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Antibiotic and antimicrobial resistance
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Prescriber-level surveillance of outpatient antimicrobial consumption to enable targeted antimicrobial stewardship: a nationwide observational study, Switzerland, 2015 to 2022
BackgroundIn Europe and other high-income countries, antibiotics are mainly prescribed in the outpatient setting, which consists of primary, specialist and hospital-affiliated outpatient care. Established surveillance platforms report antimicrobial consumption (AMC) on aggregated levels and the contribution of the different prescriber groups is unknown.
AimTo determine the contribution of different prescribers to the overall outpatient AMC in Switzerland.
MethodsWe conducted a retrospective observational study using claims data from one large Swiss health insurance company, covering the period from 2015 to 2022. We analysed antibiotic prescriptions (ATC code J01) prescribed in the Swiss outpatient setting. Results were reported as defined daily doses per 1,000 inhabitants per day (DID) and weighted according to the total population of Switzerland based on census data.
ResultsWe analysed 3,663,590 antibiotic prescriptions from 49 prescriber groups. Overall, AMC ranged from 9.12 DID (2015) to 7.99 DID (2022). General internal medicine (40.1% of all prescribed DID in 2022), hospital-affiliated outpatient care (20.6%), group practices (17.3%), paediatrics (5.4%) and gynaecology (3.7%) were the largest prescriber groups. Primary care accounted for two-thirds of the prescribed DID. Quantity and type of antibiotics prescribed varied between the prescriber groups. Broad-spectrum penicillins, tetracyclines and macrolides were the most prescribed antibiotic classes.
ConclusionPrimary care contributed considerably less to AMC than anticipated, and hospital-affiliated outpatient care emerged as an important prescriber. Surveillance at the prescriber level enables the identification of prescribing patterns within all prescriber groups, offering unprecedented visibility and allowing a more targeted antibiotic stewardship according to prescriber groups.
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Clinical isolates of ST131 blaOXA-244-positive Escherichia coli, Italy, December 2022 to July 2023
The dissemination of carbapenemase-producing Escherichia coli, although still at low level, should be continuously monitored. OXA-244 is emerging in Europe, mainly in E. coli. In Italy, this carbapenemase was reported from an environmental river sample in 2019. We report clinical isolates of OXA-244-producing ST131 E. coli in four patients admitted to an acute care hospital in Pavia, Italy. The association of this difficult-to-detect determinant with a globally circulating high-risk clone, ST131 E. coli, is of clinical relevance.
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Estimation of antimicrobial resistance of Mycoplasma genitalium, Belgium, 2022
Irith De Baetselier , Hilde Smet , Kaat Kehoe , Imelda Loosen , Marijke Reynders , Iqbal Mansoor , Lorenzo Filippin , Mathieu Cauchie , Ellen Van Even , Nadia Makki , Gilberte Schiettekatte , Wouter Vandewal , Bart Glibert , Veerle Matheeussen , Yolien Van der Beken , Reinoud Cartuyvels , Sophia Steyaert , Ann Lemmens , Maria-Grazia Garrino , Henry Paridaens , Elena Lazarova , Bénédicte Lissoir , Marine Deffontaine , Amélie Heinrichs , Veroniek Saegeman , Elizaveta Padalko , Amaryl Lecompte , Wim Vanden Berghe , Chris Kenyon and Dorien Van den BosscheBackgroundAntimicrobial resistance (AMR) of Mycoplasma genitalium (MG) is a growing concern worldwide and surveillance is needed. In Belgium, samples are sent to the National Reference Centre of Sexually Transmitted Infections (NRC-STI) on a voluntary basis and representative or robust national AMR data are lacking.
AimWe aimed to estimate the occurrence of resistant MG in Belgium.
MethodsBetween July and November 2022, frozen remnants of MG-positive samples from 21 Belgian laboratories were analysed at the NRC-STI. Macrolide and fluoroquinolone resistance-associated mutations (RAMs) were assessed using Sanger sequencing of the 23SrRNA and parC gene. Differences in resistance patterns were correlated with surveillance methodology, socio-demographic and behavioural variables via Fisher’s exact test and logistic regression analysis.
