Risk of death in Klebsiella pneumoniae bloodstream infections is associated with specific phylogenetic lineages.

BACKGROUND: Klebsiella pneumoniae species complex (KpSC) bloodstream infections (BSIs) are associated with considerable morbidity and mortality, particularly in elderly and multimorbid patients. Multidrug-resistant (MDR) strains have been associated with poorer outcome. However, the clinical impact of KpSC phylogenetic lineages on BSI outcome is unclear. METHODS: In an 18-month nationwide Norwegian prospective study of KpSC BSI episodes in adults, we used whole-genome sequencing to describe the molecular epidemiology of KpSC, and multivariable Cox regression analysis including clinical data to determine adjusted hazard ratios (aHR) for death associated with specific genomic lineages. FINDINGS: We included 1078 BSI episodes and 1082 bacterial isolates from 1055 patients. The overall 30-day case-fatality rate (CFR) was 12.5%. Median patient age was 73.4, 61.7% of patients were male. Median Charlson comorbidity score was 3. Klebsiella pneumoniae sensu stricto (Kp) (79.3%, n = 858/1082) and K. variicola (15.7%, n = 170/1082) were the dominating phylogroups. Global MDR-associated Kp clonal groups (CGs) were prevalent (25.0%, n = 270/1082) but 78.9% (n = 213/270) were not MDR, and 53.7% (n = 145/270) were community acquired. The major findings were increased risk for death within 30 days in monomicrobial BSIs caused by K. variicola (CFR 16.9%, n = 21; aHR 1.86, CI 1.10-3.17, p = 0.02), and global MDR-associated Kp CGs (CFR 17.0%, n = 36; aHR 1.52, CI 0.98-2.38, p = 0.06) compared to Kp CGs not associated with MDR (CFR 10.1%, n = 46). CONCLUSION: Bacterial traits, beyond antimicrobial resistance, have a major impact on the clinical outcome of KpSC BSIs. The global spread of MDR-associated Kp CGs is driven by other mechanisms than antibiotic selection alone. Further insights into virulence determinants, and their association with phylogenetic lineages are needed to better understand the epidemiology of KpSC infection and clinical outcome.

Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study.

BACKGROUND: The clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology. METHODS: This was a longitudinal, E coli population, genomic, cohort study that sampled isolates from 22 512 E coli bloodstream infections included in the Norwegian surveillance programme on resistant microbes (NORM) from 2002 to 2017. 15 of 22 laboratories were able to share their isolates, and the first 22·5% of isolates from each year were requested. We used whole genome sequencing to infer the population structure (PopPUNK), and we investigated the clade composition of the dominant multidrug resistant clonal complex (CC)131 using genetic markers previously reported for sequence type (ST)131, effective population size (BEAST), and presence of determinants of antimicrobial resistance (ARIBA, PointFinder, and ResFinder databases) over time. We compared these features between the 2002-10 and 2011-17 time periods. We also compared our results with those of a longitudinal study from the UK done between 2001 and 2011. FINDINGS: Of the 3500 isolates requested from the participating laboratories, 3397 (97·1%) were received, of which 3254 (95·8%) were successfully sequenced and included in the analysis. A significant increase in the number of multidrug resistant CC131 isolates from 71 (5·6%) of 1277 in 2002-10 to 207 (10·5%) of 1977 in 2011-17 (p<0·0001), was the largest clonal expansion. CC131 was the most common clone in extended-spectrum ß-lactamase (ESBL)-positive isolates (75 [58·6%] of 128) and fluoroquinolone non-susceptible isolates (148 [39·2%] of 378). Within CC131, clade A increased in prevalence from 2002, whereas the global multidrug resistant clade C2 was not observed until 2007. Multiple de-novo acquisitions of both blaCTX-M ESBL-encoding genes in clades A and C1 and gain of phenotypic fluoroquinolone non-susceptibility across the clade A phylogeny were observed. We estimated that exponential increases in the effective population sizes of clades A, C1, and C2 occurred in the mid-2000s, and in clade B a decade earlier. The rate of increase in the estimated effective population size of clade A (Ne=3147) was nearly ten-times that of C2 (Ne=345), with clade A over-represented in Norwegian CC131 isolates (75 [27·0%] of 278) compared with the UK study (8 [5·4%] of 147 isolates). INTERPRETATION: The early and sustained establishment of predominantly antimicrobial susceptible CC131 clade A isolates, relative to multidrug resistant clade C2 isolates, suggests that resistance is not necessary for clonal success. However, even in the low antibiotic use setting of Norway, resistance to important antimicrobial classes has rapidly been selected for in CC131 clade A isolates. This study shows the importance of genomic surveillance in uncovering the complex ecology underlying multidrug resistance dissemination and competition, which have implications for the design of strategies and interventions to control the spread of high-risk multidrug resistant clones. FUNDING: Trond Mohn Foundation, European Research Council, Marie Sklodowska-Curie Actions, and the Wellcome Trust.

