Automated digital reporting of clinical laboratory information to national public health surveillance systems, results of a EU/EEA survey, 2018.

BackgroundTimely reporting of microbiology test results is essential for infection management. Automated, machine-to-machine (M2M) reporting of diagnostic and antimicrobial resistance (AMR) data from laboratory information management systems (LIMS) to public health agencies improves timeliness and completeness of communicable disease surveillance.AimWe surveyed microbiology data reporting practices for national surveillance of EU-notifiable diseases in European Union/European Economic Area (EU/EEA) countries in 2018.MethodsEuropean Centre for Disease Prevention and Control (ECDC) National Microbiology and Surveillance Focal Points completed a questionnaire on the modalities and scope of clinical microbiology laboratory data reporting.ResultsComplete data were provided for all 30 EU/EEA countries. Clinical laboratories used a LIMS in 28 countries. LIMS data on EU-notifiable diseases and AMR were M2M-reported to the national level in 14 and nine countries, respectively. In the 14 countries, associated demographic data reported allowed the de-duplication of patient reports. In 13 countries, M2M-reported data were used for cluster detection at the national level. M2M laboratory data reporting had been validated against conventional surveillance methods in six countries, and replaced those in five. Barriers to M2M reporting included lack of information technology support and financial incentives.ConclusionM2M-reported laboratory data were used for national public health surveillance and alert purposes in nearly half of the EU/EEA countries in 2018. Reported data on infectious diseases and AMR varied in extent and disease coverage across countries and laboratories. Improving automated laboratory-based surveillance will depend on financial and regulatory incentives, and harmonisation of health information and communication systems.

Epidemiological situation, laboratory capacity and preparedness for carbapenem-resistant Acinetobacter baumannii in Europe, 2019.

To update information on the epidemiological situation and national capacity for detection, surveillance and containment of carbapenem-resistant Acinetobacter baumannii (CRAb) in Europe, we performed a survey in 37 countries. Nine countries reported regional or inter-regional spread and seven an endemic situation. Laboratories with a reference function, surveillance systems, and a national containment plan for CRAb existed in 30, 23 and eight countries, respectively. A pan-European molecular survey would provide in-depth understanding of the CRAb epidemiology.

Cross-border spread of blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae: a European collaborative analysis of whole genome sequencing and epidemiological data, 2014 to 2019.

Analysis of sequencing data for 143 blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outside of the European Union including Egypt, Iran, Morocco, Russia, Serbia, Tunisia and Turkey. These findings highlight the benefit of European whole genome sequencing-based surveillance and data sharing for control of antimicrobial resistance.

Worsening epidemiological situation of carbapenemase-producing Enterobacteriaceae in Europe, assessment by national experts from 37 countries, July 2018.

A survey on the epidemiological situation, surveillance and containment activities for carbapenemase-producing Enterobacteriaceae (CPE) was conducted in European countries in 2018. All 37 participating countries reported CPE cases. Since 2015, the epidemiological stage of CPE expansion has increased in 11 countries. Reference laboratory capability, dedicated surveillance and a specific national containment plan are in existence in 33, 27 and 14 countries, respectively. Enhanced control efforts are needed for CPE containment in Europe.

Candida auris: epidemiological situation, laboratory capacity and preparedness in European Union and European Economic Area countries, 2013 to 2017.

During 2013-2017, 620 cases of Candida auris were reported in the European Union/European Economic Area - 466 (75.2%) colonisations, 110 (17.7%) bloodstream infections, 40 (6.5%) other infections and four cases (0.6%) of unknown colonisation/infection status - the majority from four large outbreaks. Survey results showed that several countries lacked laboratory capacity and/or information on the occurrence of cases at national level. To prevent further spread, adequate laboratory capacity and infection control preparedness is required in Europe.

Livestock-associated meticillin-resistant Staphylococcus aureus (MRSA) among human MRSA isolates, European Union/European Economic Area countries, 2013.

