BackgroundBy using whole genome sequence data we aimed at describing a population snapshot of carbapenemase-producing K. pneumoniae isolated from hospitalized patients in Germany between 2008 and 2014.MethodsWe selected a representative subset of 107 carbapenemase-producing K. pneumoniae clinical isolates possessing the four most prevalent carbapenemase types in Germany (KPC-2, KPC-3, OXA-48, NDM-1). Isolates were processed via illumina NGS. Data were analysed using different SNP-based mapping and de-novo assembly approaches. Relevant information was extracted from NGS data (antibiotic resistance determinants, wzi gene/cps type, virulence genes). NGS data from the present study were also compared with 238 genome data from two previous international studies on K. pneumoniae.ResultsNGS-based analyses revealed a preferred prevalence of KPC-2-producing ST258 and KPC-3-producing ST512 isolates. OXA-48, being the most prevalent carbapenemase type in Germany, was associated with various K. pneumoniae strain types; most of them possessing IncL/M plasmid replicons suggesting a preferred dissemination of blaOXA-48 via this well-known plasmid type. Clusters ST15, ST147, ST258, and ST512 demonstrated an intermingled subset structure consisting of German and other European K. pneumoniae isolates. ST23 being the most frequent MLST type in Asia was found only once in Germany. This latter isolate contained an almost complete set of virulence genes and a K1 capsule suggesting occurrence of a hypervirulent ST23 strain producing OXA-48 in Germany.ConclusionsOur study results suggest prevalence of “classical” K. pneumonaie strain types associated with widely distributed carbapenemase genes such as ST258/KPC-2 or ST512/KPC-3 also in Germany. The finding of a supposed hypervirulent and OXA-48-producing ST23 K. pneumoniae isolates outside Asia is highly worrisome and requires intense molecular surveillance.Electronic supplementary materialThe online version of this article (10.1186/s13756-018-0352-y) contains supplementary material, which is available to authorized users.
Objectives: The recommended technique for colistin susceptibility testing by both EUCAST and CLSI is broth microdilution (BMD). However, many routine laboratories still use other methods such as gradient strips or semi-automated systems. The objective of this study was to compare six of the most widespread commercial products for colistin susceptibility testing in Europe with in-house prepared BMD. Methods: A collection of 325 carbapenemase-producing Enterobacterales was tested for colistin susceptibility with three semi-automated systems (Vitek 2, BD Phoenix, MicroScan WalkAway), one gradient-strip test (Etest®) and two commercial BMD products (MICRONAUT-S, TREK Sensititre). BMD, in-house prepared according to ISO standard 20776-1, served as reference. Results: The MICRONAUT-S BMD performed best with only one false-resistant (major error, ME) and four false-susceptible (very major error, VME) results while the TREK BMD performed poorer with 16 ME and seven VME. The semi-automated systems Vitek 2 and Phoenix performed poorly with 31 and 26 VME, respectively. The WalkAway semi-automated system showed 16 and 13 false results, depending on the inoculation method. The Etest® showed six ME and 10 VME. Conclusions: This study shows that colistin susceptibility testing remains a challenging task for laboratories. It emphasizes the need for selecting the most reliable test method to advocate proper treatment and shows that critical evaluation and precautious usage of colistin susceptibility testing results is constantly required.
U rinary tract infections (UTIs) are common and affect mainly women; it has been estimated that more than 50% of all women will contract a urinary tract infection at least once in their lifetimes (1, 2). Although many bacterial species may cause urinary tract infections in patients predisposed by anatomical or functional abnormalities, indwelling catheters or neurological disorders, only a subset of species/strains may cause urinary tract infections in patients without predisposing conditions (3). These organisms/strains have mostly been found to express virulence factors allowing them to adhere to the uroepithelium (4-6), to invade cells of the urinary tract (7, 8), or to degrade urea (9, 10), a component highly prevalent in urine.In staphylococci, most species do not cause urinary tract infections in the absence of predisposing factors, and Staphylococcus saprophyticus is the only species that typically causes these infections (11).We have described a number of virulence factors, such as urease (12, 13), the adhesins Aas (14) and SdrI (15,16), and the lipase Ssp (17, 18). A role for Ssp and SdrI in virulence was described in a murine model of UTI (19). Since similar proteins are present in many other staphylococci (20, 21), a factor distinguishing S. saprophyticus from other staphylococci has been sought. Interestingly, of all sequenced staphylococcal genomes, only that of S. saprophyticus possesses a gene coding for D-serine-deaminase (22), an enzyme that catabolizes D-serine to pyruvate and ammonia. This enzyme is also present in uropathogenic Escherichia coli (UPEC) but not in enterohemorrhagic E. coli (23). The amino acid D-serine is relatively prevalent in urine (3 to 115 g/ml) (24, 25) and is toxic or bacteriostatic to many bacteria, probably by inhibiting the synthesis of pantothenic acid (26)(27)(28)(29). Therefore, the presence of D-serine may be used as a cue for the presence within the urinary tract of uropathogenic microorganisms. Strains of E. coli expressing the deaminase DsdA can utilize this amino acid as a carbon and energy source (30). The operon dsdCXA comprises the regulator gene, dsdC, a specific transporter gene, dsdX, and the deaminase gene, dsdA (31, 32). In S. saprophyticus, such an operon does not exist. The dsdA gene apparently is under the control of its own promoter, and genes in the vicinity are not related to serine catabolism. Three genes in the genome are annotated as coding for D-serine/D-alanine/glycine transporters but are not located next to the dsdA gene. In UPEC, mutation of the deaminase somewhat surprisingly led to enhanced colonization of bladders and kidneys in experimentally infected mice and caused the mutants to be hyperflagellated and more motile (23). However, only wild-type (WT) UPEC strains possessing dsdA were able to grow on minimal medium containing D-serine as the sole carbon and energy source (23, 30). Later, it was shown that the high intracellular concentration of D-serine caused expression of the hypercolonization phenotype (23, 47). Regulation seems to...
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