Comparison of fast Fourier transform infrared spectroscopy biotyping with whole genome sequencing-based genotyping in common nosocomial pathogens.

Early detection of bacterial transmission and outbreaks in hospitals is important because nosocomial infections can result in health complications and longer hospitalization. Current practice to detect outbreaks uses genotyping methods amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS), which are not suitable methods for real-time transmission screening of both susceptible and resistant bacteria. The aim was to assess the typing technique Fourier transform infrared (FTIR) spectroscopy as real-time screening method to discriminate large amounts of susceptible and resistant bacteria at strain level when there is no evident outbreak in comparison with the WGS reference. Isolates of past hospital outbreak strains of Acinetobacter baumannii/calcoaceticus complex (n = 25), Escherichia coli (n = 31), Enterococcus faecium (n = 22), Staphylococcus aureus (n = 37) and Pseudomonas aeruginosa (n = 30) were used for validation of FTIR. Subsequently, Enterococcus faecalis (n = 106) and Enterococcus faecium (n = 104) isolates from weekly routine screening samples when no potential outbreak was present were analysed. FTIR showed reproducibility and congruence of cluster composition with WGS for A. baumannii/calcoaceticus complex and E. faecium outbreak isolates. The FTIR results of E. faecalis and E. faecium isolates from routine samples showed reproducibility, but the congruence of cluster composition with WGS was low. For A. baumannii/calcoaceticus complex and E. faecium outbreak isolates, FTIR appears to be a discriminatory typing tool. However, our study shows the discriminatory power is too low to screen real-time for transmission of E. faecium and E. faecalis at patient wards based on isolates acquired in routine surveillance cultures when there is no clear suspicion of an ongoing outbreak.

Rapid reinfection with SARS-CoV-2 variant-of-concern Alpha detected in a nurse during an outbreak at a non-covid inpatient ward: lessons learned.

We describe the lessons learned during a SARS-CoV-2 variant-of-concern Alpha outbreak investigation at a normal care unit in a university hospital in Amsterdam in December 2020. The outbreak consisted of nine nurses and two roomed-in patient family members. (attack rate 18%). One nurse tested positive with a phylogenetically distinct variant, after a documented infection 83 days prior. Three key points were taken from this investigation. First, it was controlled by adherence to existing guidelines, despite increased transmissibility of the variant. Second, viral sequencing can inform transmission cluster inference, but the epidemiological context is essential to draw appropriate conclusions. Third, reinfections with Alpha variants can occur rapidly after primary infection.

Wound infection following implant removal of foot, ankle, lower leg or patella; a protocol for a multicenter randomized controlled trial investigating the (cost-)effectiveness of 2 g of prophylactic cefazolin compared to placebo (WIFI-2 trial).

BACKGROUND: Elective implant removal (IR) after fracture fixation is one of the most common procedures within (orthopedic) trauma surgery. The rate of surgical site infections (SSIs) in this procedure is quite high, especially below the level of the knee. Antibiotic prophylaxis is not routinely prescribed, even though it has proved to lower SSI rates in other (orthopedic) trauma surgical procedures. The primary objective is to study the effectiveness of a single intravenous dose of 2 g of cefazolin on SSIs after IR following fixation of foot, ankle and/or lower leg fractures. METHODS: This is a multicenter, double-blind placebo controlled trial with a superiority design, including adult patients undergoing elective implant removal after fixation of a fracture of foot, ankle, lower leg or patella. Exclusion criteria are: an active infection, current antibiotic treatment, or a medical condition contraindicating prophylaxis with cefazolin including allergy. Patients are randomized to receive a single preoperative intravenous dose of either 2 g of cefazolin or a placebo (NaCl). The primary analysis will be an intention-to-treat comparison of the proportion of patients with a SSI at 90 days after IR in both groups. DISCUSSION: If 2 g of prophylactic cefazolin proves to be both effective and cost-effective in preventing SSI, this would have implications for current guidelines. Combined with the high infection rate of IR which previous studies have shown, it would be sufficiently substantiated for guidelines to suggest protocolled use of prophylactic antibiotics in IR of foot, ankle, lower leg or patella. Trial registration Nederlands Trial Register (NTR): NL8284, registered on 9th of January 2020, https://www.trialregister.nl/trial/8284.