Currently, surveillance of livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) in humans in Europe is not systematic but mainly event-based. In September 2014, the European Centre for Disease Prevention and Control (ECDC) initiated a questionnaire to collect data on the number of LA-MRSA from human samples (one isolate per patient) from national/regional reference laboratories in European Union/European Economic Area (EU/EEA) countries in 2013. Identification of LA-MRSA as clonal complex (CC) 398 by multilocus sequence typing (MLST) was preferred, although surrogate methods such as spa-typing were also accepted. The questionnaire was returned by 28 laboratories in 27 EU/EEA countries. Overall, LA-MRSA represented 3.9% of 13,756 typed MRSA human isolates, but it represented ≥ 10% in five countries (Belgium, Denmark, Spain, the Netherlands and Slovenia). Seven of the reference laboratories did not type MRSA isolates in 2013. To monitor the dispersion of LA-MRSA and facilitate targeted control measures, we advocate periodic systematic surveys or integrated multi-sectorial surveillance.

Carbapenemase-producing Enterobacteriaceae in Europe: assessment by national experts from 38 countries, May 2015.

In 2012, the European Centre for Disease Prevention and Control (ECDC) launched the 'European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE)' project to gain insights into the occurrence and epidemiology of carbapenemase-producing Enterobacteriaceae (CPE), to increase the awareness of the spread of CPE, and to build and enhance the laboratory capacity for diagnosis and surveillance of CPE in Europe. Data collected through a post-EuSCAPE feedback questionnaire in May 2015 documented improvement compared with 2013 in capacity and ability to detect CPE and identify the different carbapenemases genes in the 38 participating countries, thus contributing to their awareness of and knowledge about the spread of CPE. Over the last two years, the epidemiological situation of CPE worsened, in particular with the rapid spread of carbapenem-hydrolysing oxacillinase-48 (OXA-48)- and New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae. In 2015, 13/38 countries reported inter-regional spread of or an endemic situation for CPE, compared with 6/38 in 2013. Only three countries replied that they had not identified one single case of CPE. The ongoing spread of CPE represents an increasing threat to patient safety in European hospitals, and a majority of countries reacted by establishing national CPE surveillances systems and issuing guidance on control measures for health professionals. However, 14 countries still lacked specific national guidelines for prevention and control of CPE in mid-2015.

Prevalence, risk factors and genetic diversity of methicillin-resistant Staphylococcus aureus carried by humans and animals across livestock production sectors.

OBJECTIVES: This study aimed to assess the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in animals and humans on veal, dairy, beef and broiler farms and to compare the risk for human MRSA carriage with that of strictly horticulture farmers. The genetic background, resistance phenotypes and genotypes and toxin gene content of the isolated MRSA strains were compared with MRSA collected on MRSA clonal complex (CC)398-positive pig farms. METHODS: MRSA carriage isolates were genotyped (spa, SCCmec and multilocus sequence typing), resistance to 16 antimicrobials was determined and resistance and toxin genes were detected. RESULTS: MRSA carriage rates were higher (P<0.01) on veal farms (calves, 64%; farmers, 72%) compared with on dairy (cows, 1%), beef (cows, 5%; farmers, 11%), broiler (pooled broths, 5%; farmers, 3%) and horticulture (farmers, 3%) farms. The intensity of animal contact was identified as a risk factor for human MRSA carriage. The vast majority of MRSA (n=344), including those from pigs, were CC398 (98%). SCCmec V(5C2), V(5C2&5)c, IV(2B) and IV(2B&5) predominated. MRSA CC130 and CC599 carrying mecC were detected in beef and dairy cattle. MRSA from veal calves were significantly more resistant than MRSA from pigs (P<0.01). A few isolates, including mecC-carrying MRSA, harboured pyrogenic superantigen toxins. Human- and animal-derived MRSA from individual farms showed similar characteristics. CONCLUSIONS: This systematic cross-sector survey revealed a high prevalence of multiresistant livestock-associated MRSA on Belgian veal calf farms as compared with other farm types. MRSA harbouring mecC was detected at a low frequency in beef and dairy cows, but not in humans.

Livestock-associated methicillin-resistant Staphylococcus aureus in humans, Europe.

To estimate the proportion of methicillin-resistant Staphylococcus aureus (MRSA) isolates from humans that were sequence type (ST) 398, we surveyed 24 laboratories in 17 countries in Europe in 2007. Livestock-associated MRSA ST398 accounted for only a small proportion of MRSA isolates from humans; most were from the Netherlands, Belgium, Denmark, and Austria.

Controlled performance evaluation of the DiversiLab repetitive-sequence-based genotyping system for typing multidrug-resistant health care-associated bacterial pathogens.

