Eurosurveillance - Volume 28, Issue 20, 18 May 2023

In 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.

This study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.

We 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.

Via 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.

We validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.

Cassini 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)).

In 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.

Number 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.

DALYs 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).

The 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.

Antimicrobial resistance (AMR) is of public health concern worldwide.

We aimed to summarise the German AMR situation for clinicians and microbiologists.

We conducted a systematic review and meta-analysis of 60 published studies and data from the German Antibiotic-Resistance-Surveillance (ARS). Primary outcomes were AMR proportions in bacterial isolates from infected patients in Germany (2016–2021) and the case fatality rates (2010–2021). Random and fixed (common) effect models were used to calculate pooled proportions and pooled case fatality odds ratios, respectively.

The pooled proportion of meticillin resistance in Staphylococcus aureus infections (MRSA) was 7.9% with a declining trend between 2014 and 2020 (odds ratio (OR) = 0.89; 95% CI: 0.886–0.891; p < 0.0001), while vancomycin resistance in Enterococcus faecium (VRE) bloodstream infections increased (OR = 1.18; (95% CI: 1.16–1.21); p < 0.0001) with a pooled proportion of 34.9%. Case fatality rates for MRSA and VRE were higher than for their susceptible strains (OR = 2.29; 95% CI: 1.91–2.75 and 1.69; 95% CI: 1.22–2.33, respectively). Carbapenem resistance in Gram-negative pathogens (Klebsiella pneumoniae, Acinetobacter baumannii, Enterobacter spp. and Escherichia coli) was low to moderate (< 9%), but resistance against third-generation cephalosporins and fluoroquinolones was moderate to high (5–25%). Pseudomonas aeruginosa exhibited high resistance against carbapenems (17.0%; 95% CI: 11.9–22.8), third-generation cephalosporins (10.1%; 95% CI: 6.6–14.2) and fluoroquinolones (24.9%; 95% CI: 19.3–30.9). Statistical heterogeneity was high (I² > 70%) across studies reporting resistance proportions.

Continuous efforts in AMR surveillance and infection prevention and control as well as antibiotic stewardship are needed to limit the spread of AMR in Germany.