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Non-tuberculous mycobacteria (NTM) include more than 160 ubiquitous, environmental, acid-fast-staining bacterial species, some of which may cause disease in humans. Chronic pulmonary infection is the most common clinical manifestation. Although patients suffering from chronic lung diseases are particularly susceptible to NTM pulmonary disease, many affected patients have no apparent risk factors. Host and pathogen factors leading to NTM pulmonary disease are not well understood and preventive therapies are lacking. NTM isolation and pulmonary disease are reported to rise in frequency in Europe as well as in other parts of the world. Differentiation between contamination, infection, and disease remains challenging. Treatment of NTM pulmonary disease is arduous, lengthy, and costly. Correlations between results of in vitro antibiotic susceptibility testing and clinical treatment outcomes are only evident for the Mycobacterium avium complex, M. kansasii, and some rapidly growing mycobacteria. We describe the epidemiology of NTM pulmonary disease as well as emerging NTM pathogens and their geographical distribution in non-cystic fibrosis patients in Europe. We also review recent innovations for the diagnosis of NTM pulmonary disease, summarize treatment recommendations, and identify future research priorities to improve the management of patients affected by NTM pulmonary disease.

The aim of this study was to analyze inpatient antibiotic consumption during the first 16 months of the COVID-19 pandemic in Switzerland. The entire period (January 2018–June 2021) was divided into the prepandemic period, the first and second waves, and the intermediate period. In the first year of the pandemic, total overall inpatient antibiotic consumption measured in defined daily doses (DDD) per 100 bed-days remained stable (+1.7%), with a slight increase in ICUs of +4.2%. The increase in consumption of broad-spectrum antibiotics was +12.3% overall and 17.3% in ICUs. The segmented regression model of monthly data revealed an increase in overall antibiotic consumption during the first wave but not during the second wave. In the correlation analysis performed in a subset of the data, a significant positive association was found between broad-spectrum antibiotic consumption and an increasing number of hospitalized COVID-19 patients (p = 0.018). Restricting this dataset to ICUs, we found significant positive correlations between the number of hospitalized COVID-19 patients and total antibiotic consumption (p = 0.007) and broad-spectrum antibiotic consumption (p < 0.001). In conclusion, inpatient antibiotic use during the different periods of the COVID-19 pandemic varied greatly and was predominantly notable for broad-spectrum antibiotics.

This nation-wide survey on the epidemiology of vancomycin-resistant enterococci (VRE) included 142 healthcare institutions and showed an increasing number of VRE colonizations and infections in Switzerland, probably for the most part due to nosocomial dissemination. The introduction and spread of a new clone, gaps in VRE screening policies as well as heterogeneity regarding the management of VRE clusters may be possible explanations.

Mycobacterium genavense is a rare pathogen affecting severely immunosuppressed patients. We report the case of persistent relapsing M. genavense infection in a 48-year-old African man with a positive diagnosis of HIV infection. Despite being under effective antiretroviral therapy with partial immune reconstitution, he developed irreversible long-term abdominal complications, possibly due to persistent M. genavense infection and sustained inflammation. Case management consists of individual risk assessment, close follow-up and personalised treatment strategies concerning the duration of antimycobacterial therapy and early application of steroids. Patients with profound immunosuppression, a high viral load at HIV diagnosis and a high burden of M. genavense, appear to be at higher risk. The pathogenicity of this complication is not well known and its optimal management has still to be determined.

Chronic respiratory infectious diseases are causing high rates of morbidity and mortality worldwide. Tuberculosis, a major cause of chronic pulmonary infection, is currently responsible for approximately 1.5 million deaths per year. Although important advances in the fight against tuberculosis have been made, the progress towards eradication of this disease is being challenged by the dramatic increase in multidrug-resistant bacilli. Nontuberculous mycobacteria causing pulmonary disease and chronic pulmonary aspergillosis are emerging infectious diseases. In contrast to other infectious diseases, chronic respiratory infections share the trait of having highly variable treatment outcomes despite longstanding antimicrobial therapy. Recent scientific progress indicates that medicine is presently at a transition stage from programmatic to personalized management. We explain current state-of-the-art management concepts of chronic pulmonary infectious diseases as well as the underlying methods for therapeutic decisions and their implications for personalized medicine. Furthermore, we describe promising biomarkers and techniques with the potential to serve future individual treatment concepts in this field of difficult-to-treat patients. These include candidate markers to improve individual risk assessment for disease development, the design of tailor-made drug therapy regimens, and individualized biomarker-guided therapy duration to achieve relapse-free cure. In addition, the use of therapeutic drug monitoring to reach optimal drug dosing with the smallest rate of adverse events as well as candidate agents for future host-directed therapies are described. Taken together, personalized medicine will provide opportunities to substantially improve the management and treatment outcome of difficult-to-treat patients with chronic respiratory infections.

Background A large outbreak with different clones of vancomycin-resistant enterococci (VRE) affected the Bern University Hospital group for several months. The aim of this study was to describe the extent of the outbreak, using whole-genome sequencing (WGS). Methods Triggered by two cases of VRE bloodstream infections on our hemato-oncology ward, an outbreak investigation was started. Microbiological diagnosis of VRE was obtained by culture and PCR. Epidemiological links were assessed by meticulous chart review and supplemented with WGS analyses. Multiple infection control measures were implemented to avoid further transmissions. Results Between December 2017 and April 2018, 2,877 screening samples were obtained from 1,200 patients. Three out of six hospitals within the Bern University Hospital group were affected. Eighty-three patients (6.9%) were colonized with VR Enterococcus faecium. Of those, 76 (91.6%) had a strain carrying vanB, with 70 (84%) isolates virtually identical (separated by up to two alleles) by cgMLST and identified as MLST type ST796 (figure). The remaining seven patients (8.4%) were colonized with vanA carrying strains from five different STs. Five patients (7%) developed an invasive infection with VRE ST796. Temporo-spatial links were found in most patients carrying the outbreak strain. In order to control the outbreak, extensive infection control measures were implemented. By April 2018 the outbreak was contained with these specific measures. Conclusion This VRE outbreak was characterized by a rapid intra- and inter-institutional spread of the emergent clone ST796. This clone was recently described in Australia and New Zealand but never before in Europe.1,2 A multi-faceted infection control led to the containment of the outbreak. References 1. Mahony AA, et al. Vancomycin-resistant Enterococcus faecium sequence type 796—rapid international dissemination of a new epidemic clone. Antimicrob Resist Infect Control. 2018:7:44. 2. Leong KWC, et al. Emergence of vancomycin-resistant Enterococcus faecium at an Australian Hospital: a whole genome sequencing analysis. Sci Rep. 2018:8(1):6274. 3. de Been M, et al. Core genome multilocus sequence typing scheme for high- resolution typing of Enterococcus faecium. J Clin Microbiol. 2015:53(12):3788–97. Disclosures All authors: No reported disclosures.