Fast, reliable, and versatile typing tools are essential to differentiate among related bacterial strains for epidemiological investigation and surveillance of health care-associated infection with multidrug-resistant (MDR) pathogens. The DiversiLab (DL) system is a semiautomated repetitive-sequence-based PCR system designed for rapid genotyping. The DL system performance was assessed by comparing its reproducibility, typeability, discriminatory power, and concordance with those of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) and by assessing its epidemiological concordance on well-characterized MDR bacterial strains (n = 165). These included vanA Enterococcus faecium, extended-spectrum ß-lactamase (ESBL)-producing strains of Klebsiella pneumoniae, Escherichia coli, and Acinetobacter baumannii, and ESBL- or metallo-ß-lactamase (MBL)-producing Pseudomonas aeruginosa strains. The DL system showed very good performance for E. faecium and K. pneumoniae and good performance for other species, except for a discrimination index of <95% for A. baumannii and E. coli (93.9% and 93.5%, respectively) and incomplete concordance with MLST for P. aeruginosa (78.6%) and E. coli (97.0%). Occasional violations of MLST assignment by DL types were noted for E. coli. Complete epidemiological concordance was observed for all pathogens, as all outbreak-associated strains clustered in identical DL types that were distinct from those of unrelated strains. In conclusion, the DL system showed good to excellent performance, making it a reliable typing tool for investigation of outbreaks caused by study pathogens, even though it was generally less discriminating than PFGE analysis. For E. coli and P. aeruginosa, MLST cannot be reliably inferred from DL type due to phylogenetic group violation or discordance.

Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus.

A small number of clonal lineages dominates the global population structure of methicillin-resistant Staphylococcus aureus (MRSA), resulting in the concept that MRSA has emerged on a few occasions after penicillinase-stable beta-lactam antibiotics were introduced to clinical practice, followed by intercontinental spread of individual clones. We investigated the evolutionary history of an MRSA clone (ST5) by mutation discovery at 108 loci (46 kb) within a global collection of 135 isolates. The SNPs that were ascertained define a radial phylogenetic structure within ST5 consisting of at least 5 chains of mutational steps that define geographically associated clades. These clades are not concordant with previously described groupings based on staphylococcal protein A gene (spa) typing. By mapping the number of independent imports of the staphylococcal cassette chromosome methicillin-resistance island, we also show that import has occurred on at least 23 occasions within this single sequence type and that the progeny of such recombinant strains usually are distributed locally rather than globally. These results provide strong evidence that geographical spread of MRSA over long distances and across cultural borders is a rare event compared with the frequency with which the staphylococcal cassette chromosome island has been imported.

COVID-19 Research: Challenges to Interpret Numbers and Propose Solutions.

The response of the scientific community to the COVID-19 pandemic has been unprecedented in size, speed and discovery output. Within months of virus emergence, the SARS-CoV-2 genomics, replication, evolution and dissemination dynamics as well as natural history, infection risk and prognostic factors and biology of the disease have been gradually deciphered. More than 250 articles on COVID-19 published in Frontiers in Public Health have contributed to these insights. We discuss here some of the key research themes and challenges that have been addressed. We provide our perspective on current research issues with surveillance data quality and limitations of epidemiological methods. We warn against the potential misuse or misleading interpretation of public data of variable quality and the use of inadequate study designs for the evaluation of effect of non-pharmaceutical interventions. We conclude by interrogating possible public health strategies for pandemic control as well as discuss the ethical responsibilities and democratic accountability of researchers in their role as experts and policy advisors.

Point of Care Testing for Infectious Disease in Europe: A Scoping Review and Survey Study.

Background: Point of care testing (POCT) for infectious diseases is testing conducted near the patient. It allows clinicians to offer the most appropriate treatment more quickly. As POCT devices have increased in accuracy and become more cost-effective, their use has grown, but a systematic assessment of their use for clinical and public health management of infectious diseases in EU/EEA countries has not been previously undertaken. Methods: A scoping review of the literature on POCT in EU/ EEA countries as at November 2019, and a survey of key stakeholders. Results: 350 relevant articles were identified and 54 survey responses from 26 EU/EEA countries were analysed. POCT is available for a range of infectious diseases and in all countries responding to the survey (for at least one disease). POCT is commonly available for influenza, HIV/AIDS, Legionnaires' disease and malaria, where it is used in at least half of EU/EEA countries. While POCT has the potential to support many improvements to clinical care of infectious diseases (e.g., faster diagnosis, more appropriate use of antimicrobials), the results suggest POCT is infrequently used to support public health functions (e.g., disease surveillance and reporting). Conclusion: Although POCT is in use to some extent in all EU/EEA countries, the full benefits of POCT in wider public health functions have yet to be realised. Further research on barriers and facilitators to implementation is warranted.