Timing of Preoperative Antibiotic Prophylaxis and Surgical Site Infection: TAPAS, An Observational Cohort Study.

OBJECTIVE: To test the hypothesis that surgical site infection (SSI) risk differs, after administration of surgical antibiotic prophylaxis (SAP) within 60-30 or 30-0 minutes before incision. BACKGROUND: The importance of appropriate timing of SAP before surgery has long been recognized. However, available evidence is contradictive on the best timing within a 60-0 minutes time interval before incision. Here, we aim to evaluate previous contradictions with a carefully designed observational cohort. METHODS: An observational cohort study was conducted in a Dutch tertiary referral center. For 2 years, consecutive patients with SAP indication undergoing general, orthopedic, or gynecologic surgery were followed for the occurrence of superficial and deep SSI as defined by the Center of Disease Control and Prevention. The association between timing of SAP and SSI was assessed using multivariable logistic regression. RESULTS: After 3001 surgical procedures, 161 SSIs were detected. In 87% of the procedures, SAP was administered within 60 minutes before incision. Only antibiotics with short infusion time were used. Multivariable logistic regression indicated there was no conclusive evidence of a difference in SSI risk after SAP administration 60-30 minutes or 30-0 minutes before incision [odds ratio: 0.82; 95% confidence interval (0.57-1.19)]. CONCLUSIONS: For SAP with short infusion time no clear superior timing interval within the 60-minute interval before incision could be identified in this cohort. We were unable to reproduce differences in SSI risk found in earlier studies.

De-implementation strategy to reduce inappropriate use of intravenous and urinary catheters (RICAT): a multicentre, prospective, interrupted time-series and before and after study.

BACKGROUND: Catheter-associated bloodstream infections and urinary tract infections are frequently encountered health care-associated infections. We aimed to reduce inappropriate use of catheters to reduce health care-associated infections. METHODS: In this multicentre, interrupted time-series and before and after study, we introduced a de-implementation strategy with multifaceted interventions in seven hospitals in the Netherlands. Adult patients admitted to internal medicine, gastroenterology, geriatic, oncology, or pulmonology wards, and non-surgical acute admission units, and who had a (central or peripheral) venous or urinary catheter were eligible for inclusion. One of the interventions was that nurses in the participating wards attended educational meetings on appropriate catheter use. Data on catheter use were collected every 2 weeks by the primary research physician during the baseline period (7 months) and intervention period (7 months), which were separated by a 5 month transition period. The primary outcomes were percentages of short peripheral intravenous catheters and urinary catheters used inappropriately on the days of data collection. Indications for catheter use were based on international guidelines. This study is registered with Netherlands Trial Register, NL5438. FINDINGS: Between Sept 1, 2016, and April 1, 2018, we screened 6157 patients for inclusion, of whom 5696 were enrolled: 2650 patients in the baseline group, and 3046 in the intervention group. Inappropriate use of peripheral intravenous catheters occurred in 366 (22·0%, 95% CI 20·0 to 24·0) of 1665 patients in the baseline group and in 275 (14·4%, 12·8 to 16·0) of 1912 patients in the intervention group (incidence rate ratio [IRR] 0·65, 95% CI 0·56 to 0·77, p<0·0001). Time-series analyses showed an absolute reduction in inappropriate use of peripheral intravenous catheters from baseline to intervention periods of 6·65% (95% CI 2·47 to 10·82, p=0·011). Inappropriate use of urinary catheters occurred in 105 (32·4%, 95% CI 27·3 to 37·8) of 324 patients in the baseline group compared with 96 (24·1%, 20·0 to 28·6) of 398 patients in the intervention group (IRR 0·74, 95% CI 0·56 to 0·98, p=0·013). Time-series analyses showed an absolute reduction in inappropriate use of urinary catheters of 6·34% (95% CI -12·46 to 25·13, p=0·524). INTERPRETATION: Our de-implementation strategy reduced inappropriate use of short peripheral intravenous catheters in patients who were not in the intensive care unit. The reduction of inappropriate use of urinary catheters was substantial, yet not statistically significant in time-series analysis due to a small sample size. The strategy appears well suited for broad-scale implementation to reduce health care-associated infections. FUNDING: Netherlands Organisation for Health Research and Development.

