Characterization of Carbapenemase producing Acinetobacter baumannii Isolates from Danish Patients 2014-2021 - Detection of a New International Clone - IC11

The aim of this study was to characterize carbapenemase producing Acinetobacter baumannii isolates from Danish patients using whole genome sequencing (WGS). Furthermore, we compared typing- and epidemiological data for further investigation of the spread and origin of the carbapenemase producing A. baumannii isolates. From January 1^st 2014 through September 30^th 2021, 141 carbapenemase producing A. baumannii isolates, received at the national reference laboratory at Statens Serum Institut, were investigated using WGS. MLST and cgMLST data, obtained by the SeqSphere+ software, were linked to data related to source of isolation, patient age and gender, hospital admission and travel history. The majority of the carbapenemase producing A. baumannii isolates were from males (n=100, 71%). The majority of patients (n=88, 63%) had travelled outside Scandinavia before admission to a Danish hospital. The most prevalent carbapenemase gene was bla_OXA-23 (n=124). Isolates belonging to the dominating international clone IC2 accounted for 78% of all isolates. A new international ST164/OXA-91 clone, proposedly named IC11, was recognized and described. cgMLST analysis revealed 17 clusters, reflecting both sporadic travel to similar geographical areas as well as confirmed outbreaks in Danish hospitals. The occurrence of carbapenemase producing A. baumannii in Denmark was still low; however, isolates belonging to major international clones with a high potential to spread within hospitals, mainly IC2, dominated. OXA-23 was by far the most prevalent carbapenemase detected. Sporadic and travel related introductions to Danish hospitals, but also intra-hospital transmission could be confirmed, emphasizing the need for continuing vigilance.

Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019

Background

Carbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark.

Aim

Molecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019.

Methods

For the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST).

Results

In total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark.

Conclusion

Import of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.

LRE-Finder, a Web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences

OBJECTIVES

In enterococci, resistance to linezolid is often mediated by mutations in the V domain of the 23S rRNA gene (G2576T or G2505A). Furthermore, four genes [optrA, cfr, cfr(B) and poxtA] encode linezolid resistance in enterococci. We aimed to develop a Web tool for detection of the two mutations and the four genes encoding linezolid resistance in enterococci from whole-genome sequence data.

METHODS

LRE-Finder (where LRE stands for linezolid-resistant enterococci) detected the fraction of Ts in position 2576 and the fraction of As in position 2505 of the 23S rRNA and the cfr, cfr(B), optrA and poxtA genes by aligning raw sequencing reads (fastq format) with k-mer alignment. For evaluation, fastq files from 21 LRE isolates were submitted to LRE-Finder. As negative controls, fastq files from 1473 non-LRE isolates were submitted to LRE-Finder. The MICs of linezolid were determined for the 21 LRE isolates. As LRE-negative controls, 26 VRE isolates were additionally selected for linezolid MIC determination.

RESULTS

LRE-Finder was validated and showed 100% concordance with phenotypic susceptibility testing. A cut-off of 10% mutations in position 2576 and/or position 2505 was set in LRE-Finder for predicting a linezolid resistance phenotype. This cut-off allows for detection of a single mutated 23S allele in both Enterococcus faecalis and Enterococcus faecium, while ignoring low-level sequencing noise.

CONCLUSIONS

A Web tool for detection of the 23S rRNA mutations (G2576T and G2505A) and the optrA, cfr, cfr(B) and poxtA genes from whole-genome sequences from enterococci is now available online.

Molecular characterization of Danish ESBL/AmpC-producing Klebsiella pneumoniae from bloodstream infections, 2018

OBJECTIVES

The aim of the study was to molecularly characterize third-generation cephalosporin-resistant Klebsiella pneumoniae isolated from bloodstream infections in Denmark in 2018 using whole-genome sequencing (WGS) data, and to compare these isolates to the most common clones detected in 2006 and 2008.

METHODS

Sixty-two extended-spectrum beta-lactamase (ESBL)/AmpC-producing K. pneumoniae isolates from Danish blood cultures from 2018 were analysed using WGS to obtain multilocus sequence typing (MLST), core genome MLST (cgMLST), resistance profile and phylogeny. These were compared to the most common ESBL K. pneumoniae clones detected in 2006 and 2008.