An Estimate of the Burden of Fungal Disease in Norway.

The aim of this study was to examine the burden of fungal disease in Norway, contributing to a worldwide effort to improve awareness of the needs for better diagnosis and treatment of such infections. We used national registers and actual data from the Departments of Microbiology from 2015 and estimated the incidence and/or prevalence of superficial, allergic and invasive fungal disease using published reports on specific populations at risk. One in 6 Norwegians suffered from fungal disease: Superficial skin infections (14.3%: 745,600) and recurrent vulvovaginal candidiasis in fertile women (6%: 43,123) were estimated to be the most frequent infections. Allergic fungal lung disease was estimated in 17,755 patients (341/100,000). Pneumocystis jirovecii was diagnosed in 262 patients (5/100,000), invasive candidiasis in 400 patients (7.7/100,000), invasive aspergillosis in 278 patients (5.3/100,000) and mucormycosis in 7 patients (0.1/100,000). Particular fungal infections from certain geographic areas were not observed. Overall, 1.79% of the population was estimated to be affected by serious fungal infections in Norway in 2015. Even though estimates for invasive infections are small, the gravity of such infections combined with expected demographic changes in the future emphasizes the need for better epidemiological data.

A long-term low-frequency hospital outbreak of KPC-producing Klebsiella pneumoniae involving Intergenus plasmid diffusion and a persisting environmental reservoir.

BACKGROUND: To study the molecular characteristics of a long-term, low frequency outbreak of bla KPC-2 in a low prevalence setting involving the hospital environment. METHODOLOGY/PRINCIPAL FINDINGS: KPC-producing bacteria were screened by selective chromogenic agar and Real-Time PCR. The presence of antibiotic resistance genes was ascribed by PCRs and subsequent sequencing, and the KPC-producing isolates were phylogenetically typed using PFGE and multi-locus sequence typing. Bla KPC-2-plasmids were identified and analysed by S1-nuclease-PFGE hybridization and PCR based replicon typing. A ∼97 kb IncFII plasmid was seen to carry bla KPC-2 in all of the clinical isolates, in one of the isolates recovered from screened patients (1/136), and in the Klebsiella pneumoniae and Enterobacter asburiae isolates recovered from the environment (sinks) in one intensive care unit. The K. pneumoniae strain ST258 was identified in 6 out of 7 patients. An intergenus spread to E. asburiae and an interspecies spread to two different K. pneumoniae clones (ST27 and ST461) of the bla KPC-2 plasmid was discovered. K. pneumoniae ST258 and genetically related E. asburiae strains were found in isolates of both human and environmental origins. CONCLUSIONS/SIGNIFICANCE: We document a clonal transmission of the K. pneumoniae ST258 strain, and an intergenus plasmid diffusion of the IncFII plasmid carrying bla KPC-2 in this outbreak. A major reservoir in the patient population could not be unveiled. However, the identification of a persisting environmental reservoir of strains with molecular determinants linked to human isolates, suggests a possible role of the environment in the maintenance of this long-term outbreak.

A nationwide study of mechanisms conferring reduced susceptibility to extended-spectrum cephalosporins in clinical Escherichia coli and Klebsiella spp. isolates.