Amplified fragment length polymorphism and whole genome sequencing: a comparison of methods in the investigation of a nosocomial outbreak with vancomycin resistant enterococci.

Background: Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months. Methods: Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors. Results: Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4-5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward. Conclusion: AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.

Pre-Use Ureteroscope Contamination after High Level Disinfection: Reprocessing Effectiveness and the Relation with Cumulative Ureteroscope Use.

PURPOSE: We assessed the frequency of preoperative and persistent microbial contamination of flexible ureteroscopes after reprocessing and the relation of contamination to cumulative ureteroscope use. MATERIALS AND METHODS: We evaluated the effectiveness of high level disinfection with peracetic acid as well as data on ureteroscope use for 20 new flexible ureteroscopes from December 2015 to December 2017 at a single center. In the operating room pre-use and postuse microbial samples of the ureteroscope shaft and working channel were collected to evaluate microbial contamination after reprocessing. Positive cultures were defined as 30 cfu/ml or greater of skin flora, or 10 cfu/ml or greater of uropathogenic microorganisms. A generalized estimating equation model was used to analyze whether cumulative ureteroscope use was associated with positive pre-use cultures. RESULTS: Microbial samples were collected during 389 procedures. Pre-use ureteroscope cultures were positive in 47 of 389 procedures (12.1%), of which uropathogens were found in 9 of 389 (2.3%) and skin flora in 38 of 389 (9.8%). Urinary tract infection symptoms did not develop in any of the patients who underwent surgery with a uropathogen contaminated ureteroscope. In 1 case the pre-use culture contained the same bacteria type as the prior postuse culture. Cumulative ureteroscope use was not associated with a higher probability of positive cultures. CONCLUSIONS: Microbial contamination of reprocessed ureteroscopes was found in an eighth of all procedures. Notably uropathogenic microorganisms were discovered in a small proportion of all procedures. Persistent ureteroscope contamination with uropathogens was only rarely encountered. Cumulative ureteroscope use was not associated with a higher probability of microbial contamination.

Preoperative disinfection of foot and ankle: microbiological evaluation of two disinfection methods.

BACKGROUND: The aim of the current study was to investigate the effect of a footbath in alcohol prior to preoperative disinfection on bacterial flora of the foot and ankle. METHODS: Twenty-two volunteers underwent skin preparation mimicking pre-surgical disinfection. One foot was submerged in a bag filled with 70% ethanol containing 10% IPA for 5 min after which it was painted with regular 0.5% chlorhexidine in 70% alcohol. The other foot was only painted with 0.5% chlorhexidine in 70% alcohol. Swabs were taken at four locations: (1) under the nailfold of the first toe, (2) first webspace, (3) sinus tarsi and (4) pre-tibial. A quantitative and qualitative analysis of the cultures was performed. RESULTS: No statistically significant difference between the number of positive cultures between the two methods was observed. The number of colony forming units was statistically significantly lower on two locations in the footbath group (i.e., subungual and the first webspace) (median 1 versus median 92 p =0.03 and median 0 versus median 1 p =0.03, respectively). The number of cultures with heavy growth was lower in the footbath group under the nailfold of the first toe (5 versus 13 p =0.008). Thirty-eight different microorganisms were cultured. CONCLUSION: A footbath in alcohol prior to regular preoperative skin antisepsis significantly reduces the amount of bacteria under the nailfold and in the first webspace. The number of cultures with heavy growth is lower after a footbath in alcohol. LEVEL OF EVIDENCE: IV.