ResultsOf the 244 MG-positive samples received, 232 could be sequenced for macrolide and fluoroquinolone RAMs. Over half of the sequenced samples (55.2%) were resistant to macrolides. All sequenced samples from men who have sex with men (MSM) (24/24) were macrolide-resistant. Fluoroquinolone RAMs were found in 25.9% of the samples and occurrence did not differ between socio-demographic and sexual behaviour characteristics.
ConclusionAlthough limited in sample size, our data suggest no additional benefit of testing MG retrieved from MSM for macrolide resistance in Belgium, when making treatment decisions. The lower occurrence of macrolide resistance in other population groups, combined with emergence of fluoroquinolone RAMs support macrolide-resistance testing in these groups. Continued surveillance of resistance in MG in different population groups will be crucial to confirm our findings and to guide national testing and treatment strategies.
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Rethinking Clostridioides difficile infection (CDI) surveillance definitions based on changing healthcare utilisation and a more realistic incubation period: reviewing data from a tertiary-referral hospital, Ireland, 2012 to 2021
More LessBackgroundCommunity-associated Clostridioides difficile infections (CA-CDI) have increased worldwide. Patients with CDI-related symptoms occurring < 48 hours after hospitalisation and no inpatient stay 12 weeks prior are classified as CA-CDI, regardless of hospital day attendances 3 months before CDI onset. Healthcare-associated (HA) CDIs include those with symptom onset ≥ 48 hours post hospitalisation.
AimTo consider an incubation period more reflective of CDI, and changing healthcare utilisation, we measured how varying surveillance specifications to categorise patients according to their CDI origin resulted in changes in patients’ distribution among CDI origin categories.
MethodsNew CDI cases between 2012–2021 from our hospital were reviewed. For patients with CA-CDI, hospital day attendances in the 3 months prior were recorded. CA-CDI patients with hospital day attendances and recently discharged CDI patients (RD-CDI; CDI onset 4–12 weeks after discharge) were combined into a new ‘healthcare-exposure’ category (HE-CDI). Time from hospitalisation to disease onset was varied and the midpoint between optimal and balanced cut-offs was used instead of 48 hours to categorise HA-CDI.
ResultsOf 1,047 patients, 801 (76%) were HA-CDI, 205 (20%) CA-CDI and 41 (4%) were RD-CDI. Of the CA-CDI cohort, 45 (22%) met recent HE-CDI criteria and, when reassigned, reduced CA-CDI to 15%. Sensitivity analysis indicated a day 4 cut-off for assigning HA-CDI. Applying this led to 46 HA-CDI reassigned as CA-CDI. Applying both HE and day 4 criteria led to 72% HA-CDI, 20% CA-CDI, and 8% HE-CDI (previously RD-CDI).
ConclusionCDI surveillance specifications reflecting healthcare exposure and an incubation period more characteristic of C. difficile may improve targeted CDI prevention interventions.
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Impact of the COVID-19 pandemic on prevalence of highly resistant microorganisms in hospitalised patients in the Netherlands, March 2020 to August 2022
BackgroundThe COVID-19 pandemic resulted in adaptation in infection control measures, increased patient transfer, high occupancy of intensive cares, downscaling of non-urgent medical procedures and decreased travelling.
AimTo gain insight in the influence of these changes on antimicrobial resistance (AMR) prevalence in the Netherlands, a country with a low AMR prevalence, we estimated changes in demographics and prevalence of six highly resistant microorganisms (HRMO) in hospitalised patients in the Netherlands during COVID-19 waves (March–June 2020, October 2020–June 2021, October 2021–May 2022 and June–August 2022) and interwaves (July–September 2020 and July–September 2021) compared with pre-COVID-19 (March 2019–February 2020).
MethodsWe investigated data on routine bacteriology cultures of hospitalised patients, obtained from 37 clinical microbiological laboratories participating in the national AMR surveillance. Demographic characteristics and HRMO prevalence were calculated as proportions and rates per 10,000 hospital admissions.
