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Additional file 4. “Thematic analysis of open questions”. Description of data: “A full list of identified themes and the coded text”.

Additional file 3. “Full responses to questionnaire”. Description of data: “Full responses to all questions included in the survey”.

Additional file 2. “Selection of target groups for the survey”. Description of data: “An overview of existing surveillance systems to identify all public health professionals who (would potentially) generate or use NGS data for the surveillance of infectious diseases based in different institutes and organizations in Belgium.”

Enhanced oral (po) bioavailability of antimicrobial drugs allows conversion to po therapy once a patient meets defined clinical criteria. This can reduce length of hospital stay, healthcare costs and risk of complications related to intravenous (iv) access. We developed a quality indicator for assessing the appropriate iv-to-po switch of bioavailable antibiotics and evaluated its feasibility and clinical relevance across acute healthcare systems. The study was designed as a multicentre, multinational observational audit. The indicator was the proportion of inappropriate iv treatments at any point in time in adult patients treated with fluoroquinolones, clindamycin, linezolid or metronidazole. Treatments were prospectively evaluated by a trained physician or clinical pharmacist using predefined clinical criteria. The feasibility of the indicator was evaluated by measuring data availability, data collection workload and sensitivity to improvement Data were collected over a 3 month period in five university hospitals in Austria, Belgium and Germany and iv treatment was assessed in 211 patients. The indicator was measurable in 99.1 of cases. By intention-to-treat analysis, 37.0 (95 CI 30.543.9) of treatments were inappropriate, ranging from 17.5 to 53.8 across hospitals. The median time needed for case assessment and documentation was 29 min. This quality indicator was found to be generally feasible in hospitals across three European countries, and informative about the local need for clinical quality improvement.

This study describes the development of structure indicators for hospital antimicrobial stewardship programmes and pilot validation across European hospitals. A multi-disciplinary panel from four European countries developed structure indicators in three steps: identification and listing of indicators, remote ranking of indicators using multi-criteria scoring, selection of indicators in a face-to-face consensus meeting. Additionally, the top-ten indicators were identified as a minimal set of key indicators. A survey was sent to the directors of antimicrobial stewardship programmes in European hospitals. The yes/no answers for the indicators were transformed into numbers in order to calculate the total scores. A list of 58 indicators was selected and categorised into the following topics: antimicrobial stewardship services (12 items), tools (16 items), human resources and mandate (6 items), health care personnel development (4 items), basic diagnostic capabilities (6 items), microbiological rapid tests (2 items), evaluation of microbiological drug resistance data (3 items), antibiotic consumption control (5 items) and drug use monitoring (4 items). The indicator scores, reported by 11 pilot hospitals from five European countries, ranged from 32 to 50 (maximum score = 58) and from 5 to 10 points (maximum score = 10) for, respectively, the complete and the top-ten list. An international panel selected 58 potential structure indicators, among which was a minimal set of ten key structure indicators, that could be useful for assessment of the comprehensiveness and resource-intensity of antimicrobial stewardship programmes. There was significant heterogeneity among participating centres with regard to their score for structural components of effective antimicrobial stewardship.

A rapid survey by the European Centre for Disease Prevention and Control (ECDC) and the World Health Organization (WHO) Regional Office for Europe ascertained the availability of national reference laboratory testing for a recently detected novel coronavirus as of 28 November 2012. Screening by internal quality controlled upE-RT-PCR assay was available in 23/46 of responding countries in the WHO European Region, of which 19/30 in European Union (EU) and European Economic Area (EEA) countries. Confirmation of positive screened samples by either ORF1b - RT-PCR, or other target RT-PCR assays with sequence analysis or whole-genome sequence analysis was available in 22/46 responding countries of which 18/30 in EU/EEA countries.