Effect of Antibiotic Prophylaxis on Surgical Site Infections Following Removal of Orthopedic Implants Used for Treatment of Foot, Ankle, and Lower Leg Fractures: A Randomized Clinical Trial.

Importance: Following clean (class I, not contaminated) surgical procedures, the rate of surgical site infection (SSI) should be less than approximately 2%. However, an infection rate of 12.2% has been reported following removal of orthopedic implants used for treatment of fractures below the knee. Objective: To evaluate the effect of a single dose of preoperative antibiotic prophylaxis on the incidence of SSIs following removal of orthopedic implants used for treatment of fractures below the knee. Design, Setting, and Participants: Multicenter, double-blind, randomized clinical trial including 500 patients aged 18 to 75 years with previous surgical treatment for fractures below the knee who were undergoing removal of orthopedic implants from 19 hospitals (17 teaching and 2 academic) in the Netherlands (November 2014-September 2016), with a follow-up of 6 months (final follow-up, March 28, 2017). Exclusion criteria were an active infection or fistula, antibiotic treatment, reimplantation of osteosynthesis material in the same session, allergy for cephalosporins, known kidney disease, immunosuppressant use, or pregnancy. Interventions: A single preoperative intravenous dose of 1000 mg of cefazolin (cefazolin group, n = 228) or sodium chloride (0.9%; saline group, n = 242). Main Outcomes and Measures: Primary outcome was SSI within 30 days as measured by the criteria from the US Centers for Disease Control and Prevention. Secondary outcome measures were functional outcome, health-related quality of life, and patient satisfaction. Results: Among 477 randomized patients (mean age, 44 years [SD, 15]; women, 274 [57%]; median time from orthopedic implant placement, 11 months [interquartile range, 7-16]), 470 patients completed the study. Sixty-six patients developed an SSI (14.0%): 30 patients (13.2%) in the cefazolin group vs 36 in the saline group (14.9%) (absolute risk difference, -1.7 [95% CI, -8.0 to 4.6], P = .60). Conclusions and Relevance: Among patients undergoing surgery for removal of orthopedic implants used for treatment of fractures below the knee, a single preoperative dose of intravenous cefazolin compared with saline did not reduce the risk of surgical site infection within 30 days following implant removal. Trial Registration: clinicaltrials.gov Identifier: NCT02225821.

De-implementation strategy to Reduce the Inappropriate use of urinary and intravenous CATheters: study protocol for the RICAT-study.

BACKGROUND: Urinary and (peripheral and central) intravenous catheters are widely used in hospitalized patients. However, up to 56% of the catheters do not have an appropriate indication and some serious complications with the use of these catheters can occur. The main objective of our quality improvement project is to reduce the use of catheters without an appropriate indication by 25-50%, and to evaluate the affecting factors of our de-implementation strategy. METHODS: In a multicenter, prospective interrupted time series analysis, several interventions to avoid inappropriate use of catheters will be conducted in seven hospitals in the Netherlands. Firstly, we will define a list of appropriate indications for urinary and (peripheral and central) intravenous catheters, which will restrict the use of catheters and urge catheter removal when the indication is no longer appropriate. Secondly, after the baseline measurements, the intervention will take place, which consists of a kick-off meeting, including a competitive feedback report of the baseline measurements, and education of healthcare workers and patients. Additional strategies based on the baseline data and local conditions are optional. The primary endpoint is the percentage of catheters with an inappropriate indication on the day of data collection before and after the de-implementation strategy. Secondary endpoints are catheter-related infections or other complications, catheter re-insertion rate, length of hospital (and ICU) stay and mortality. In addition, the cost-effectiveness of the de-implementation strategy will be calculated. DISCUSSION: This study aims to reduce the use of urinary and intravenous catheters with an inappropriate indication, and as a result reduce the catheter-related complications. If (cost-) effective it provides a tool for a nationwide approach to reduce catheter-related infections and other complications. TRIAL REGISTRATION: Dutch trial registry: NTR6015 . Registered 9 August 2016.

