Concomitant carriage of KPC-producing and non-KPC-producing Klebsiella pneumoniae ST512 within a single patient.

BACKGROUND: KPC-producing Klebsiella pneumoniae of clonal group 258 are prominent in healthcare settings in many regions of the world. The blaKPC gene is mostly carried by a multireplicon IncFIIk-IncFI plasmid suspected to be highly compatible and stable in this genetic background. Here, we analysed the genetic diversity of an ST512 K. pneumoniae population in a single patient. METHODS: Twelve K. pneumoniae isolates (n = 5 from urine samples and n = 7 from rectal swabs) were recovered from one patient over a 2 month period. Antimicrobial susceptibility testing, plasmid extraction and WGS were performed on all isolates. The first K. pneumoniae isolate, D1, was used as a reference for phylogenetic analysis. RESULTS: Antimicrobial susceptibility testing, plasmid analysis and WGS revealed concomitant carriage of carbapenem-resistant and carbapenem-susceptible K. pneumoniae isolates of ST512, with the absence of the entire blaKPC-carrying plasmid in the susceptible population. Furthermore, 14 other genetic events occurred within the genome, including 3 chromosomal deletions (of 71 kb, 33 kb and 11 bp), 2 different insertions of ISKpn26 and 9 SNPs. Interestingly, most of the events occurred in the same chromosomal region that has been deleted independently several times, probably after homologous recombination involving 259 bp repeated sequences. CONCLUSIONS: Our study revealed (to the best of our knowledge) the first case of in vivo blaKPC-carrying plasmid curing and a wide within-patient genetic diversity of a single K. pneumoniae ST512 clone over a short period of carriage. This within-patient diversity must be taken into account when characterizing transmission chains using WGS during nosocomial outbreaks.

Molecular characterization of plasmid-encoded Tripoli MBL 1 (TMB-1) in Enterobacteriaceae.

Objectives: Available commercial tools (molecular methods or immunochromatographic assays) usually allow the detection of the five most prevalent carbapenemases (KPC, NDM, VIM, IMP and OXA-48-like), but miss minor carbapenemases. Here, we characterize two enterobacterial isolates with reduced susceptibility to carbapenems and negative for the most commonly encountered carbapenemase genes. Methods: Enterobacter hormaechei and Citrobacter freundii isolates were recovered from a bile sample and rectal screening, respectively. Both isolates were investigated by WGS. Resistance genes were detected using ResFinder. The blaTMB-1-harbouring plasmid was reconstructed using CLC genomic workbench 10.0 and was annotated using the RAST tool. Transfer frequency was determined by conjugation experiments using the laboratory strain Escherichia coli J53. Results: The two isolates were resistant to broad-spectrum cephalosporins and carbapenems. WGS revealed the presence of blaTMB-1, which has previously only been described in non-fermenters. blaTMB-1 was located within an ISKpn19-based composite class 1 transposon. Comparative genomics revealed that this structure was carried on a conjugative IncN-type plasmid within an integration hotspot. Conjugation experiments revealed high transfer frequencies of ∼1 × 10-3. Conclusions: To the best of our knowledge, this study corresponds to the first report of Tripoli MBL 1-producing Enterobacteriaceae. Despite always being described as likely to be chromosomally located in non-fermenters, the blaTMB-1 gene is now found to be carried by a conjugative plasmid among Enterobacteriaceae, raising concern about the possible dissemination of this carbapenemase. The blaTMB-1 gene should now be suspected when PCRs targeting the main carbapenemases remain negative.

Fungal complications after Candida preservation fluid contamination in liver transplant recipients.

Donor-derived fungal infections can be associated with severe complications in transplant recipients. Donor-derived candidiasis has been described in kidney transplant recipients where contamination of the preservation fluid (PF) was a commonly proposed source. In liver transplantation, these fungal infections have been less explored. The aim of this study was therefore to determine the incidence and clinical relevance of Candida contamination of preservation fluid in the context of liver transplantation. A 5-year (2008-2012) retrospective multicentre study involving six French liver transplantation centers was performed to determine the incidence of Candida PF contamination. Postoperative clinical features, outcomes in recipients, and risk factors for Candida-related complications of liver transplantation were studied. Candida sp. was isolated from 28 of 2107 preservation fluid samples (1.33%). Candida albicans was the most common yeast (n = 18, 64%). Twenty-two recipients (78.5%) received antifungal therapy (echinocandins in 68%) for 7-37 days. Eight patients developed yeast-related complications (28.6%) including hepatic artery aneurysms (n = 6) and Candida peritonitis (n = 2). The 1-year mortality rate among patients after a yeast-related complication was 62.5%. The incidence of Candida PF contamination was low, but was associated with dramatic postoperative complications and high mortality. Close radiological follow-up may enable early recognition of the arterial complications associated with PF contamination by Candida.