Nationwide implementation of antibiotic management teams in Belgian hospitals: a self-reporting survey.

OBJECTIVES: Antibiotic management teams (AMTs) have been advocated to optimize the use of antimicrobials in hospitals. Since 2002, the Belgian Antibiotic Policy Coordination Committee (BAPCOC) has supported the development of AMTs in Belgian hospitals with policy guidance and federal funding for antibiotic managers. We performed a national, self-reporting survey to assess the level of AMT activities in 2007. METHODS: A structured questionnaire survey was performed on the composition, organization and service activities of the AMT in all acute care and larger chronic care hospitals in the country in 2007. Descriptive statistics were stratified by duration of AMT funding. RESULTS: Completed questionnaires were provided by 112 of 116 hospitals (response rate, 96.6%). Mutidisciplinary AMTs varied in size (mean 10, range 2-28 members). Antibiotic stewardship tools used by AMTs included: hospital antibiotic formulary (96.3% of hospitals); practice guidelines for antibiotic therapy and surgical prophylaxis (91.6% and 96.3%, respectively); list of 'restricted' antimicrobial agents (75.9%); concurrent review of antibiotic therapies (64.2%); de-escalation of therapy after a few days (63.9%); sequential intravenous/oral therapy for antibiotics with equivalent bioavailability (78.7%); dedicated antimicrobial order forms (36.1%); automatic stop of delivery (43.5%); analysis of antibiotic consumption data (96.2%); and analysis of microbial resistance data (89.8%). CONCLUSIONS: These data demonstrate a well-developed structure of AMTs in Belgian hospitals and the broad range of services provided. Technical and financial support by healthcare authorities was key to the extensive implementation of antimicrobial stewardship programmes across the national hospital care system.

The bacterial envelope as a target for novel anti-MRSA antibiotics.

Methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-intermediate S. aureus (VISA) are spreading worldwide, making the search for antibiotics directed against new targets a high priority. Drugs that anchor in the bacterial membrane (e.g. ceragenins and lipopeptides) or that target the bacterial membrane and proteic (lipoglycopeptides) or lipidic (glycodepsipeptides) cell wall precursors seem to have the most potential because they show a fast and extensive bactericidal effect and are probably less prone to select for resistance owing to the difficulty in modifying their targets in a way that is compatible with bacterial survival. The efficacy of lipopeptides and lipoglycopeptides has been demonstrated in the treatment of skin and skin structure infections, and bacteremia caused by resistant S. aureus. Ceragenins and glycodepsipeptides are restricted to topical applications because of their unsatisfactory safety profile. The mode of action, pharmacological and microbiological properties and target indications of these anti-MRSA agents, which function by disturbing membrane integrity, are reviewed in this article.

Methicillin-resistant Staphylococcus aureus ST398 in swine farm personnel, Belgium.

We assessed methicillin-resistant Staphylococcus aureus (MRSA) in persons on 49 swine farms in Belgium. Surveys showed that 48 (37.8%) persons carried MRSA ST398 and 1 (0.8%) had concurrent skin infection. Risk factors for carriage were MRSA carriage by pigs, regular contact with pigs and companion animals, and use of protective clothing.

Intracellular activity of antibiotics in a model of human THP-1 macrophages infected by a Staphylococcus aureus small-colony variant strain isolated from a cystic fibrosis patient: pharmacodynamic evaluation and comparison with isogenic normal-phenotype and revertant strains.

