete nucleotide sequences of two NDM-1-encoding plasmids from the same sequence type 11 Klebsiella pneumoniae strain.

The sequence type 11 Klebsiella pneumoniae strain Kpn-3002cz was confirmed to harbor two NDM-1-encoding plasmids, pB-3002cz and pS-3002cz. pB-3002cz (97,649 bp) displayed extensive sequence similarity with the blaNDM-1-carrying plasmid pKPX-1. pS-3002cz (73,581 bp) was found to consist of an IncR-related sequence (13,535 bp) and a mosaic region (60,046 bp). A 40,233-bp sequence of pS-3002cz was identical to the mosaic region of pB-3002cz, indicating the en bloc acquisition of the NDM-1-encoding region from one plasmid by the other.

Survey of metallo-ß-lactamase-producing Enterobacteriaceae colonizing patients in European ICUs and rehabilitation units, 2008-11.

OBJECTIVES: The objective of this study was to perform a multinational survey of patients' colonization by metallo-ß-lactamase (MBL)-producing Enterobacteriaceae, including their molecular characterization. METHODS: Patients in 18 hospital units across Europe and Israel (n = 17 945) were screened between mid-2008 and mid-2011. MBL-producing isolates were typed by PFGE and MLST. MBL genes were amplified and sequenced within their integrons. Plasmids with MBL genes were analysed by nuclease S1 plus hybridization profiling, mating and transformation assays, and by PCR-based replicon typing. RESULTS: Ninety-one patients in nine centres (six countries), including 62 patients in two Greek ICUs, carried 94 non-duplicate MBL-producing organisms. Klebsiella pneumoniae isolates from Greece dominated (n = 57) and belonged mainly to ST147, ST36 and ST383. All but one of the isolates expressed VIM-1-type MBLs. Isolates of Greek origins produced five enzymes, including new VIM-39, encoded by class 1 integrons of four types. In-e541-like elements prevailed, comprising six variants located on IncR, IncFIIK, IncR + FIIK, IncR + A/C or non-typeable plasmids. The other group were new In4873 and In4863, being the first In416-like elements identified in Greece, which were present on IncA/C or non-typeable plasmids. Isolates from other countries produced only VIM-1 and the major integron was In916, identified in 16 organisms from France, Italy and Spain. In916 was carried by four plasmid types, including IncA/C, IncFIIK and IncHI2. Other integrons included a new element, In3103, in Spain and In110 identified only in Latvia. CONCLUSIONS: This study provided fully comparable data on the occurrence and molecular characteristics of VIM-producing Enterobacteriaceae in a group of hospital units across Europe, documenting recent changes in their epidemiology.

Prevalence study on carbapenemase-producing Escherichia coli and Klebsiella pneumoniae isolates in Czech hospitals--results from Czech Part of European Survey on Carbapenemase--Producing Enterobacteriaceae (EuSCAPE).

OBJECTIVE: One of the most important threats of current medicine is the spread of multiresistant Gram-negative bacteria. We report here data from a six-month prevalence study on carbapenemase-producing K. pneumoniae and E. coli performed in Czech hospitals participating on European Survey on Carbapenemase-Producing Enterobacteriaceae (EuSCAPE). METHODS: Ten hospitals covering all regions of the Czech Republic were selected. During the study period (1st November 2013 to 30th April 2014), first ten carbapenem non-susceptible isolates of K. pneumoniae or E. coli isolated from non-surveillance specimens (i.e., blood, lower respiratory tract secretions, urine, puncture fluids, and wound secretions) of single successive patients were collected. Successive carbapenem-susceptible isolates of the same species were also preserved as controls. Susceptibility to 15 antibiotics was determined using EUCAST recommendations. Carbapenemase activity was detected by MALDI-TOF MS meropenem hydrolysis assay. Positive isolates were subjected for molecular typing (multi-locus sequence typing, identification of carbapenemase gene). RESULTS: During the study period, thirty non-susceptible isolates (K. pneumoniae n=28, E. coli n=2) were identified in 5 hospitals. Only two of them were confirmed to be carbapenemase producers. A NDM-1-producing K. pneumoniae ST11 was recovered from a patient, transferred from Ukraine, being injured during a Maidan revolution. The second isolate, an OXA-48-producing K. pneumoniae, belonging to ST101, was recovered from a patient admitted to a hospital for an ischemic stroke. CONCLUSIONS: This study again confirmed that the Czech Republic still belongs to the countries with low prevalence of carbapenemase-producing Enterobacteriaceae (CPE). Cases of CPE are usually restricted to an import from high-prevalence countries or countries with unknown epidemiological situation.

