Molecular characterization and phylogeny of Shiga toxin–producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing

AbstractShiga toxin–producing Escherichia coli (STEC) is one of the major causes of human gastrointestinal disease and has been implicated in sporadic cases and outbreaks of diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome worldwide. In this study, we determined the molecular characteristics and phylogenetic relationship of STEC isolates, and their genetic diversity was compared to that of other E. coli populations. Whole genome sequencing was performed on 132 clinical STEC isolates obtained from the faeces of 129 Dutch patients with gastrointestinal complaints. STEC isolates of this study belonged to 44 different sequence types (STs), 42 serogenotypes and 14 stx subtype combinations. Antibiotic resistance genes were more frequently present in stx1-positive isolates compared to stx2 and stx1 + stx2–positive isolates. The iha, mchB, mchC, mchF, subA, ireA, senB, saa and sigA genes were significantly more frequently present in eae-negative than in eae-positive STEC isolates. Presence of virulence genes encoding type III secretion proteins and adhesins was associated with isolates obtained from patients with bloody diarrhoea. Core genome phylogenetic analysis showed that isolates clustered according to their ST or serogenotypes irrespective of stx subtypes. Isolates obtained from patients with bloody diarrhoea were from diverse phylogenetic backgrounds. Some STEC isolates shared common ancestors with non-STEC isolates. Whole genome sequencing is a powerful tool for clinical microbiology, allowing high-resolution molecular typing, population structure analysis and detailed molecular characterization of strains. STEC isolates of a substantial genetic diversity and of distinct phylogenetic groups were observed in this study

Thirteen years of antibiotic susceptibility surveillance of Pseudomonas aeruginosa from intensive care units and urology services in the Netherlands

The purpose of this study was the evaluation of trends in the antimicrobial resistance of Pseudomonas aeruginosa from intensive care unit (ICU) patients and urology patients in the Netherlands. From 1998 to 2010, 1,927 consecutive P. aeruginosa isolates from ICU (n = 1,393) and urology service patients (n = 534) of 14 university and referral hospitals all over the Netherlands were collected and their susceptibility to relevant antibiotics was determined according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Over time, a significant upward trend in the resistance of P. aeruginosa strains collected from ICUs to piperacillin (1.2 % to 10.6 %, p = 0.0175), piperacillin-tazobactam (1.2 % to 12.1 %, p = 0.0008), ceftazidime (1.2 % to 7.8 %, p = 0.0064), cefepime (4.8 % to 6.4 %, p = 0.0166), imipenem (6 % to 19.1 %, p < 0.0001), meropenem (8.3 % to 17 %, p = 0.0022) and ciprofloxacin (13.1 % to 31.2 %, p = 0.0024) was observed, as was the prevalence of multi-resistance (1.2 % to 8.5 %, p = 0.0002). For P. aeruginosa isolates from the urology services, the resistance to imipenem increased (4.1 % to 7.8 %, p = 0.0006) and to ciprofloxacin it decreased (22.4 % to 18.8 %, p = 0.025). Like in other countries, in the Netherlands, an increase in multi-resistant Gram-negatives is observed, suggesting the presence and dissemination of several mechanisms of resistance. Our findings emphasise the importance of local surveillance for the setting up of local antibiotic guidelines and to support optimal empiric therapy. With the observed increase in multi-resistance, the direct testing of alternative antibiotics like polymyxins and fosfomycin is essential. Our data also illustrate the importance of adequate outbreak control measures

Timing of debridement, antibiotics, and implant retention (DAIR) for early post-surgical hip and knee prosthetic joint infection (PJI) does not affect 1-year re-revision rates

Debridement, antibiotics, and implant retention (DAIR) is a procedure to treat a periprosthetic joint infection (PJI) after total hip arthroplasty (THA) or total knee arthroplasty (TKA). The timing between the primary procedure and the DAIR is likely a determinant for its successful outcome. However, the optimal timing of a DAIR and the chance of success still remain unclear. We aimed to assess the risk of re-revision within 1 year after a DAIR procedure and to