Small-colony variant (SCV) strains of Staphylococcus aureus show reduced antibiotic susceptibility and intracellular persistence, potentially explaining therapeutic failures. The activities of oxacillin, fusidic acid, clindamycin, gentamicin, rifampin, vancomycin, linezolid, quinupristin-dalfopristin, daptomycin, tigecycline, moxifloxacin, telavancin, and oritavancin have been examined in THP-1 macrophages infected by a stable thymidine-dependent SCV strain in comparison with normal-phenotype and revertant isogenic strains isolated from the same cystic fibrosis patient. The SCV strain grew slowly extracellularly and intracellularly (1- and 0.2-log CFU increase in 24 h, respectively). In confocal and electron microscopy, SCV and the normal-phenotype bacteria remain confined in acid vacuoles. All antibiotics tested, except tigecycline, caused a net reduction in bacterial counts that was both time and concentration dependent. At an extracellular concentration corresponding to the maximum concentration in human serum (total drug), oritavancin caused a 2-log CFU reduction at 24 h; rifampin, moxifloxacin, and quinupristin-dalfopristin caused a similar reduction at 72 h; and all other antibiotics had only a static effect at 24 h and a 1-log CFU reduction at 72 h. In concentration dependence experiments, response to oritavancin was bimodal (two successive plateaus of -0.4 and -3.1 log CFU); tigecycline, moxifloxacin, and rifampin showed maximal effects of -1.1 to -1.7 log CFU; and the other antibiotics produced results of -0.6 log CFU or less. Addition of thymidine restored intracellular growth of the SCV strain but did not modify the activity of antibiotics (except quinupristin-dalfopristin). All drugs (except tigecycline and oritavancin) showed higher intracellular activity against normal or revertant phenotypes than against SCV strains. The data may help rationalizing the design of further studies with intracellular SCV strains.

Intracellular activity of antibiotics in a model of human THP-1 macrophages infected by a Staphylococcus aureus small-colony variant strain isolated from a cystic fibrosis patient: study of antibiotic combinations.

In a companion paper (H. A. Nguyen et al., Antimicrob. Agents Chemother. 53:1434-1442, 2009), we showed that vancomycin, oxacillin, fusidic acid, clindamycin, linezolid, and daptomycin are poorly active against the intracellular form of a thymidine-dependent small-colony variant (SCV) strain isolated from a cystic fibrosis patient and that the activity of quinupristin-dalfopristin, moxifloxacin, rifampin, and oritavancin remains limited (2- to 3-log CFU reduction) compared to their extracellular activity. Antibiotic combination is a well-known strategy to improve antibacterial activity, which was examined here against an intracellular SCV strain using combinations with either rifampin or oritavancin. Time-kill curve analysis using either concentrations that caused a static effect for each antibiotic individually or concentrations corresponding to the maximum concentration in human serum showed largely divergent effects that were favorable when antibiotics were combined with rifampin at low concentrations only and with oritavancin at both low and high concentrations. The nature of the interaction between rifampin, oritavancin, and moxifloxacin was further examined using the fractional maximal effect method, which allows categorization of the effects of combinations when dose-effect relationships are not linear. Rifampin and oritavancin were synergistic at all concentration ratios investigated. Oritavancin and moxifloxacin were also synergistic but at high oritavancin concentrations only. Rifampin and moxifloxacin were additive. This approach may help in better assessing and improving the activity of antibiotics against intracellular SCV strains.

Epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among residents of nursing homes in Belgium.

OBJECTIVES: A national survey was conducted to determine the prevalence, risk factors and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) carriage among nursing home (NH) residents in Belgium. METHODS: A random stratified, cross-sectional prevalence survey was conducted in NH residents who were screened for MRSA carriage by multisite enriched culture. Characteristics of NHs and residents were collected by a questionnaire survey and analysed by two-stage logistic regression modelling. MRSA isolates were genotyped by PFGE, staphylococcal cassette chromosome mec (SCCmec) typing, multilocus sequence typing (MLST) and resistance genes. RESULTS: Of 2953 residents screened in 60 NHs, 587 (19.9%) were MRSA carriers. Risk factors included hospital contact, antibiotic exposure, impaired mobility and skin lesions at the resident level, and lack of MRSA surveillance, lack of antibiotic therapeutic formulary and the combination of less-developed infection control activities and a high ratio of physicians to residents at the institution level. MRSA isolates showed eight major types, three of which were predominant: B2-ST45-SCCmec IV (49%; where ST stands for sequence type); A21-ST8-SCCmec IV (13%); and A20-ST8-SCCmec IV (10%). Each was recovered in 55, 21 and 25 NHs, respectively. The geographical distribution of NH genotypes paralleled that of acute-care hospitals. CONCLUSIONS: A high prevalence of MRSA carriage in NH residents was associated with hospital care, co-morbidities and less-developed coordination of institutional care. The predominant MRSA strains from NH residents and hospitalized patients of the same area were identical. Strengthening and coordination of MRSA surveillance and control activities are warranted within and between NHs and hospitals.