Staphylococcus aureus and coagulase-negative species of staphylococci (CNS), particularly S epidermidis, are among the most frequently isolated bacteria from patients with nosocomial infection. Conventional methods used in the clinical microbiology laboratory for identification, susceptibility testing, and epidemiologic typing of staphylococci have several limitations Identification to species level is often limited to S. aureus, based on ability to produce coagulase, thermostable nuclease, and clumping factor. However, several newly-described species of staphylococci may express some of these characters, whereas atypical strains of S. aureus do not, leading to misidentification (1,2). Furthermore, among the 17 species of staphylococci currently recognized to be indigenous to humans, the potential of S. lugdunensis to cause serious infections is being increasingly recognized (1,2) Therefore, further speciation of CNS is clinically relevant. Distinction of true CNS infection from specimen contamination by skin flora can be addressed by demonstrating the repeated isolation of the same clone from multiple specimens, e g., blood cultures (1). Currently available, rapid biochemical test systems enable identification of staphylococci to species level with 60-90% accuracy (1). Antimicrobial susceptibility pattern, the only routinely available strain marker, is not reliable for clonal delmeation because of phenotypic variation among clonally derived isolates (1).

A multicenter preclinical evaluation was conducted to evaluate the performance of two Cepheid Xpert assays for detection of methicillin-resistant Staphylococcus aureus (MRSA) and S. aureus. Sensitivity was 97.1% and 98.3% for MRSA in wound and blood culture specimens, respectively. Sensitivity was 100% for S. aureus from both specimen types.

One of the principal objectives of tuberculosis (TB) control is to minimise the emergence of drug resistance. The first national survey was conducted in Rwanda to determine the prevalence of M. tuberculosis drug resistance.Sputum samples were collected from all new and retreatment cases in the health districts from November 2004 to February 2005. Drug susceptibility testing of isolates against first-line drugs was performed by the proportion method.Of 616 strains from new cases, 6.2% were resistant to isoniazid, 3.9% to rifampicin and 3.9% were multidrug-resistant TB. Among 85 strains from previously treated cases, the prevalence of resistance was respectively 10.6%, 10.6% and 9.4% (MDR-TB strains). Eight MDR cases showed additional resistance to ethambutol and streptomycin.The level of MDR-TB among TB patients in Rwanda is high. The main reasons of this emergence of MDR-TB can be attributed to the disorganisation of the health system, migration of the population during the 1994 civil war and poor success rates, with a high number of patients transferred out and lost to follow-up. On the other hand, the use of treatment regimens administered twice weekly during the continuation phase could be another important factor and merit further investigations.

The worldwide emergence of community-acquired methicillin resistant Staphylococcus aureus infections caused by hypervirulent strains producing Panton-Valentine leukocidin is a cause for considerable concern

Surveillance of antibiotic resistance is especially important in intensive care units (ICUs) because the infection rates are much higher there than in other hospital wards and most epidemics with multiresistant bacteria originate in ICUs.To evaluate the incidence of decreased antibiotic susceptibility among aerobic gram-negative bacilli isolated from patients in ICUs.Consecutive specimens collected on clinical indications from ICU patients were cultured and tested. Minimum inhibitory concentrations for amikacin, ceftazidime, ceftriaxone, ciprofloxacin, gentamicin, imipenem, piperacillin, and piperacillin-tazobactam were determined using E test.Eighteen hospitals in Belgium, 40 in France, 20 in Portugal, 30 in Spain, and 10 in Sweden.A total of 9166 gram-negative strains were initially isolated from 7308 patients between June 1994 and June 1995.The incidence of decreased susceptibility, defined as the sum of resistant and intermediate categories with use of the minimum inhibitory concentration break points recommended by the National Committee for Clinical Laboratory Standards.The most frequently isolated organisms were Enterobacteriaceae (59%) followed by Pseudomonas aeruginosa (24%). The main sources were respiratory tract (42%), urine (26%), blood (14%), abdomen (11%), and skin and soft tissue (7%). Decreased antibiotic susceptibility across all species and drugs was highest in Portuguese ICUs followed by French, Spanish, Belgian, and Swedish ICUs. The highest incidence of resistance was seen in all countries among P aeruginosa (up to 37% resistant to ciprofloxacin in Portuguese ICUs and 46% resistant to gentamicin in French ICUs), Enterobacter species, Acinetobacter species, and Stenotrophomonas maltophilia, and in Portugal and France among Klebsiella species.The high incidence of reduced antibiotic susceptibility among gram-negative bacteria in these ICUs suggests that more effective strategies are needed to control the selection and spread of resistant organisms.