RESULTS

The most common ESBL clone was ST15 CTX-M-15, the DHA-1 enzyme was the most common in AmpC isolates, and the OXA-48-like group was the most common carbapenemase. Thirty-nine different sequence types (STs) were found, with the most frequent being ST14, ST15 and ST37, accounting for 24% of the isolates. The isolates were subdivided into 55 complex types (CTs) of which 49 were singletons, with the most frequent being ST14-CT2080. Two of the CTX-M-15-producing isolates from 2018 belonged to the ST15-CT105/CT3078 clone, which was first detected in 2006.

CONCLUSIONS

The ESBL/AmpC K. pneumoniae isolates detected in Danish blood cultures belonged to many different types. No dominant clones were circulating in Danish hospitals, but the ST15-CT105/CT3078 CTX-M-15 K. pneumoniae clone was seen 13 years after its first detection.

Investigation of possible clonal transmission of carbapenemase-producing Klebsiella pneumoniae complex member isolates in Denmark using core genome MLST and National Patient Registry Data

OBJECTIVES

The aim of this study was to identify clonally-related carbapenemase-producing Klebsiella pneumoniae complex members that could be involved in outbreaks among hospitalized patients in Denmark, and to identify possible epidemiological links.

METHODS

From January 2014 to June 2018, 103 isolates belonging to the K. pneumoniae complex were collected from 102 patients. From the whole-genome sequencing (WGS) data, presence of genes encoding carbapenemase and multilocal sequence typing (MLST) data were extracted. Core genome MLST (cgMLST) cluster analysis was performed. Using data from the Danish National Patient Registry (DNPR) and reported travel history, presumptive outbreaks were investigated for possible epidemiological links.

RESULTS

The most common detected carbapenemase gene was bla_OXA-48, followed by bla_NDM-1. The 103 K. pneumoniae complex isolates belonged to 47 sequence types (STs) and cgMLST subdivided the isolates into 80 different complex types. cgMLST identified 13 clusters with 2-4 isolates per cluster. For five of the 13 clusters, a direct link (the patients stayed at the same ward on the same day) could be detected between at least some of the patients. In two clusters, the patients resided simultaneously at the same hospital, but not the same ward. A possible link (same ward within 1-13 days) was detected for the patients in one cluster. For five clusters detected by cgMLST, no epidemiological link could be detected using data from DNPR.

CONCLUSION

In this study, cgMLST combined with patient hospital admission data and travel information was found to be a reliable and detailed approach to detect possible clonal transmission of carbapenemase-producing K. pneumoniae complex members.

WGS-based surveillance of third-generation cephalosporin-resistant Escherichia coli from bloodstream infections in Denmark

Objectives

To evaluate a genome-based surveillance of all Danish third-generation cephalosporin-resistant Escherichia coli (3GC-R Ec ) from bloodstream infections between 2014 and 2015, focusing on horizontally transferable resistance mechanisms.

Methods

A collection of 552 3GC-R Ec isolates were whole-genome sequenced and characterized by using the batch uploader from the Center for Genomic Epidemiology (CGE) and automatically analysed using the CGE tools according to resistance profile, MLST, serotype and fimH subtype. Additionally, the phylogenetic relationship of the isolates was analysed by SNP analysis.

Results

The majority of the 552 isolates were ESBL producers (89%), with bla CTX-M-15 being the most prevalent (50%) gene, followed by bla CTX-M-14 (14%), bla CTX-M-27 (11%) and bla CTX-M-101 (5%). ST131 was detected in 50% of the E. coli isolates, with the remaining isolates belonging to 73 other STs, including globally disseminated STs (e.g. ST10, ST38, ST58, ST69 and ST410). Five of the bloodstream isolates were carbapenemase producers, carrying bla OXA-181 (3) and bla OXA-48 (2). Phylogenetic analysis revealed 15 possible national outbreaks during the 2 year period, one caused by a novel ST131/ bla CTX-M-101 clone, here observed for the first time in Denmark. Additionally, the analysis revealed three individual cases with possible persistence of closely related clones collected more than 13 months apart.

Conclusions

Continuous WGS-based national surveillance of 3GC-R Ec , in combination with more detailed epidemiological information, can improve the ability to follow the population dynamics of 3GC-R Ec , thus allowing for the detection of potential outbreaks and the effects of changing treatment regimens in the future.