Campylobacter coli enteritis associated with Campylobacter fetus bacteremia, spondylodiscitis, and late CIED-related endocarditis, a case report.

Campylobacter sp. is widely considered a leading causative agent of bacterial food-borne gastrointestinal illness. Discitis and endocarditis caused by Campylobacter spp. are extremely rare. We describe the case of a 94-year-old man who was admitted for recent lumbar pain, diarrhea, and fever. C. fetus and C. coli were identified by MALDI-TOF from blood and stool samples respectively. MRI of the spine showed L5-S1 discitis. Patient was treated with 6 weeks of amoxicillin with clinical and microbiological response until cardiac implantable electronic device (CIED) related endocarditis occurred four weeks after the end of the antibiotic treatment. He was treated with another 6 weeks amoxicillin regimen, with a favorable outcome after a 6-month follow-up. Enteric infection with Campylobacter spp. in a debilitated patient should raise the possibility of a co-infection with another more invasive species such as C. fetus, leading to systemic invasion. In case of Campylobacter fetus bacteremia, a search for endocarditis and spondylodiscitis is recommended even in the absence of specific clinical signs.

Fungal infections after liver transplantation: outcomes and risk factors revisited in the MELD era.

Antifungal prophylaxis is recommended in high-risk patients, but risk criteria remain unclear and the predictive value of Model of End-Stage Liver Disease (MELD) score is unknown. In a retrospective, single-center analysis of 667 liver transplants, potential risk factors for fungal infection were assessed, including MELD score. Antifungal prophylaxis was administered in 198 patients (29.4%). During follow-up (mean 43.6 ± 29.6 months), 263 patients (39.4%) developed ≥ 1 episode of fungal infection, and 187 (28.0%) patients developed a probable or proven invasive fungal infection requiring systemic antifungal treatment. Patients receiving antifungal prophylaxis had a lower incidence of fungal infection (29.8% vs. 43.5% without prophylaxis, p < 0.001) and invasive fungal infection (17.7% vs. 32.4%, p < 0.001). One-yr patient survival was 91%, 85% and 69%, respectively, in patients with no fungal infection, fungal colonization and treated invasive fungal infection (p < 0.001); graft survival was 88%, 85% and 66% (p < 0.001). Multivariate analysis indicated that MELD score of 20-30 or ≥ 30 was associated with a 2.0-fold or 4.3-fold increase in relative risk of fungal infection, respectively, and a 2.1-fold or 3.1-fold increase in relative risk of invasive fungal infection. In conclusion, liver transplant patients with a MELD score ≥ 20, and particularly patients with a score ≥ 30, are candidates for antifungal prophylaxis.

Outcomes associated with amphotericin B lipid complex (ABLC) prophylaxis in high-risk liver transplant patients.

Antifungal prophylaxis with liposomal amphotericin B in high-risk liver transplant recipients is recommended, but experience with amphotericin B lipid complex (ABLC, Abelcet(®)) in this setting is limited. Data from 615 liver transplants performed during 1999-2005 were analyzed retrospectively. High-risk patients (n = 146) received a mean cumulative ABLC dose of 955 ± 609 mg (mean duration of 23.3 ± 11.9 days). Low-risk patients (n = 469) received no prophylaxis. During a mean follow-up of 43.8 ± 29.2 months, fungal infections occurred in 32.2% of ABLC patients versus 43.5% of non-prophylaxis patients (P = 0.015). The overall rate of invasive fungal infection was 12.3% in the ABLC group versus 15.6% in the non-prophylaxis patients (P = 0.34). Any Candida infection (ABLC 29.5%, non-prophylaxis 41.2%, P = 0.011), probable or proven invasive Candida infection requiring systemic antifungal treatment (ABLC 18.5%, non-prophylaxis 32.4%, P = 0.001) and invasive abdominal candidiasis during the first 3 months (ABLC 4.1%, non-prophylaxis 9.2%, P = 0.049) were significantly less frequent in the ABLC group. There was no significant difference between groups in the incidence of Aspergillus infections. The ABLC group showed no evidence of nephrotoxicity. In conclusion, the marked and significant differences in infection rates and requirement for systemic treatment in this large population suggest that targeted use of low-dose ABLC therapy to high-risk patients is a valid prophylactic strategy following liver transplantation.