Identification of CMY-2-type cephalosporinases in clinical isolates of Enterobacteriaceae by MALDI-TOF MS.

This study exploited the possibility to detect Citrobacter freundii-derived CMY-2-like cephalosporinases in Enterobacteriaceae clinical isolates using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Periplasmic proteins were prepared using a modified sucrose method and analyzed by MALDI-TOF MS. A ca. 39,850-m/z peak, confirmed to represent a C. freundii-like ß-lactamase by in-gel tryptic digestion followed by MALDI-TOF/TOF MS, was observed only in CMY-producing isolates. We have also shown the potential of the assay to detect ACC- and DHA-like AmpC-type ß-lactamases.

[Identification of Mycobacterium spp. isolates using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)]. / Identifikace izolátu Mycobacterium spp. pomocí MALDI-TOF hmotnostní spektrometrie.

STUDY OBJECTIVE: Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has recently been widely used in diagnostic microbiological laboratories. It is a cheap and rapid method for the identification of bacteria and micromycetes. Apart from this purpose, it is also used for the detection of antibiotic resistance mechanisms. It has the potential to be extended for other purposes in microbiology. The aim of this study was to validate MALDI-TOF MS for the identification of mycobacteria. MATERIAL AND METHODS: Thirty isolates of Mycobacterium spp. isolated in the Laboratory of Mycobacteriology of the Plzen University Hospital were included in the study. The isolates were identified to the species level using biochemical tests, gene probes, and sequencing of the gene encoding 16S rRNA. The identification by MALDI-TOF MS was performed with the use of silica beads. Strain identification by sequencing the gene encoding 16S rRNA was considered as the reference method. RESULTS: MALDI-TOF MS correctly identified all isolates of Mycobacterium spp. (score range 1.461 - 2.168). The species identified were Mycobacterium tuberculosis (n= 5), Mycobacterium kansasii (n=5), Mycobacterium avium (n=6), Mycobacterium intracelullare (n=3), Mycobacterium xenopi (n=3), Mycobacterium gordonae (n=1), Mycobacterium abscessus (n=1), Mycobacterium kumamotonense (n=2), Mycobacterium mantenii (n=1), Mycobacterium lentiflavum (n=1), Mycobacterium fortuitum (n=1), and Mycobacterium scrofulaceum (n=1). CONCLUSION: MALDI-TOF MS is a suitable tool for the routine identification of Mycobacterium spp. in laboratories using this method for the conventional identification of microbes.

Carbapenemase-producing Klebsiella pneumoniae in the Czech Republic in 2011.

Carbapenemase-producing Enterobacteriaceae and Pseudomonas spp. are increasingly reported in many countries all over the world. Due to the resistance of those bacteria to almost all antibiotics (e.g.beta-lactams, aminoglycosides, fluoroquinolones),treatment options are seriously limited. In the Czech Republic, the incidence of carbapenemase-producing Enterobacteriaceae seems to be low, restricted to only three cases detected between 2009 and 2010.Here, we describe molecular typing of 15 carbapenemase-producing Klebsiella pneumoniae isolates identified in the Czech Republic during 2011. Five VIM-1-producing isolates belonging to sequence type (ST)11 and one VIM-4-producing isolate of ST1029 have been detected. blaVIM-1 and blaVIM-4 as a part of class 1 integrons were chromosomally located or carried by a plasmid belonging to A/C replicon type (blaVIM-4). KPC-3-producing isolates of ST512, recovered from six patients, caused an outbreak. Three more isolates producing KPC-2 enzyme belonged to ST258. Both blaKPCgenes were part of the Tn4401a transposon carried on plasmids of the pKpQIL type. The isolates were resistant to all antibiotics tested except colistin and/or gentamicin.Four of these 15 strains were recovered from patients repatriated to the Czech Republic from Greece and Italy. This is the first report of outbreaks caused by carbapenemase-producing Enterobacteriaceae in the Czech Republic.