BACKGROUND: Enterobacteriaceae exerting a high level of extended-spectrum cephalosporin (ESC) resistance have increased significantly in Norway in the last decade. Various mechanisms acting alone or in concert mediate variable levels of ESC resistance and pose great challenges in the implementation of screening strategies and treatment. This study was undertaken to document the prevalence of underlying mechanisms conferring resistance to ESCs in a nationwide collection of clinical isolates of Escherichia coli, Klebsiella pneumoniae, and Klebsiella oxytoca, before the increase in extended-spectrum ß-lactamase (ESBL)-producing strains. METHODS: Consecutive E. coli (n = 2213), K. pneumoniae (n = 303), and K. oxytoca (n = 66) isolates from 23 Norwegian diagnostic laboratories were collected and examined for reduced susceptibility to ESCs. Isolates displaying minimum inhibitory concentrations (MICs) of > 2 mg/l by Etest to cefpodoxime and/or MICs > 1 mg/l to any other ESCs were included (n = 54; 35 E. coli, 11 K. pneumoniae, and 8 K. oxytoca). Isoelectric focusing for the detection of ß-lactamases, and polymerase chain reactions (PCRs) with subsequent sequencing for detection of ESBLs CTX-M, TEM, and SHV, plasmid-mediated AmpC, OXA subtypes, and alterations of porin genes ompC and ompF, and quantitative reverse transcriptase (RT)-PCR for investigation of enhanced expression of chromosomal ampC were performed. RESULTS: Eight E. coli isolates (0.4%) were ESBL producers and 20 (1.0%) were hyperproducers of the chromosomal ampC. Three K. pneumoniae isolates (1.1%) were ESBL producers, and all K. oxytoca isolates (n = 8; 13.6%) were OXY-hyperproducers. No definite mechanisms for reduced susceptibility to ESCs could be inferred for 7 E. coli (0.4%) and 8 K. pneumoniae (3.0%) isolates. CONCLUSIONS: This study identified chromosomal AmpC-hyperproducing E. coli and OXY-hyperproducing K. oxytoca in addition to ESBLs in Enterobacteriaceae as major mechanisms of resistance to ESC, and documented their rates of prevalence for the first time in Norway.

[Young girl with abscesses in the face]. / Ung jente med abscesser i ansiktet.

Skin and soft tissue infections are most often caused by Staphylococcus aureus or various species of streptococcus. This case report summarizes the clinical features, diagnosis, treatment and clinical outcome of a facial infection presenting as multiple abscesses in a young and otherwise healthy girl. Nocardia brasiliensis was recovered from abscess aspiration, and treatment failure was eventually recognized for the recommended empirical antibiotic treatment, broad-spectrum antibiotics and surgery.

Emergence of OXA-carbapenemase- and 16S rRNA methylase-producing international clones of Acinetobacter baumannii in Norway.

This study was designed to investigate the molecular epidemiology and antibiotic-resistance characteristics of 11 carbapenem-resistant clinical isolates of Acinetobacter baumannii obtained in Norway between 2004 and 2009. Interestingly, all the isolates were linked with recent hospitalization outside Norway. The epidemiological status was investigated by multilocus sequence typing (MLST), multiplex PCR assays for major international clones, typing of blaOXA-51-like variants and PFGE. The genotypic-resistance characteristics, including the occurrence of OXA-carbapenemase-encoding and 16S rRNA methylase-encoding genes and class 1 integrons, were investigated by PCR assays and sequencing. Seven isolates were found to harbour blaOXA-66 and belong to MLST clonal complexes (CCs) CC2P (Pasteur Institute scheme) and CC92B (Bartual scheme), and international clone II. One isolate harboured blaOXA-69, and belonged to CC1P, CC109B and international clone I. Two isolates belonged to sequence group 9, probably a subgroup of international clone I, and one isolate belonged to sequence group 4, a proposed novel international clone. All isolates contained an acquired OXA-carbapenemase-encoding gene: blaOXA-23-like (n=9), blaOXA-24-like (n=1) and blaOXA-58-like (n=1). Four isolates with high-level aminoglycoside-resistance contained the 16S rRNA methylase-encoding armA gene. Class 1 integrons with six different variable regions were detected. Sequence analysis of gene cassettes identified four aminoglycoside (aacA4, aac(6')-Im, aadA1 and aacC1), two chloramphenicol (catB8 and cm1A5), one ß-lactamase (blaOXA-20) and one rifampicin (arr-2) resistance gene in various combinations. In conclusion, the occurrence of A. baumannii isolates producing OXA carbapenemase and 16S rRNA methylase in Norway was related to the worldwide distribution of international clones I and II, and the emergence of novel international clones.

Molecular characterization of CTX-M-15-producing clinical isolates of Escherichia coli reveals the spread of multidrug-resistant ST131 (O25:H4) and ST964 (O102:H6) strains in Norway.