Eradication of carriage with methicillin-resistant Staphylococcus aureus: determinants of treatment failure.

BACKGROUND: Using data from an observational study in which the effectiveness of a guideline for eradication of methicillin-resistant Staphylococcus aureus (MRSA) carriage was evaluated, we identified variables that were associated with treatment failure. METHODS: A multivariate logistic regression model was performed with subgroup analyses for uncomplicated and complicated MRSA carriage (the latter including MRSA infection, skin lesions, foreign-body material, mupirocin resistance and/or exclusive extranasal carriage) and for those treated according to the guideline (i.e. mupirocin nasal ointment and chlorhexidine soap solution for uncomplicated carriage, in combination with two oral antibiotics for complicated carriage). RESULTS: Six hundred and thirteen MRSA carriers were included, of whom 333 (54%) had complicated carriage; 327 of 530 patients (62%) with known complexity of carriage were treated according to the guideline with an absolute increase in treatment success of 20% (95% confidence interval 12%-28%). Among those with uncomplicated carriage, guideline adherence [adjusted odds ratio (OR(a)) 7.4 (1.7-31.7)], chronic pulmonary disease [OR(a) 44 (2.9-668)], throat carriage [OR(a) 2.9 (1.4-6.1)], perineal carriage [OR(a) 2.2 (1.1-4.4)] and carriage among household contacts [OR(a) 5.6 (1.2-26)] were associated with treatment failure. Among those with complicated carriage, guideline adherence was associated with treatment success [OR(a) 0.2 (0.1-0.3)], whereas throat carriage [OR(a) 4.4 (2.3-8.3)] and dependence in activities of daily living [OR(a) 3.6 (1.4-8.9)] were associated with failure. CONCLUSIONS: Guideline adherence, especially among those with complicated MRSA carriage, was associated with treatment success. Adding patients with extranasal carriage or dependence in daily self-care activities to the definition of complicated carriage, and treating them likewise, may further increase treatment success.

Eradication of carriage with methicillin-resistant Staphylococcus aureus: effectiveness of a national guideline.

BACKGROUND: We evaluated the effectiveness of eradication of methicillin-resistant Staphylococcus aureus (MRSA) carriage in the Netherlands after the introduction of a guideline in 2006. The guideline distinguishes complicated (defined as the presence of MRSA infection, skin lesions, foreign-body material, mupirocin resistance and/or exclusive extranasal carriage) and uncomplicated carriage (not meeting criteria for complicated carriage). Mupirocin nasal ointment and chlorhexidine soap solution are recommended for uncomplicated carriers and the same treatment in combination with two oral antibiotics for complicated carriage. METHODS: A prospective cohort study was performed in 18 Dutch centres from 1 October 2006 until 1 October 2008. RESULTS: Six hundred and thirteen MRSA carriers underwent one or more decolonization treatments during the study period, mostly after hospital discharge. Decolonization was achieved in 367 (60%) patients with one eradication attempt and ultimately 493 (80%) patients were decolonized, with a median time until decolonization of 10 days (interquartile range 7-43 days). Three hundred and twenty-seven (62%) carriers were treated according to the guideline, which was associated with an absolute increase in treatment success of 20% [from 45% (91/203) to 65% (214/327)]. CONCLUSIONS: Sixty percent of MRSA carriers were successfully decolonized after the first eradication attempt and 62% were treated according to the guideline, which was associated with an increased treatment success.

