The objective of this study was to perform molecular surveillance for assessing the spread of carbapenemase-producing in Czech hospitals. One hundred thirty-six carbapenemase-producing isolates were recovered from 22 hospitals located throughout the country. Sequence type 357 (ST357) dominated ( = 120) among carbapenemase producers. One hundred seventeen isolates produced IMP-type (IMP-7 [ = 116] and IMP-1 [ = 1]) metallo-β-lactamases (MβLs), 15 produced the VIM-2 MβL, and the remaining isolates expressed the GES-5 enzyme. The -like genes were located in three main integron types, with In-p110-like being the most prevalent ( = 115). The two other IMP-encoding integrons (In1392 and In1393) have not been described previously. -carrying integrons included In59-like, In56, and a novel element (In1391). was carried by In717. Sequencing data showed that In-p110-like was associated with a Tn-like transposon inserted in genomic island LESGI-3 in the chromosome. The other integrons were also integrated into the chromosome. These findings indicated the clonal spread of ST357 , carrying the IMP-7-encoding integron In-p110, in Czech hospitals. Additionally, the sporadic emergence of producing different carbapenemase types, associated with divergent or novel integrons, punctuated the ongoing evolution of these bacteria.
Strains of genus Citrobacter (152 isolates from 1950 to 1988 deposited in the Czech National Collection of Type Cultures, Prague) were re-classified using biological and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) methods. One-hundred thirty-six strains (ca. 90 %) were identified to the species level using the biological method with evaluation by Farmer matrix. MALDI-TOF MS exhibited better identification capability, the data being more compact; the method was unambiguously successful in typing 145 (95 %) strains. Comparison of the results of identification by the two methods revealed differences (for 12 samples) in identified species which, considering all biochemical and/or MS characteristics, could be attributed to the natural variability of strains and close relation of the misidentified species (all of them belonged to the Citrobacter freundii complex). Taking into account all the above data, both methods can be considered reliable; however, the MALDI-TOF MS exhibits higher accuracy, efficiency, and rapidity.
PurposeThe aim of this study was to characterize serogroup 19 isolates resistant to macrolides and/or penicillin found among pneumococci recovered from cases of invasive and respiratory tract disease in the Czech Republic in 2014.MethodsPneumococcal isolates of serotypes 19A (n=26) and 19F (n=10) that were non-susceptible to penicillin and/or macrolides and had been collected in 2014 were analysed using multi-locus sequence typing (MLST). Four isolates representing the major clones were subjected to whole-genome sequencing (WGS).ResultsThe penicillin-susceptible macrolide-resistant isolates of serotype 19A were mainly associated with sequence type (ST) 416 belonging to clonal complex (CC) 199, and the penicillin-resistant isolates were of serotype 19F belonging to ST1464 (CC 320). WGS revealed the presence of pilus 1, in association with pilus 2, in serotype19F isolates belonging to CC 320. Another adhesin, pneumococcal serine-rich protein (PsrP), was only present in serotype 19A isolates of ST416. Analysis of the penicillin-binding proteins (PBPs) of serotype 19F penicillin-resistant isolates (ST1464 and ST271) performed on PBP1a, 2b and 2x identified a large number of mutations in comparison to the reference strain, R6. Both isolates contained a unique PBP profile; however, they were highly similar to PBP sequences of the Taiwan19F-14 reference strain. The Pbp2b sequences of both 19F isolates showed the lowest similarity to those of the Taiwan19F-14 strain (91 % similarity), while they were also found to be distantly related to each other (94 % similarity).ConclusionsWGS revealed specific virulence factors in antibiotic-resistant pneumococcal clones that spread rapidly in the post-vaccine era in the Czech Republic.
