Vlaminckx, B. J. M. | bioRxiv Science

bioRxiv2023

Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022

Invasive group A streptococcal (iGAS) disease cases increased in the first half year of 2022 in the Netherlands with a remarkably high proportion of emm4 isolates. Whole-genome sequence analysis of 66 emm4 isolates, 40 isolates from the pre-COVID-19-pandemic period 2009-2019 and 26 contemporary isolates from 2022, identified a novel Streptococcus pyogenes lineage (M4NL22), which accounted for 85% emm4 iGAS cases in 2022. Surprisingly, we detected few isolates of the emm4 hypervirulent clone, which has replaced nearly all other emm4 in the USA and the UK. M4NL22 displayed genetic differences compared to other emm4 strains, although these were of unclear biological significance. In publicly available data, we identified a single Norwegian isolate belonging to M4NL22, which was sampled after the isolates from this study, possibly suggesting export of M4NL22 to Norway. In conclusion, our study identified a novel S. pyogenes emm4 lineage underlying an increase of iGAS disease in early 2022 in the Netherlands and results have been promptly communicated with public health officials. Impact statementGroup A Streptococcus (predominantly comprising Streptococcus pyogenes) has a long history of causing disease in humans. Over the past decades, researchers have described various changes in the S. pyogenes population circulating in humans. In this study, we describe a shift in the S. pyogenes population within type emm4 in the Netherlands in early 2022. A novel lineage, which we termed M4NL22, became the predominant emm4 lineage during this period. This was surprising, as in other countries such as the USA and the UK, another recently emerged lineage became dominant. Our work informed public health officials on the possible causes of increased S. pyogenes cases in the Netherlands and underlines the added value of continued active bacteriological surveillance. Data summaryCode is freely available from https://github.com/boasvdp/GAS_M4. All sequencing data is freely available from BioProject PRJEB58654.

microbiology↗

bioRxiv2017

Diagnostic Prediction Tools For Bacteraemia Caused By 3rd Generation Cephalosporin-Resistant Enterobacteriaceae In Suspected Bacterial Infections: A Nested Case-Control Study

ObjectivesCurrent guidelines for empirical antibiotic treatment poorly predict the presence of 3rd generation cephalosporin resistant Enterobacteriaceae (3GC-R EB) as a cause of infection, thereby increasing unnecessary carbapenem use. We aimed to develop diagnostic scoring systems to better predict the presence of 3GC-R EB as a cause of bacteraemia.\n\nMethodsA retrospective nested case-control study was performed that included patients [≥]18 years in whom blood cultures were obtained and intravenous antibiotics were initiated. Each patient with 3GC-R EB bacteraemia was matched to four control infection episodes within the same hospital, based on blood culture date and onset location (community or hospital). Starting from 32 described clinical risk factors at infection onset, selection strategies were used to derive scoring systems for the probability of community- and hospital-onset 3GC-R EB bacteraemia.\n\nResults3GC-R EB bacteraemia occurred in 90 of 22,506 (0.4%) community-onset and in 82 of 8,110 (1.0%) hospital-onset infections, and these cases were matched to 360 community-onset and 328 hospital-onset control episodes, respectively. The derived community-onset and hospital-onset scoring system consisted of 6 and 9 predictors, respectively, with c-statistics of 0.807 (95% confidence interval 0.756-0.855) and 0.842 (0.794-0.887). With selected score cutoffs, the models identified 3GC-R EB bacteraemia with equal sensitivity as existing guidelines, but reduced the proportion of patients classified as at risk for 3GC-R EB bacteraemia (i.e. eligible for empiric carbapenem therapy) with 40% in patients with community-onset and 49% in patients with hospital-onset infection.\n\nConclusionsThese prediction rules for 3GC-R EB bacteraemia may reduce unnecessary empiric carbapenem use.

epidemiology↗