Over a 3-month period, six immunocompromised patients developed one or more episodes of Burkholderia pickettii bacteremia and/or catheter infection. Vials of a commercially available, "sterile" saline for injection which had been used for flushing the patients' indwelling intravenous devices were implicated as the common source of the organisms. No further cases were diagnosed once the use of this saline was discontinued. Twenty-six isolates, including 9 outbreak-related strains from case patients and contaminated saline as well as 17 control strains, were tested comparatively by biotyping, ribotyping with EcoRI and HindIII, and pulsed-field gel electrophoresis (PFGE) with SpeI. Macrorestriction analysis revealed nine PFGE groups and was more discriminating than ribotyping (seven ribotypes) and biotyping (two biovars). Among the outbreak-related isolates, one B. pickettii type was found by the three typing methods. Furthermore, PFGE was useful for subdividing ribotypes and for distinguishing isolates involved in the outbreak from all epidemiologically unrelated strains.

To describe the Belgian methicillin-resistant Staphylococcus aureus (MRSA) surveillance network, the evolution of methods used in Belgian hospitals for MRSA detection and control, and MRSA incidence from 1994 to 1995.Questionnaire surveys; infection control physicians from acute-care hospitals in Belgium.Publication of national guidelines for MRSA control in 1993.The participation rate in surveys ranged from 42% to 57% of hospitals. In 1995, 88% of participants detected MRSA strains by disk diffusion tests, with little improvement in standardization since 1991. More centers employed the oxacillin agar screen method (27%), automated systems (29%), or a combination of methods (29%) than in 1991 (P.005). Between 1991 and 1995, the proportion of hospitals reporting MRSA control measures increased from 68% to 95% (P.01). Practices that were used increasingly included patient placement in private room (from 50% to 93%, P.01) and hand decontamination with antiseptic (from 43% to 87%, P.01). The proportion of centers that reported screening MRSA carriers and treating them topically increased two- and threefold, respectively (P.05). Surveillance data from 1994 to 1995 showed that MRSA represented a mean of 21.3% of S aureus clinical isolates (range, 1.6% to 62.4%). The median incidence of nosocomial MRSA acquisition was 2.8 per 1,000 admissions, with a wide range (0 to 13.7 per 1,000 admissions) across hospitals of all sizes. The median incidence decreased over the first three semesters of surveillance in hospitals with continuous participation.MRSA detection and control measures have improved in Belgian hospitals after publication of national guidelines. However, MRSA incidence rates show the persistence of nosocomial transmission, with large variations between centers. The national MRSA surveillance network should indicate whether control efforts eventually will curb the problem.

Arbitrarily primed PCR fingerprinting was carried out on 43 Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients. Seventeen major groups of strains that coincided with groups also distinguished by macrorestriction (pulsed-field gel electrophoresis) typing were identified. Our results illustrated that a CF patient can carry more than one strain and can carry a given strain for long periods of time and that strains can evolve by changes in drug resistance or other phenotypic traits during long-term colonization. The arbitrarily primed PCR method is recommended for first-pass screening of P. aeruginosa isolates from CF patients, especially when many strains are to be typed, because of its sensitivity and efficiency.

A questionnaire survey of Belgian acute care hospitals was conducted to determine the methods used for detection of methicillin-resistant Staphylococcus aureus (MRSA), to estimate the prevalence of this organism during the period 1989-1991 and to describe the infection control measures used locally for limiting its spread. Questionnaires were returned by 144 acute care hospitals, with a coverage of 41 to 72% of hospitals by province. Methods used for detection of MRSA included disk diffusion (91%), microdilution panels (8%) and oxacillin agar screen (9%). Only 34% of laboratories performed disk diffusion testing under optimal conditions for detection of heterogenous resistance. Among 36 hospitals reporting complete susceptibility data of Staphylococcus aureus isolates tested during the study period (n = 24,153), a mean MRSA prevalence of 14% was found (range: 0-70%). The median prevalence increased from 9.5% in 1989 to 13.7% in 1991 and showed a significant linear increase during this period in 30% of these hospitals (p0.01). Precautions used for controlling spread of MRSA included hand decontamination using either soap and water or antimicrobial preparations (68% of hospitals), room decontamination (62%), patient isolation (55%) and various barrier precautions (24-49%). Carrier screening was performed in 37% of hospitals, but antibiotic decolonization was attempted in only 24%. This survey identified areas for improvement in MRSA detection methods and underscored the need for multicentric surveillance of MRSA prevalence and a reappraisal of MRSA control strategies in Belgian hospitals.