ResultsAlthough no significant persistent changes in HRMO prevalence were detected, some relevant non-significant patterns were recognised in intensive care units. Compared with pre-COVID-19 we found a tendency towards higher prevalence of meticillin-resistant Staphylococcus aureus during waves and lower prevalence of multidrug-resistant Pseudomonas aeruginosa during interwaves. Additionally, during the first three waves, we observed significantly higher proportions and rates of cultures with Enterococcus faecium (pooled 10% vs 6% and 240 vs 120 per 10,000 admissions) and coagulase-negative Staphylococci (pooled 21% vs 14% and 500 vs 252 per 10,000 admissions) compared with pre-COVID-19.
ConclusionWe observed no substantial changes in HRMO prevalence in hospitalised patients during the COVID-19 pandemic.
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Assessing the impact of a national social marketing campaign for antimicrobial resistance on public awareness, attitudes, and behaviour, and as a supportive tool for healthcare professionals, England, 2017 to 2019
BackgroundPrevious United Kingdom campaigns targeting antimicrobial resistance (AMR) recommended running multimedia campaigns over an increased timeframe. The 3-year-long Keep Antibiotics Working (KAW) campaign was a mass media campaign in England targeting the public and general practitioners (GPs).
MethodsEvery year, pre- and post-campaign questionnaire data were collected from the public, whereas post-campaign interview data were obtained from GPs. Data were weighted to allow pre- and post-campaign comparisons between independent samples. Significant changes in nominal and ordinal data were determined using Pearson’s chi-squared (X2) and Mann–Whitney U tests, respectively.
ResultsPrompted campaign recognition was high, increasing by 6% from 2018 to 2019 (2017: data unavailable; 2018: 68% (680/1,000); 2019: 74% (740/1,000); X2 = 8.742, p = 0.003). Knowledge regarding declining antibiotic effectiveness when taken inappropriately improved following the campaign (net true: pre-2017 = 69.1% (691/1,000); post-2019 = 77.6%; (776/1,000); X2 = 5.753, p = 0.016). The proportion of individuals reporting concern for themselves or for children (≤ 16 years) about AMR increased by 11.2% (Z = −5.091, p < 0.001) and 6.0% (Z = −3.616, p < 0.001) respectively, pre- to post-campaign. Finally, in 2017, reported confidence to say no to patients requesting antibiotics differed significantly between GPs who were and were not aware of the campaign (net agree: 98.9% (182/184) vs 92.4% (97/105) respectively; X2 = 4.000, p = 0.045).
ConclusionA high level of prompted campaign recognition was achieved. The KAW campaign improved aspects of AMR knowledge and certain attitudes towards appropriate antimicrobial use. It increased awareness of and concern about AMR, supporting GP confidence to appropriately prescribe antibiotics. Future determination of measurable behaviour changes resulting from AMR campaigns is important.
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Emergence and persistent spread of carbapenemase-producing Klebsiella pneumoniae high-risk clones in Greek hospitals, 2013 to 2022
Kyriaki Tryfinopoulou , Marius Linkevicius , Olga Pappa , Erik Alm , Kleon Karadimas , Olov Svartström , Michalis Polemis , Kassiani Mellou , Antonis Maragkos , Alma Brolund , Inga Fröding , Sophia David , Alkiviadis Vatopoulos , Daniel Palm , Dominique L Monnet , Theoklis Zaoutis , Anke Kohlenberg and Greek CCRE study groupBackgroundPreliminary unpublished results of the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey) showed the expansion of carbapenemase-producing Klebsiella pneumoniae (CPKP) sequence type (ST) 39 in 12 of 15 participating Greek hospitals in 2019.
AimWe conducted a rapid survey to determine the extent of spread of CPKP high-risk clones in Greek hospitals in 2022 and compare the distribution of circulating CPKP clones in these hospitals since 2013.