A total of 2,683 nonrepetitive Escherichia coli isolates were collected from microbiological laboratories covering all regions of the Czech Republic, during April 2011. Antimicrobial susceptibility patterns of E. coli were assessed. All 38 cefotaxime-resistant (CTX-R) isolates were found to be extended-spectrum β-lactamase (ESBL)-positive by the double-disc synergy test. Thirty-two of those isolates produced enzymes of CTX-M-1 family, five of CTX-M-9 family, and one isolate both CTX-M types. Genotyping by multilocus sequence typing classified all ESBL-producing isolates into 13 sequence types (STs). ST131 was the most prevalent and was exclusively correlated with E. coli belonging to the more-virulent phylogroup B2. blaCTX-M-15 and blaCTX-M-9-like genes were mainly carried by plasmids belonging to the IncF group, while replicon I1 was predominant among CTX-M-1-encoding plasmids. Additionally, 63% of the ESBL-producing isolates were also resistant to ciprofloxacin. Sequence analysis of quinolone resistance-determining regions of gyrA and parC revealed the presence of amino acid substitutions in 22 out of 23 ciprofloxacin-resistant isolates. The acc(6')-Ib-cr and qnrB1 plasmid-mediated quinolone resistance genes were also detected in some of the isolates. This is the first report on the emergence and spread of CTX-M-producing E. coli in the community of the Czech Republic, indicating the high prevalence of ST131 clone among CTX-M producers.
We studied a novel taxon of the genus Acinetobacter , which comprised six strains collected in Czechia, Germany, Indonesia and Turkey between 2015 and 2021. The organisms were isolated from environmental soil, water samples and cow faeces. Their genome sizes varied between 3.3 and 3.5 Mb, with a G+C content of 40.4–40.8 mol%. Based on genus-wide core genome analysis, the taxon formed a distinct clade, with Acinetobacter gandensis being the phylogenetically closest related species. The intrataxon genomic average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values reached 95.3–97.4% and 62.5–77.8 %, respectively, whereas its ANIb/dDDH values against the known Acinetobacter type strains were ≤82.7 %/≤25.7 %. Cluster analysis of whole-cell MALDI-TOF mass spectra corroborated the distinctness and cohesiveness of the taxon. The novel strains were non-glucose-oxidizing, non-haemolytic and non-proteolytic, growing at up to 37–41 °C but not at 44 °C and utilizing 8–10 of the 36 carbon sources tested. Growth on glutarate, tricarballylate and at 37 °C combined with the inability to assimilate 4-aminobutyrate and d-malate differentiated them from all validly named Acinetobacter species. The inspection of genome sequences in the NCBI database revealed the existence of numerous strains conspecific with this group, which were collected from pig faeces and environmental samples in China. We conclude that the taxon represents an ecologically and geographically widespread species, for which we propose the name Acinetobacter amyesii sp. nov., with ANC 5579T (= CCM 9242T=CCUG 76274T=CNCTC 8134T) as the type strain.
We investigated a taxonomically novel group of the genus Acinetobacter , which included five strains isolated from soil and water samples collected in preserved forest areas in Czechia between 2013 and 2021. The whole-genome sequences of the strains were 3.1–3.2 Mb in size, with G+C contents of 38.0–38.2 mol%. Core genome-based phylogenetic analysis showed that they formed a compact and deeply branched clade within the genus. The genomic average nucleotide identity based on blast/digital DNA–DNA hybridization values for the novel strains were 99.2–99.6 %/95.2–98.4 %, whereas those between the novel strains and the type strains of the known Acinetobacter species reached <78 %/<24 %. The results of the genus-wide analysis of whole-cell MALDI-TOF mass spectra supported the sharp distinctness of the group. The five strains were non-glucose acidifying, nonhaemolytic, nonproteolytic and growing at 28 °C, but not at 32 °C; they assimilated acetate, benzoate, ethanol, l-histidine, 4-hydroxybenzoate, dl-lactate and malonate but not 4-aminobutyrate, l-aspartate or 2,3-butanediol; this phenotype is unique among the known Acinetobacter species. We conclude that the five strains represent a novel environmental species, for which the name Acinetobacter silvestris sp. nov. is proposed, with the type strain ANC 4999T (=CCM 9207T=CCUG 75877T=CNCTC 8124T).
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