Polyclonal Spread of Fosfomycin Resistance among Carbapenemase-Producing Members of the Enterobacterales in the Czech Republic.

Fosfomycin (FOS) has been recently reintroduced into clinical practice, but its effectiveness against multidrug-resistant (MDR) Enterobacterales is reduced due to the emergence of FOS resistance. The copresence of carbapenemases and FOS resistance could drastically limit antibiotic treatment. The aims of this study were (i) to investigate fosfomycin susceptibility profiles among carbapenem-resistant Enterobacterales (CRE) in the Czech Republic, (ii) to characterize the genetic environment of fosA genes among the collection, and (iii) to evaluate the presence of amino acid mutations in proteins involved in FOS resistance mechanisms. During the period from December 2018 to February 2022, 293 CRE isolates were collected from different hospitals in the Czech Republic. FOS MICs were assessed by the agar dilution method (ADM), FosA and FosC2 production was detected by the sodium phosphonoformate (PPF) test, and the presence of fosA-like genes was confirmed by PCR. Whole-genome sequencing was conducted with an Illumina NovaSeq 6000 system on selected strains, and the effect of point mutations in the FOS pathway was predicted using PROVEAN. Of these strains, 29% showed low susceptibility to fosfomycin (MIC, ≥16 µg/mL) by ADM. An NDM-producing Escherichia coli sequence type 648 (ST648) strain harbored a fosA10 gene on an IncK plasmid, while a VIM-producing Citrobacter freundii ST673 strain harbored a new fosA7 variant, designated fosA7.9. Analysis of mutations in the FOS pathway revealed several deleterious mutations occurring in GlpT, UhpT, UhpC, CyaA, and GlpR. Results regarding single substitutions in amino acid sequences highlighted a relationship between ST and specific mutations and an enhanced predisposition for certain STs to develop resistance. This study highlights the occurrence of several FOS resistance mechanisms in different clones spreading in the Czech Republic. IMPORTANCE Antimicrobial resistance (AMR) currently represents a concern for human health, and the reintroduction of antibiotics such as fosfomycin into clinical practice can provide further option in treatment of multidrug-resistant (MDR) bacterial infections. However, there is a global increase of fosfomycin-resistant bacteria, reducing its effectiveness. Considering this increase, it is crucial to monitor the spread of fosfomycin resistance in MDR bacteria in clinical settings and to investigate the resistance mechanism at the molecular level. Our study reports a large variety of fosfomycin resistance mechanisms among carbapenemase-producing Enterobacterales (CRE) in the Czech Republic. Our study summarizes the main achievements of our research on the use of molecular technologies, such as next-generation sequencing (NGS), to describe the heterogeneous mechanisms that reduce fosfomycin effectiveness in CRE. The results suggest that a program for widespread monitoring of fosfomycin resistance and epidemiology fosfomycin-resistant organisms can aide timely implementation of countermeasures to maintain the effectiveness of fosfomycin.

NDM-1 producing Acinetobacter baumannii isolated from a patient repatriated to the Czech Republic from Egypt, July 2011.

We describe the isolation of an NDM-1-producing Acinetobacter baumannii in a Czech patient repatriated in July 2011 from Egypt. The infection spread to another patient on the same ward. Both isolates showed the same resistance pattern and were susceptible only to colistin. They had an identical PFGE pattern and belonged to the same sequence type ST 1. Sequencing of the blaNDM gene identified the NDM-1 variant of the carbapenemase, surrounded by two copies of insertion sequence ISAba125.

[Interpretation of the susceptibility test results in enterobacteria producing 3rd- and 4th-generation cephalosporin- or carbapenem-hydrolyzing beta-lactamases]. / Interpretace výsledku vysetrení citlivosti k beta-laktamim u enterobakterií produkujících beta-laktamázy hydrolyzující cefalosporiny III. a IV. generace a karbapenemy.

The interpretation of the susceptibility of Gram-negative rods to beta-lactams is currently under discussion in CLSI and EUCAST--two authorities on determination of clinical breakpoints. This article summarizes the current knowledge about clinical breakpoints in enterobacteria and proposes guidance for clinical microbiology laboratories in the Czech Republic.

[Mobile genetic elements in the epidemiology of bacterial resistance to antibiotics]. / Mobilní genetické elementy v epidemiologii rezistence bakterií k antibiotikum.