MethodsWe analysed whole genome sequences and epidemiological data of 310 K. pneumoniae isolates that were carbapenem-resistant or ‘susceptible, increased exposure’ from Greek hospitals that participated in the European survey of carbapenemase-producing Enterobacteriaceae (EuSCAPE, 2013–2014), in the CCRE survey (2019) and in a national follow-up survey (2022) including, for the latter, an estimation of transmission events.
ResultsFive K. pneumoniae STs including ST258/512 (n = 101 isolates), ST11 (n = 93), ST39 (n = 56), ST147 (n = 21) and ST323 (n = 13) accounted for more than 90% of CPKP isolates in the dataset. While ST11, ST147 and ST258/512 have been detected in participating hospitals since 2013 and 2014, KPC-2-producing ST39 and ST323 emerged in 2019 and 2022, respectively. Based on the defined genetic relatedness cut-off, 44 within-hospital transmission events were identified in the 2022 survey dataset, with 12 of 15 participating hospitals having at least one within-hospital transmission event.
ConclusionThe recent emergence and rapid spread of new high-risk K. pneumoniae clones in the Greek healthcare system related to within-hospital transmission is of concern and highlights the need for molecular surveillance and enhanced infection prevention and control measures.
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Multidrug-resistant Corynebacterium diphtheriae in people with travel history from West Africa to France, March to September 2023
We describe 10 unlinked cases of Corynebacterium diphtheriae infection (nine cutaneous, one respiratory) in France in 2023 in persons travelling from Guinea, Mali, Senegal, Niger or Nigeria and Central African Republic. Four isolates were toxigenic. Seven genomically unrelated isolates were multidrug-resistant, including a toxigenic respiratory isolate with high-level resistance to macrolides and beta-lactams. The high rates of resistance, including against first-line agents, call for further microbiological investigations to guide clinical management and public health response in ongoing West African outbreaks.
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Rebound in community antibiotic consumption after the observed decrease during the COVID-19 pandemic, EU/EEA, 2022
We observed a rebound in consumption of antibacterials for systemic use (ATC J01) in the community sector in the European Union/European Economic Area during 2021 and 2022, after an observed decrease between 2019 and 2020. The rates in 2022 returned to pre-COVID-19-pandemic levels and were exceeded in 13 countries. Although these patterns could partly be a result of changes in disease transmission during the study period, it could also reflect a lost opportunity to strengthen and reinforce prudent antibiotic use.
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Increasing proportions of extended-spectrum β-lactamase-producing isolates among Escherichia coli from urine and bloodstream infections: results from a nationwide surveillance network, Finland, 2008 to 2019
BackgroundEscherichia coli is the leading cause of urinary tract infections (UTI) and bloodstream infections (BSI), and the emergence of antimicrobial resistance (AMR) in E. coli causes concern.
AimTo investigate changes in the proportion of extended-spectrum β-lactamase (ESBL) producing isolates among E. coli isolated from urine and blood in Finland during 2008–2019.
MethodsSusceptibility testing of 1,568,488 urine (90% female, 10% male) and 47,927 blood E. coli isolates (61% female, 39% male) from all Finnish clinical microbiology laboratories during 2008–2019 was performed according to guidelines from the Clinical and Laboratory Standard Institute during 2008–2010 and the European Committee on Antimicrobial Susceptibility Testing during 2011–2019. A binomial regression model with log link compared observed trends over time and by age group and sex.
ResultsThe annual proportion of ESBL-producing E. coli isolates among E. coli from blood cultures increased from 2.4% (23/966) to 8.6% (190/2,197) among males (average annual increase 7.7%; 95% CI: 4.4–11.0%, p < 0.01) and from 1.6% (28/1,806) to 6.4% (207/3,218) among females (9.3%; 95% CI: 4.8–14.0%, p < 0.01). In urine cultures, the proportion of ESBL-producing E. coli isolates increased from 2.2% (239/10,806) to 7.2% (1,098/15,297) among males (8.8%; 95% CI: 6.5–11.3%, p < 0.01) and from 1.0% (1,045/108,390) to 3.1% (3,717/120,671) among females (8.6%; 95% CI: 6.3–11.0%, p < 0.01). A significant increase was observed within most age groups.