Treatment of acute hepatitis C virus infection in HIV-infected MSM: the effect of treatment duration.

We evaluated hepatitis C virus (HCV) treatment and the effect of treatment duration (24 versus 48 weeks) on treatment outcome among 50 HIV-infected men who have sex with men with acute HCV infection in Amsterdam. Overall sustained virological response (SVR) rate was 76%. Treatment duration was not significantly associated with SVR (adjusted odds ratio = 2.32; 95% confidence interval 0.39-13.97), suggesting that 24-week treatment may be sufficient for acute HCV infection in HIV-coinfected patients.

Human parechoviruses as an important viral cause of sepsislike illness and meningitis in young children.

BACKGROUND: Enteroviruses (EVs) belong to the family Picornaviridae and are a well-known cause of neonatal sepsis and viral meningitis. Human parechoviruses (HPeVs) type 1 and 2, previously named echovirus 22 and 23, have been associated with mild gastrointestinal or respiratory symptoms in young children. Six HPeV genotypes are currently known, of which HPeV3 is associated with neonatal sepsis and meningitis. METHODS: Cerebrospinal fluid samples from children aged <5 years previously tested by EV-specific polymerase chain reaction (PCR) during 2004-2006 were selected (N= 761). Samples from 716 of those children were available for retrospective testing by HPeV-specific real-time PCR. The prevalence of EV and HPeV in these samples was compared. Data on clinical presentation of children infected with HPeV were retrospectively documented. RESULTS: HPeV was found in cerebrospinal fluid samples from 33 (4.6%) of the children. Yearly prevalence of HPeV in cerebrospinal fluid varied remarkably: 8.2% in 2004, 0.4% in 2005, and 5.7% in 2006. EV was detected in 14% (108 of 761 samples), with no variation in yearly prevalence. Children with HPeV in cerebrospinal fluid presented with clinical symptoms of sepsislike illness and meningitis, which led to hospitalization and antibiotic treatment. CONCLUSION: EV-specific PCRs do not detect HPeVs. The addition of an HPeV-specific PCR has led to a 31% increase in detection of a viral cause of neonatal sepsis or central nervous system symptoms in children aged <5 years. HPeV can be considered to be the second cause of viral sepsis and meningitis in young children, and rapid identification of HPeV by PCR could contribute to shorter duration of both antibiotic use and hospital stay.

Transmission of hepatitis B virus from a surgeon to his patients during high-risk and low-risk surgical procedures during 4 years.

OBJECTIVE: We investigated cases of acute hepatitis B in The Netherlands that were linked to the same general surgeon who was infected with hepatitis B virus (HBV). DESIGN: A retrospective cohort study was conducted of 1,564 patients operated on by the surgeon. Patients were tested for serologic HBV markers. A case-control study was performed to identify risk factors. RESULTS: The surgeon tested positive for hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) with a high viral load. He was a known nonresponder after HBV vaccination and had apparently been infected for more than 10 years. Forty-nine patients (3.1%) were positive for HBV markers. Transmission of HBV from the surgeon was confirmed in 8 patients, probable in 2, and possible in 18. In the remaining 21 patients, the surgeon was not implicated. Two patients had a chronic HBV infection. One case of secondary transmission from a patient to his wife was identified. HBV DNA sequences from the surgeon were completely identical to sequences from 7 of the 28 patients and from the case of secondary transmission. The duration of the operation and the occurrence of complications during or after surgery were identified as independent risk factors. Although the risk of HBV infection during high-risk procedures was 7 times higher than that during low-risk procedures, at least 8 (28.6%) of the 28 patients were infected during low-risk procedures. CONCLUSIONS: Transmission of HBV from surgeons to patients at a low rate can remain unnoticed for a long period of time. Prevention requires a more stringent strategy for vaccination and testing of surgeons and optimization of infectious disease surveillance. Policies allowing HBV-infected surgeons to perform presumably low-risk procedures should be reconsidered.