The study of the role of mobile elements and mobilization of resistance genes is crucial for understanding the epidemiology of antibiotic resistance. This review summarizes recent data on the insertion sequences, transposons, integrons and plasmids that are involved in the mobilization of bacterial antibiotic resistance genes.

[The use of molecular genetics techniques in clinical microbiology--final report from the workshop of the Molecular Microbiology Working Group TIDE]. / Aplikace metod molekulární genetiky v klinické mikrobiologii: zpráva z jednání Pracovní skupiny molekulárni mikrobiologie--TIDE.

In the last decade, there has been a rapid development in the use of molecular genetics methods in clinical microbiology. Novel technologies bring new knowledge and approaches to various disciplines of microbiology--taxonomy, identification of microbes, clinical diagnosis, epidemiology of infectious diseases and antibiotic resistance. This article summarizes the conclusions from the workshop of the Molecular Microbiology Working Group TIDE held during the Second Annual Meeting of the Society for Medical Microbiology of the J. E. Purkyne Czech Medical Association.

First identification of metallo-beta-lactamase-producing Pseudomonas aeruginosa in the Czech Republic.

Since 2005, invasive isolates of Pseudomonas aeruginosa have been collected in the Czech Republic as part of the European Antibiotic Resistance Surveillance System (EARSS). Forty-eight microbiology laboratories throughout the country including approximately 81% of the population provide consecutive isolates from blood and cerebrospinal fluid. Surprisingly, no metallo-beta-lactamase (MBL) was found in 1,259 invasive isolates tested over the past three years until the detection of two MBL-producing strains in mid-2008. Both strains were isolated from patients hospitalised in one regional hospital. The MBL was identified as IMP-7, which had been seen previously in Canada, Japan, Malaysia and Slovakia.

Antimicrobial susceptibility and mechanisms of resistance of Greek Clostridium difficile clinical isolates.

OBJECTIVES: This study examined the antimicrobial susceptibility and resistance mechanisms of Clostridium difficile recovered in Greek hospitals during 2012-2015. METHODS: C. difficile isolates (n=88) were collected from clinically-confirmed C. difficile infection from symptomatic patients in 10 Greek hospitals. Minimum inhibitory concentrations (MICs) of various antimicrobial agents were determined by Etest. Isolates were typed by multilocus sequence typing (MLST). Toxin and resistance genes were detected by PCR. Chromosomal mutations in gyrA, gyrB and rpoB were identified by PCR and sequencing. The genetic environment of resistance genes was characterised by Illumina sequencing. RESULTS: The 88 C. difficile isolates comprised 27 sequence types (STs), with ST37 (n=26) and ST11 (n=21) being the most prevalent. All isolates were susceptible to vancomycin and metronidazole, with variable resistance rates to other antimicrobials. Of the 88 isolates, 45.5% were multidrug-resistant and the majority belonged to ST11 and ST37. The presence of chromosomal mutations in gyrA, gyrB and rpoB was mainly observed in high-risk clones such as ST11 and ST37. The antimicrobial resistance genes ermB, mefA, msrA and tetM were identified at different prevalences and combinations. Additionally, cfrB and cfrC were identified for the first time in Greece and were carried by a Tn6218 transposon and a novel plasmid, respectively. CONCLUSIONS: To our knowledge, this is the first study examining the resistance profiles and respective mechanisms of C. difficile recovered in Greek hospitals. Gut commensals such as C. difficile may serve as hubs for further transfer of antimicrobial resistance genes.

[Carbapenem resistance in enterobacteria]. / Rezistence enterobakterii ke karbapenemum.

Carbapenems are the drugs of choice in the treatment of serious infections caused by multiresistant Gram-negative bacteria. Clinically and epidemiologically, resistance to these beta-lactams poses the highest risk. In enterobacteria, two common mechanisms can cause the resistance to carbapenems: (1) hydrolysis of carbapenems by beta-lactamases and (2) outer membrane impermeability. The focus is on types of carbapenemases described so far, detection methods, epidemiology of and therapeutic options for infections caused by carbapenemase-producing enterobacteria. Attention is also paid to the mechanisms involved in the control of outer membrane permeability, i.e., reduced porin expression or changes in the porin structure that prevent carbapenems from entering the Gram-negative bacterial periplasmic space.