ConclusionsConsidering the ageing population and their risk of E. coli BSI and UTI, the increase in the annual proportions of ESBL-producing E. coli is concerning, and these increasing trends should be carefully monitored.
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Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022
BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.
AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.
MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.
ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene blaNDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known blaNDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.
ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
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Rapid spread of a novel NDM-producing clone of Klebsiella pneumoniae CC147, Northern Italy, February to August 2023
New Delhi metallo-beta-lactamase (NDM)-producing Klebsiella pneumoniae (Kp) ST147 caused a large multi-hospital outbreak in Italy from 2018 to 2021. We describe a new ST6668 NDM-producing Kp clone, belonging to CC147, which rapidly spread across hospitals in the Pavia province (Northern Italy) from February to August 2023. Genomic analyses revealed that ST6668 is different from ST147 and fast evolving. As shown here, genomic surveillance programmes are useful for tracking the spread of new clones with reduced susceptibility to most antibiotics.
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Healthcare-associated infections by multidrug-resistant bacteria in Andalusia, Spain, 2014 to 2021
BackgroundMultidrug-resistant (MDR) bacteria are among chief causes of healthcare-associated infections (HAIs). In Spain, studies addressing multidrug resistance based on epidemiological surveillance systems are lacking.
AimIn this observational study, cases of HAIs by MDR bacteria notified to the epidemiological surveillance system of Andalusia, Spain, between 2014−2021, were investigated. Notified cases and their spatiotemporal distribution were described, with a focus on social determinants of health (SDoH).
MethodsNew cases during the study period of HAIs caused by extended-spectrum β-lactamase (ESBL)-/carbapenemase-producing Enterobacterales, MDR Acinectobacter baumannii, MDR Pseudomonas aeruginosa or meticillin resistant Staphylococcus aureus were considered. Among others, notification variables included sex and age, while socio-economic variables comprised several SDoH. Cases’ spatial distribution across municipalities was assessed. The smooth standardised incidence ratio (sSIR) was obtained using a Bayesian spatial model. Association between municipalities’ sSIR level and SDoH was evaluated by bivariate analysis.
ResultsIn total, 6,389 cases with a median age of 68 years were notified; 61.4% were men (n = 3,921). The most frequent MDR bacteria were ESBL-producing Enterobacterales (2,812/6,389; 44.0%); the main agent was Klebsiella spp. (2,956/6,389; 46.3%). Between 2014 and 2021 case numbers appeared to increase. Overall, up to 15-fold differences in sSIR between municipalities were observed. In bivariate analysis, there appeared to be an association between municipalities’ sSIR level and deprivation (p = 0.003).
ConclusionThis study indicates that social factors should be considered when investigating HAIs by MDR bacteria. The case incidence heterogeneity between Andalusian municipalities might be explained by SDoH, but also possibly by under-notification. Automatising reporting may address the latter.
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Deciphering mechanisms of blaNDM gene transmission between human and animals: a genomics study of bacterial isolates from various sources in China, 2015 to 2017
More LessBackgroundIn China, the blaNDM gene has been recovered from human bacterial isolates since 2011. After 2014, detections of this gene in animal and food bacterial isolates have increasingly been reported.
AimWe aimed to understand how blaNDM-bearing bacteria could spread between humans, animals, and animal-derived food.
MethodsA total of 288 non-duplicate Escherichia coli strains, including 130 blaNDM-carrying and 158 blaNDM-negative strains were collected from clinical (humans), food-producing animals (pigs) and food (retail pork) sources between 2015 and 2017. The strains were whole genome sequenced. Core-genome-multilocus-sequence-typing was conducted. To investigate if sequence types (STs) found in human, animal or food samples could have a prior origin in a clinical, animal or food-borne animal reservoir, discriminant analysis of principal components (DAPC) was used. Plasmids bearing blaNDM were characterised.