[Staphylococcus aureus endocarditis in Denmark 1982-1991. Clinical picture, complications and antibiotic therapy in non-drug addicts]

The central S. aureus surveillance in Denmark made it possible to analyze the clinical features of S. aureus endocarditis in a nation-wide population of non-drug addicts. Almost all cases of bacteraemia with S. aureus are reported to the Staphylococcus laboratory, Copenhagen. The medical records were reviewed in cases from 1982 to 1991 in which the diagnosis of endocarditis was reported or suspected. Two hundred and sixty patients fulfilled the diagnostic criteria. In 83 patients the diagnosis of endocarditis was not suspected clinically. The overall mortality rate among those patients whose disease was diagnosed clinically was 46% and significantly associated with late congestive heart failure, age and involvement of the central nervous system. A more frequent use of echocardiography as a screening method seems essential to improve the prognosis of patients with S. aureus endocarditis. Involvement of the CNS constitutes a relative indication for early valve replacement.

Clinical features of Staphylococcus aureus endocarditis: a 10-year experience in Denmark

BACKGROUND

Both morbidity and mortality resulting from Staphylococcus aureus endocarditis are known to be high, and the incidence of this disease seems to increase. The Statens Serum Institut, Copenhagen, Denmark, made it possible for us to analyze the clinical features of S aureus endocarditis in a nation-wide population of non-drug addicts.

METHODS

Almost all Danish cases of bacteremia due to S aureus are reported to the Staphylococcus laboratory, Statens Serum Institut. The medical records were reviewed in cases reported from 1982 to 1991 in which the diagnosis of endocarditis was reported or suspected.

RESULTS

A total of 260 patients, 145 males and 115 females, fulfilled the diagnostic criteria. The median age was 67.5 years. In 83 patients, the diagnosis of endocarditis was not suspected clinically. The overall mortality rate among those patients whose disease was diagnosed clinically was 46%. Among the subset of patients who received medical therapy only and appropriate antistaphylococcal treatment, mortality was significantly associated with late congestive heart failure, age, and involvement of the central nervous system.

CONCLUSIONS

A raised awareness of the paucity of clinical findings and a more frequent use of echocardiography as a screening method seem essential to improve the prognosis of patients with S aureus endocarditis. Involvement of the central nervous system constitutes a relative indication of early valve replacement.

A study of 47 bacteremic Staphylococcus aureus endocarditis cases: 23 with native valves treated surgically and 24 with prosthetic valves

A retrospective review of medical records from the Staphylococcus Laboratory, Copenhagen, 1982-1991, was carried out at the Department of Clinical Microbiology, Statens Serum Institut, 1994-1995, to investigate the clinical features and outcome of two subgroups of bacteremic Staphylococcus aureus endocarditis cases in non-drug addicts: patients with prosthetic valve endocarditis (PVE) and patients with native valve endocarditis treated surgically. Twenty-four cases of PVE were included. Six cases were early (within 60 days of valve implantation) and 18 were late. The overall in-hospital mortality was 42%. Surgical treatment resulted in a non-significantly lower mortality as compared with medical treatment alone (0% vs 50%, p = 0.19). Medical treatment of aortic and mitral valve endocarditis resulted in similar mortality rates (44% and 50%, respectively). Twenty-three cases of native valve infective endocarditis had the valve replaced surgically. The in-hospital mortality was 22%, which was significantly lower as compared with medical therapy (69%, p < 0.0001). The treatment changed significantly during the study period: 6 of 112 patients (5%) were treated surgically in the first half of the period (1982-1986) compared to 17 of 124 patients (14%) in the second half (1987-1991, p = 0.049). Severe congestive heart failure was the main indication for cardiac surgery in 21 patients. In conclusion, a shift towards a more aggressive surgical approach has taken place in the 10-year period. This development should be strengthened in the future as surgical intervention may improve survival in patients with infective endocarditis caused by S. aureus whether the infected valve is prosthetic or native.

Neurologic manifestations in Staphylococcus aureus endocarditis: a review of 260 bacteremic cases in nondrug addicts

PURPOSE

To investigate the neurologic manifestations of infective endocarditis caused by Staphylococcus aureus in a population of nondrug addicts with special emphasis on the clinical presentation, epidemiology, and mortality.

PATIENTS AND METHODS

During the period from 1982 to 1991 a total of 8,514 cases of bacteremia with S aureus were reported to the Staphylococcus Laboratory, Copenhagen, Denmark. The medical records of cases of suspected infective endocarditis were retrospectively reviewed and classified according to the new diagnostic criteria for endocarditis proposed by Durack.