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

BACKGROUND: The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. AIMS: The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. SOURCES: Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. CONTENT: Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. IMPLICATIONS: Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner.

[Clinically important beta-lactamases of gram-negative bacteria: AmpC]. / Klinicky významné beta-laktamázy gramnegativních bakterii: AmpC.

Beta-lactamases are the most common cause of beta-lactam resistance in Gram-negative bacteria. With third-generation and fourth-generation cephalosporins being introduced into practice, new beta-lactamases have evolved, able to hydrolyze these antibiotics. AmpC-type beta lactamases (cephalosporinases) are serine enzymes with the ability to hydrolyze penicillins, monobactams and cephalosporins of all generations, including cephamycins. Over the last two decades, transferable plasmid-mediated class C beta-lactamases have been reported with increasing frequency. The genes for resistance to other groups of antibiotics are usually carried on the same mobile element as the AmpC genes. A reliable method for AmpC detection in routine diagnosis has not been available yet. The issue of AmpC-type beta lactamases is summarized, including their identification, interpretation of susceptibility test results and recommended treatment of infection caused by AmpC producers.

[Clinically important beta-lactamases of gram-negative bacteria: extended-spectrum beta-lactamases (ESBL)]. / Klinicky významné beta-laktamázy gramnegativních bakterií: sirokospektré beta-laktamázy (ESBL).

Beta-lactamases are the commonest cause of a resistance of gram-negative bacteria to beta-lactam antimicrobial agents. The introduction of the third- and fourth-generation cephalosporins into clinical practise is the reason of an evolution of new beta-lactamases being able to hydrolyze these antibiotics. Extended-spectrum beta-lactamases (ESBLs) are the major group of these enzymes. Most of the ESBLs are mainly structural mutants of penicillinases TEM-1, TEM-2 and SHV-1. For several reasons, ESBL-producing isolates should, by definition, be reported as resistant to all penicillins, cephalosporins and monolactams. Due to seriously reduced antibiotic choice for infections caused by ESBL-producing bacteria, ESBLs pose a serious clinical problem. This review will focus on the characterization and identification of ESBLs, interpretation of sensitivity testing results of ESBL producing bacteria and an appropriate treatment of infections caused by ESBL-producers.

First description in Europe of the emergence of Enterococcus faecium ST117 carrying both vanA and vanB genes, isolated in Greece.

OBJECTIVES: An Enterococcus faecium isolate (Efa-125) carrying both the vanA and vanB genes was recovered from a patient with bacteraemia treated in a Greek hospital. Since this is the first description in Europe of E. faecium carrying both vanA and vanB genes, the isolate was further studied. METHODS: Susceptibility to several antibiotics was determined using the VITEK®2 automated system. The isolate was typed by multilocus sequence typing (MLST). To define the genetic units of the vanA and vanB genes, the plasmid content of Efa-125 was analysed by pulsed-field gel electrophoresis (PFGE) of total DNA digested with S1 nuclease followed by hybridisation with digoxigenin-labelled vanA and vanB probes. In addition, plasmids and chromosomes were sequenced using the Illumina MiSeq platform. RESULTS: E. faecium Efa-125 belonged to ST117 and expressed resistance both to vancomycin and teicoplanin, with minimum inhibitory concentrations (MICs) for both of 256mg/L. The vanA gene was carried on a 29 320-bp plasmid exhibiting high similarity to pA6981 previously characterised from Enterococcus gallinarum A6981, whereas vanB was part of a Tn1549-like transposon integrated into the chromosome. Expression of the VanA phenotype was correlated with the presence of intact vanZ and vanS genes. CONCLUSIONS: This is the first detection in Greece of vanA-vanB genotype/VanA phenotype E. faecium and indicates an evolving epidemiology of vancomycin-resistant enterococci.

Emergence of sequence type 11 Klebsiella pneumoniae coproducing NDM-1 and VIM-1 metallo-ß-lactamases in a Greek hospital.

Sequence type 11 Klebsiella pneumoniae, coproducing NDM-1 and VIM-1 metallo-ß-lactamases, were isolated in a Greek hospital. blaNDM-1 was part of a Tn125 derivative, located on an ~90-kb plasmid similar to the NDM-1-encoding plasmid pB-3002cz. blaVIM-1 was located in an In-e541-like integron, carried on a multireplicon (IncA/C and IncR) plasmid of ~180kb.