ResultsThe 130 blaNDM-carrying E. coli strains comprised a total of 60 STs, with ST167 (10/51), ST77 (6/33) and ST48 (6/46) being most prevalent in clinical, animal and food sources, respectively. Some ST10 and ST167 strains were respectively found among all three sources sampled, suggesting they might enable transfer of blaNDM between sources. DAPC analysis indicated possible transmissions of ST167 from humans to animals and ST10 from animals to human. In 114 of 130 blaNDM-carrying isolates, blaNDM was located on an IncX3 plasmid.
ConclusionThis study in a Chinese context suggests that cross-species transmission of certain STs of E. coli harbouring blaNDM on mobile elements, may facilitate the spread of carbapenem-resistant Enterobacteriaceae. Stringent monitoring of blaNDM-bearing E. coli in ecosystems is important.
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Two cases of extensively drug-resistant (XDR) Neisseria gonorrhoeae infection combining ceftriaxone-resistance and high-level azithromycin resistance, France, November 2022 and May 2023
We report two extensively drug-resistant (XDR) Neisseria gonorrhoeae (NG) isolates combining high-level resistance to azithromycin and resistance to ceftriaxone, obtained in France from two heterosexual patients, one of whom returned from Cambodia. Whole genome sequencing identified MLST ST16406, the mosaic penA-60.001 which caused ceftriaxone resistance in the internationally spreading FC428 clone, and the A2059G mutation in the 23S rRNA gene. The NG isolates F93 and F94 were related to XDR isolates detected in Austria and the United Kingdom in 2022.
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Antimicrobial susceptibility testing and reporting practices of public hospital microbiology laboratories in Greece, 2022: A national observational survey and call for action
Antimicrobial resistance (AMR) in Greece is among the highest across the European Union/European Economic Area (EU/EEA), with high AMR rates even to last-line antibiotics. To better understand the clinical microbiology laboratory practices and capacities in species identification and antimicrobial susceptibility testing (AST) across public healthcare establishments in Greece, we sent a questionnaire to 98 of 128 public hospital microbiology laboratories between 1 February and 1 April 2022. Of the 73.5% (72/98) that responded, 51.4% (37/72) reported using EUCAST guidelines. Two of three laboratories used an automated instrument for species identification and AST for all laboratory samples. Broth microdilution for colistin susceptibility testing was used by 46 of the laboratories, more frequently in larger (> 400 beds) versus smaller (< 400 beds) hospitals (90.5% (19/21) vs 52.9% (27/51) respectively, p = 0.011). MALDI-TOF mass spectrometry was available in one of 10 laboratories, and more often in larger compared to smaller hospitals (p = 0.035). Although the majority of laboratories had a laboratory information system (LIS) in place, only half had the capacity to extract data directly from the LIS for the purpose of AMR surveillance; 73.6% (53/72) used restrictive antibiograms. Public microbiology laboratory AMR capacities in Greece require improvement, prioritising interventions for EUCAST guidelines implementation.
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Intraregional hospital outbreak of OXA-244-producing Escherichia coli ST38 in Norway, 2020
Infections with OXA-244-carbapenemase-producing Escherichia coli with sequence type (ST)38 have recently increased in Europe. Due to its low-level activity against carbapenems, OXA-244 can be difficult to detect. Previous assessments have not revealed a clear source and route of transmission for OXA-244-producing E. coli, but there are indications of non-healthcare related sources and community spread. Here we report a hospital-associated outbreak of OXA-244-producing E. coli ST38 involving three hospitals in Western Norway in 2020. The outbreak occurred over a 5-month period and included 12 cases identified through clinical (n = 6) and screening (n = 6) samples. The transmission chain was unclear; cases were identified in several wards and there was no clear overlap of patient stay. However, all patients had been admitted to the same tertiary hospital in the region, where screening revealed an outbreak in one ward (one clinical case and five screening cases). Outbreak control measures were instigated including contact tracing, isolation, and screening; no further cases were identified in 2021. This outbreak adds another dimension to the spread of OXA-244-producing E. coli ST38, illustrating this clone’s ability to establish itself in the healthcare setting. Awareness of challenges concerning OXA-244-producing E. coli diagnostic is important to prevent further spread.