RESULTS

A total of 260 cases from 63 hospitals fulfilled the diagnostic criteria. Overall, 91 patients (35%) experienced neurologic manifestations. Sixty-one presented with neurologic symptoms, whereas 30 patients developed neurologic complications at various intervals (median: 10 days) after the debut of the disease. The most frequent neurologic manifestation was unilateral hemiparesis, which occurred in 41 patients (45%). Forty-two percent of the females had neurologic manifestations compared to only 30% of the males (P = 0.06). Cases with native mitral valve infection had a significantly higher frequency of neurologic manifestations compared with all other valvular involvement (44% versus 29%, P = 0.02) but the frequency of neurologic complications was only nonsignificantly higher in those patients with native mitral valve infection than in those patients with native aortic valve infection (44% versus 31%, P = 0.10). Only two of the patients with tricuspid valve infection and none of those with congenital heart disorder experienced neurologic manifestations. A neurologic manifestation occurred in 22 (35%) of the 63 episodes in which vegetations were detected on the echocardiograms, compared with 17 (26%) of the 65 episodes without vegetations (P = 0.38). The mortality was 74% in patients with major neurologic manifestations and 56% in patients without neurologic manifestations (P = 0.008). In patients with neurologic complications the mortality was significantly higher among those treated with antibiotics alone as compared with those treated surgically (65 of 81, 80% versus 2 of 10, 20%; P = 0.0003).

CONCLUSIONS

In a population of nondrug addicts with infective endocarditis caused by S aureus the following main conclusions can be drawn: neurologic manifestations occur with a higher frequency in patients with native mitral valve infection. The presence of vegetations on echocardiograms is not a risk factor for developing neurologic complications but this conclusion is based on the results of transthoracic echocardiograms performed in only one half of the patients. The majority of the neurologic manifestations occur on presentation or shortly thereafter and the risk of recurrent embolism is low. Mortality is increased in patients with neurologic manifestations. A neurologic event per se may constitute an indication for surgical treatment.

Dicloxacillin and flucloxacillin: pharmacokinetics, protein binding and serum bactericidal titers in healthy subjects after oral administration

The pharmacokinetics of dicloxacillin and flucloxacillin were studied in 12 healthy volunteers after oral administration. The participants received a single dose of either dicloxacillin (0.5 g, 0.75 g or 1.0 g) or flucloxacillin (0.75 g) in a cross-over fashion. Antibiotic concentrations were determined in serum and urine by bioassay and followed for 8 and 24 h, respectively. The three dicloxacillin dosages showed no significant differences for the serum elimination half-lives (t1/2 beta, median: 72 min). Comparing 0.75 g flucloxacillin with the same dose of dicloxacillin, no significant differences between the values of Cmax, t1/2 beta and AUC were found. Protein binding as determined by ultrafiltration in pooled serum was 94.7-96.2% for flucloxacillin and 96.4-97.2% for dicloxacillin. The serum bactericidal titers were similar for the two drugs. In conclusion, dicloxacillin and flucloxacillin showed similar pharmacokinetic behavior after 0.75 g doses in human volunteers.

No difference in enterotoxin production among Staphylococcus aureus strains isolated from blood compared with strains isolated from healthy carriers

The production of enterotoxin A, B, C and D by 196 Staphylococcus aureus strains isolated from blood cultures and 95 strains from nasal carriers was investigated. Half of the bacteraemia strains were from patients who died with or because of their infection, the other half from patients who survived. The nasal strains were selected to match the bacteraemia strains regarding phage types. Overall, 30.6% of the bacteraemia strains and 40.0% of the nasal strains produced enterotoxins; enterotoxins B and C were the toxins produced most frequently in both groups. A similar incidence and pattern of enterotoxin production was found among the bacteraemia strains of S. aureus regardless of acquisition of the infection, the portal of entry, presence or absence of endocarditis and outcome of the infection. Thus, the concept that the enterotoxins play an important role in staphylococcal infections, apart from the diseases caused by the toxins per se such as food poisoning and toxic shock syndrome, cannot be substantiated by the results of the present study.