Evaluation of CHROMagar™ LIN-R for the Screening of Linezolid Resistant Staphylococci from Positive Blood Cultures and Nasal Swab Screening Samples.

The increasing number of nosocomial pathogens with resistances towards last resort antibiotics, like linezolid for gram positive bacteria, leads to a pressing need for screening and, consequently, suitable screening media. Some national guidelines on infection prevention (e.g., in Germany) have already recommended screening for linezolid-resistant bacteria, despite an accurate screening medium that was not available yet. In this study, we analyzed the performance and reliability of the first commercial chromogenic medium, CHOMagar™ LIN-R, for screening of linezolid-resistant gram-positive isolates. Thirty-four pure bacterial cultures, 18 positive blood cultures, and 358 nasal swab screening samples were tested. This medium efficiently detected linezolid-resistant S. epidermidis isolates from pure bacterial cultures and from positive blood cultures with a high sensitivity (100%) and specificity (100%). Among the 358 nasal swab screening samples prospectively tested, 10.9% were cultured with linezolid-resistant isolates (mostly S. epidermidis). Of note, slight growth was observed for 7.5% samples with linezolid-susceptible isolates of S. epidermidis (n = 1), S. aureus (n = 1), Enterococcus faecalis (n = 4), Lactobacillus spp. (n = 3), gram negatives (n = 18). Moreover, few Candida spp. also cultured on this medium (1.4%).

Susceptibility Testing Is Key for the Success of Cefiderocol Treatment: A Retrospective Cohort Study.

Cefiderocol is a novel siderophore cephalosporin, which has proven in vitro activity against carbapenem-resistant (CR) Gram-negative pathogens and stability towards all carbapenemases. The aim of this study was to describe the first cases of prescriptions and the efficacy of cefiderocol for compassionate use in the 2 months following its access in France. We performed a national retrospective study of all patients who received at least one dose of cefiderocol from 2 November 2018 to 5 November 2019. We collected clinical characteristics and outcome through a standard questionnaire. Bacterial isolates from 12 patients were centralized and analyzed in the French National Reference Center for Antimicrobial Resistance, and sequenced using Illumina technology. Finally, 13 patients from 7 French university hospitals were included in the study. The main type of infection treated by cefiderocol was respiratory tract infections (RTI, n = 10). The targeted bacteria were Pseudomonas aeruginosa (n = 12), including carbapenemase-producing P. aeruginosa (n = 9), Acinetobacter baumannii (n = 2), Klebsiella pneumoniae (n = 1), and Enterobacter hormaechei (n = 1). Overall, of the 12 patients whose samples were analyzed, 5 P. aeruginosa strains were not susceptible to cefiderocol (4 categorized as resistant and 1 as intermediate) according to Clinical and Laboratory Standards Institute (CLSI) breakpoints. If considering susceptible strains, the cure rate was 6/7, while being 0/5 among not-susceptible strains. This study underlines the necessity to test strains in adequate conditions.

Streptococcus sinensis: an emerging agent of infective endocarditis.

The identification by conventional methods of viridans streptococcal species, which are rarely encountered clinically, requires confirmation by genomic methods. We characterized a strain of Streptococcus sinensis responsible for infective endocarditis by sequencing both the 16S rRNA and the manganese-dependent superoxide dismutase genes.

Bacteremia caused by an undescribed species of Janibacter.

A yellow-pigmented rod- to coccoid-shaped coryneform microorganism was isolated from the blood of a patient with acute myeloid leukemia. It was identified by 16S rRNA gene sequencing as a previously undescribed species of Janibacter. The isolate was susceptible to penicillins, aminoglycosides, fluoroquinolones, and glycopeptides.