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Nationwide, population-based observational study of the molecular epidemiology and temporal trend of carbapenemase-producing Enterobacterales in Norway, 2015 to 2021
IntroductionNational and regional carbapenemase-producing Enterobacterales (CPE) surveillance is essential to understand the burden of antimicrobial resistance, elucidate outbreaks, and develop infection-control or antimicrobial-treatment recommendations.
AimThis study aimed to describe CPE and their epidemiology in Norway from 2015 to 2021.
MethodsA nationwide, population-based observational study of all verified clinical and carriage CPE isolates submitted to the national reference laboratory was conducted. Isolates were characterised by antimicrobial susceptibility testing, whole genome sequencing (WGS) and basic metadata. Annual CPE incidences were also estimated.
ResultsA total of 389 CPE isolates were identified from 332 patients of 63 years median age (range: 0–98). These corresponded to 341 cases, 184 (54%) being male. Between 2015 and 2021, the annual incidence of CPE cases increased from 0.6 to 1.1 per 100,000 person-years. For CPE-isolates with available data on colonisation/infection, 58% (226/389) were associated with colonisation and 38% (149/389) with clinical infections. WGS revealed a predominance of OXA-48-like (51%; 198/389) and NDM (34%; 134/389) carbapenemases in a diversified population of Escherichia coli and Klebsiella pneumoniae, including high-risk clones also detected globally. Most CPE isolates were travel-related (63%; 245/389). Although local outbreaks and healthcare-associated transmission occurred, no interregional spread was detected. Nevertheless, 18% (70/389) of isolates not directly related to import points towards potentially unidentified transmission routes. A decline in travel-associated cases was observed during the COVID-19 pandemic.
ConclusionsThe close-to-doubling of CPE case incidence between 2015 and 2021 was associated with foreign travel and genomic diversity. To limit further transmission and outbreaks, continued screening and monitoring is essential.
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Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018
BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.
AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.
MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999–2004 and 2015–2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.
ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015–2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3–6 months.
ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.
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Associated deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in Switzerland, 2010 to 2019
BackgroundCassini et al. (2019) estimated that, in 2015, infections with 16 different antibiotic-resistant bacteria resulted in ca 170 disability-adjusted life-years (DALYs) per 100,000 population in the European Union and European Economic area (EU/EEA). The corresponding estimate for Switzerland was about half of this (87.8 DALYs per 100,000 population) but still higher than that of several EU/EEA countries (e.g. neighbouring Austria (77.2)).
AimIn this study, the burden caused by the same infections due to antibiotic-resistant bacteria (‘AMR burden’) in Switzerland from 2010 to 2019 was estimated and the effect of the factors ‘linguistic region’ and ‘hospital type’ on this estimate was examined.
MethodsNumber of infections, DALYs and deaths were estimated according to Cassini et al. (2019) whereas separate models were built for each linguistic region/hospital type combination.
ResultsDALYs increased significantly from 3,995 (95% uncertainty interval (UI): 3;327–4,805) in 2010 to 6,805 (95% UI: 5,820–7,949) in 2019. Linguistic region and hospital type stratifications significantly affected the absolute values and the slope of the total AMR burden estimates. DALYs per population were higher in the Latin part of Switzerland (98 DALYs per 100,000 population; 95% UI: 83–115) compared with the German part (57 DALYs per 100,000 population; 95% UI: 49–66) and in university hospitals (165 DALYs per 100,000 hospitalisation days; 95% UI: 140–194) compared with non-university hospitals (62 DALYs per 100,000 hospitalisation days; 95% UI: 53–72).
ConclusionsThe AMR burden estimate in Switzerland has increased significantly between 2010 and 2019. Considerable differences depending on the linguistic region and the hospital type were identified – a finding which affects the nationwide burden estimation.
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