Antibiotic usage in an intensive care unit in a Danish university hospital

We report a study of antimicrobial use in patients admitted to the Intensive Care Unit (ICU) in a Danish university hospital during the course of 1 year. Of 615 patients admitted, 434 (71%) received antibiotics, 220 (36%) for infections and 222 (36%) for prophylaxis. Therapy for suspected infection accounted for 67% of the total consumption of antibiotics and prophylaxis for 33%. Ampicillin was the drug most frequently used; 43% of the patients treated for infection received this drug. One hundred and thirty-one patients (60%) were treated for suspected lower respiratory tract infection. Relevant microbiological specimens were obtained from 120 (92%) of these patients and a possible pathogen was isolated in 92 patients (77%, 92/120). Staphylococcus aureus and Streptococcus pneumoniae were each isolated in almost a quarter of the patients, and Enterobacteriaceae in 53%. However, many of the pathogens isolated were of no clinical relevance and merely reflected a state of colonization. Most treatments were given during the first few days following admission. Of 220 patients receiving antibiotics for an infection, 87% were treated on day 1, but only 34% (14 of 41) on day 11. The frequent use of laboratory investigations combined with good communication between clinicians and microbiologists probably resulted in rapid cessation of unnecessary therapy. Fifty-two per cent of the antibiotics given for prophylaxis were administered later than the first postoperative day. This study emphasizes the need for consultation between surgeons and clinical microbiologists to supervise postoperative antibiotic use.

The effect of antistaphylococcal agents used alone and in combinations on the survival of Staphylococcus aureus ingested by human polymorphonuclear leukocytes

The intracellular activity of a number of drugs used alone and in combinations against Staphylococcus aureus was investigated using an experimental design which imitates the clinical situation and differs from other published methods. Staphylococci were phagocytosed by human polymorphonuclear leukocytes and, after differential centrifugation and washing, the granulocytes were incubated in 90% pooled human serum with clinically relevant drug concentrations. When exposed to antibiotics, more than 40-50% of the bacteria were located intracellularly. Fusidic acid (100 mg/l), erythromycin (20 mg/l), and clindamycin (20 mg/l) all had a bacteriostatic effect during the first 6 h of incubation, whereas rifampicin (1 and 5 mg/l), vancomycin (5 and 20 mg/l), and ciprofloxacin (2 mg/l) all acted bactericidally with decreases in viable counts between 1.3-1.9 log10. The greatest bactericidal effect was achieved with tobramycin (10 mg/l), which produced more than a 4 log10 decrease in viable counts at 6 h. Combinations of fusidic acid with other antibiotics all resulted in killing kinetics different from those achieved with the drugs used individually. The bactericidal effect of ciprofloxacin and dicloxacillin during the first 6 h was abolished when these drugs were combined with fusidic acid. However, at 24 h no significant difference was found between the effect of dicloxacillin alone versus the combination dicloxacillin and fusidic acid. The combination of fusidic acid and rifampicin resulted in a killing identical to that achieved with rifampicin used alone during the first 6 h, but at 24 h the killing by the combination was significantly greater. The bactericidal effect of the combination dicloxacillin (20 mg/l) and tobramycin (10 mg/l) equalled that obtained with tobramycin (10 mg/l) used alone. Rifampicin (5 mg/l) antagonized the bactericidal effect of ciprofloxacin (2 mg/l) during the first 6 h of incubation but at 24 h the combination acted synergistically. The results obtained are partly in agreement and partly in conflict with previous results.

In-vitro activity of ciprofloxacin combined with either fusidic acid or rifampicin against Staphylococcus aureus

Killing kinetic experiments were performed with ciprofloxacin, fusidic acid and rifampicin alone and with ciprofloxacin combined with either fusidic acid or rifampicin against ten strains of Staphylococcus aureus. The strains were all clinical isolates and two strains were methicillin-resistant. The antibiotic concentrations tested were in the range obtainable in the serum with recommended doses. The early bactericidal effect of ciprofloxacin alone was substantially greater than that of fusidic acid or rifampicin; thus the extent of killing after 6 h exposure to these antibiotics was 3.4 log10, 0.8 log10 and 0.6 log10, respectively. Fusidic acid as well as rifampicin antagonized the bactericidal activity of ciprofloxacin. Each combination killed 2 log10 cfu less than ciprofloxacin alone. For each combination the mean decrease in the number of organisms was comparable to that achieved with fusidic acid or rifampicin used alone.