Nationwide, CTX-M-producing clinical Escherichia coli isolates from the Norwegian ESBL study in 2003 (n=45) were characterized on strain and plasmid levels. Bla(CTX-M) allele typing, characterization of the genetic environment, phylogenetic groups, pulsed field gel electrophoresis (PFGE), serotyping and multilocus sequence typing were performed. Plasmid analysis included S1-nuclease-PFGE, polymerase chain reaction-based replicon typing, plasmid transfer and multidrug resistance profiling. Bla(CTX-M-15) (n=23; 51%) and bla(CTX-M-14) (n=11; 24%) were the major alleles of which 18 (78%) and 6 (55%), respectively, were linked to ISEcp1. Thirty-two isolates were of phylogenetic groups B2 and D. Isolates were of 29 different XbaI-PFGE-types including six regional clusters. Twenty-three different O:H serotypes were found, dominated by O25:H4 (n=9, 20%) and O102:H6 (n=9, 20%). Nineteen different STs were identified, where ST131 (n=9, 20%) and ST964 (n=7, 16%) were dominant. Bla(CTX-M) was found on > or =100 kb plasmids (39/45) of 10 different replicons dominated by IncFII (n=39, 87%), FIB (n=20, 44%) and FIA (n=19, 42%). Thirty-nine isolates (87%) displayed co-resistance to other classes of antibiotics. A transferable CTX-M phenotype was observed in 9/14 isolates. This study reveals that the majority of CTX-M-15-expressing strains in Norway are part of the global spread of multidrug-resistant ST131 and ST-complex 405, associated with ISEcp1 on transferrable IncFII plasmids.

Emergence of clonally related Klebsiella pneumoniae isolates of sequence type 258 producing plasmid-mediated KPC carbapenemase in Norway and Sweden.

BACKGROUND: The class A carbapenemase KPC has disseminated rapidly worldwide, challenging the treatment of Gram-negative infections. This report describes the first KPC-producing Klebsiella pneumoniae isolates identified in Norway (n=6) and the second isolate from Sweden. METHODS: Antimicrobial susceptibility profiles were determined using Etest. PCR and sequencing were used to determine the bla(KPC) variant, the surrounding genetic structure and the presence of AmpC and extended-spectrum beta-lactamase genes. PFGE and multilocus sequence typing (MLST) were used for epidemiological comparisons. Localization of bla(KPC) was investigated by S1 nuclease digestion, followed by PFGE and Southern blot hybridization. RESULTS: All isolates expressed a multidrug-resistant phenotype with some variability in the carbapenem susceptibility profile. The Norwegian isolates carried bla(KPC-2), while the Swedish isolate carried bla(KPC-3). All isolates carried TEM-1, but were negative for bla(CTX-M) and bla(AmpC) genes. SHV-11 and SHV-12 were detected in the Norwegian isolates, while the Swedish isolate carried only SHV-11. Isolates from four patients were associated with import from Greece (n=3) and Israel. The other isolates were probably associated with local transmissions. PFGE and MLST showed that the isolates were clonally related, with three isolates displaying ST258, a single locus variant of ST11 previously associated with the clonal spread of CTX-M-15-producing K. pneumoniae in Hungary. In all isolates, bla(KPC) was located on plasmids as part of isoform a of Tn4401. CONCLUSIONS: The emergence of KPC-producing isolates of K. pneumoniae in Norway and Sweden is associated with multiple import events and probable local transmission of a successful multiresistant ST258 clone, closely related to the CTX-M-15-producing ST11 clone previously described in Hungary.

Effects of phenotype and genotype on methods for detection of extended-spectrum-beta-lactamase-producing clinical isolates of Escherichia coli and Klebsiella pneumoniae in Norway.

Consecutive clinical isolates of Escherichia coli (n = 87) and Klebsiella pneumoniae (n = 25) with reduced susceptibilities to oxyimino-cephalosporins (MICs > 1 mg/liter) from 18 Norwegian laboratories during March through October 2003 were examined for bla(TEM/SHV/CTX-M) extended-spectrum-beta-lactamase (ESBL) genes, oxyimino-cephalosporin MIC profiles, ESBL phenotypes (determined by the ESBL Etest and the combined disk and double-disk synergy [DDS] methods), and susceptibility to non-beta-lactam antibiotics. Multidrug-resistant CTX-M-15-like (n = 23) and CTX-M-9-like (n = 15) ESBLs dominated among the 50 ESBL-positive E. coli isolates. SHV-5-like (n = 9) and SHV-2-like (n = 4) ESBLs were the most prevalent in 19 ESBL-positive K. pneumoniae isolates. Discrepant ESBL phenotype test results were observed for one major (CTX-M-9) and several minor (TEM-128 and SHV-2/-28) ESBL groups and in SHV-1/-11-hyperproducing isolates. Negative or borderline ESBL results were observed when low-MIC oxyimino-cephalosporin substrates were used to detect clavulanic acid (CLA) synergy. CLA synergy was detected by the ESBL Etest and the DDS method but not by the combined disk method in SHV-1/-11-hyperproducing strains. The DDS method revealed unexplained CLA synergy in combination with aztreonam and cefpirome in three E. coli strains. The relatively high proportion of ESBL-producing E. coli organisms with a low ceftazidime MIC in Norway emphasizes that cefpodoxime alone or both cefotaxime and ceftazidime should be used as substrates for ESBL detection.