Abstract Background The wide adoption of whole genome sequencing has enabled the implementation of genomics-based systems, which provide unparalleled resolution for the surveillance and outbreak investigation of bacterial pathogens. To fully exploit the wealth and complexity of genomics data, bioinformatics methods need to be highly scalable, provide accurate and extensive data for potential downstream analyses, as well as analytic capabilities. Here, we present chewBBACA 3, a suite of modules for scalable and comprehensive bacterial whole- and core-genome multilocus sequence typing (wg/cgMLST) with built-in features to create new schemas, evaluate loci diversity and strain similarity. Results chewBBACA 3 enables faster and more accurate schema creation and allele calling by complementing an alignment-based approach with alignment-free methods, including hash-based comparisons and minimizer-based clustering. Schema creation is up to 55-fold faster and identifies up to 10% more loci than its predecessor, chewBBACA 2. Furthermore, chewBBACA 3 can quickly adapt or import schemas available on external wg/cgMLST platforms or Chewie-NS, promoting interoperability. The efficiency of allele calling allows processing larger genome collections, from thousands to tens of thousands of genomes, at the whole- and core-genome levels without requiring high computational resources and being up to 52-fold faster than similar tools. chewBBACA 3’s enhanced sensitivity allows it to identify and classify more schema loci and coding sequences than the compared methods, resulting in higher resolution for strain comparison. Moreover, the allelic profiles, classification statistics and associated sequence data produced by chewBBACA 3 can be the basis for detailed analyses that provide added value in surveillance and outbreak investigation settings. New modules leverage the potential of the schema and allele call results data to create interactive reports that enable an intuitive and in-depth analysis of allele diversity in loci of interest and allow assessing strain similarity based on loci presence, allelic distances and phylogenetic analysis. Conclusions chewBBACA 3 provides functionalities for complete wg/cgMLST analysis at scale, lowering the barrier for the use of wg/cgMLST and offering extensive results and analytic capabilities for streamlined, comprehensive, and local analyses. chewBBACA 3 is freely available at https://github.com/B-UMMI/chewBBACA .

[This corrects the article DOI: 10.3389/fmicb.2025.1712362.].

Streptococcus pyogenes cause invasive infections with variable incidence over time. In 2023, an increase in invasive S. pyogenes infections caused by emm-types 1 and 12 was reported globally. In Southern Sweden an increase in S. pyogenes emm12 severe infections was also noted and we set out to determine if this increase was caused by a single genetic sublineage. Data on severe S. pyogenes infections notified between July 1st 2016 and June 30th 2023, including emm-types, was obtained from the Regional Centre for Communicable Disease Control. All emm12 isolates recovered during November-April each season were sequenced, analysed by core genome multilocus sequence typing (cgMLST), and compared with international emm12 isolates. Clinical information was obtained from the medical records. During the 2022/23 season, 157 cases of severe S. pyogenes infection were reported, of which 32 (20

Abstract The third Bacterial Genome Sequencing Pan-European Network conference, held in Engelberg, Switzerland (12–15 January 2026), brought together experts from six European countries to discuss the implementation of bacterial genome sequencing in clinical microbiology and public health. Key themes included regulatory frameworks (In Vitro Diagnostic Regulation, General Data Protection Regulation), standardization, quality control, data sharing, economic evaluation, and the integration of artificial intelligence and long-read sequencing into diagnostic workflows. Across presentations, panel discussions, and workshops, participants emphasized that successful implementation of genome sequencing requires more than technical capacity: it depends on robust validation, sustainable funding, interoperable data standards, ethical governance, and interdisciplinary collaboration. The meeting highlighted that sequencing should remain question-driven and clinically meaningful, balancing cost, turnaround time, and public health impact. Overall, the conference reinforced the need for coordinated European efforts to advance responsible, standardized, and sustainable genomic surveillance and diagnostics.

The importance of invasive Streptococcus agalactiae (Lancefield group B streptococci - GBS) disease among adults is increasingly recognized worldwide. Acquisition from other humans or an individual's own microbiota is thought to be the origin of the diverse GBS lineages causing these infections. We report two cases in three consecutive years (2016-2018) of invasive GBS disease in Portugal due to the unusual ST283 lineage, a hypervirulent clone circulating in Southeast Asia (SEA) and associated to foodborne transmission and large disease outbreaks among previously healthy younger adults. The need for genetic analyses, which are infrequently performed, to identify ST283 may mean that cases of ST283 occur sporadically outside SEA but go undetected.

Background: Genome-based epidemiological surveillance of Streptococcus pyogenes (Lancefield Group A Streptococcus, GAS) infections facilitated the detection of emergent successful lineages, such as the M1UK sublineage. This sublineage dominated the post-COVID-19 upsurge of invasive GAS infections (iGAS) in multiple countries, including Portugal. Here, we characterized the genetic lineages causing iGAS in Portugal during 2016-2019 to evaluate possible temporal trends and compare them with internationally circulating lineages. Methods: Whole-genome sequencing and antimicrobial susceptibility testing were performed for 273 iGAS isolates. Results: The dominant emm types were emm1 (n = 87), emm3 (n = 37), and emm89 (n = 26), collectively comprising 55 % of all isolates (n = 273). Throughout the study, the M1UKsublineage increased in prevalence, accounting for 48 % of all emm1 isolates. Core-genome multilocus sequence typing supports multiple introductions of M1UKin Portugal pre-COVID-19, and a limited relatedness to the M1UKisolates recovered during the post-COVID-19 surge in pediatric iGAS. Several internationally disseminated lineages expressing various emm types were identified. Mutations inactivating key regulators of virulence (CovRS and RopB) and in the capsule locus were found in a significant fraction of isolates. Macrolide resistance was primarily associated with the erm(A) and erm(B) genes and remained low (4 %), highlighting differences between Europe and North America. Conclusions: Despite adult iGAS in Portugal being caused by geographically widespread, successful GAS lineages that may be repeatedly introduced in the country, including M1UK, there was no apparent increase in disease. This is consistent with upsurges of iGAS post-COVID-19 not being driven primarily by the emergence or introduction of novel GAS clones.

Abstract Background Streptococcus pneumoniae serotype 3 (Spn3) is included in the pneumococcal 13-valent conjugate vaccine (PCV13) but carriage and invasive disease persist worldwide. Previous work showed that the prevalent clonal complex 180 (CC180) of Spn3 is comprised of 3 genetically distinct lineages: clade Iα, Iβ, and II; a post-PCV13 shift towards increased incidence of clade II strains with a concomitant decrease in clade Iα and 1β incidence has been observed in the United States, England, and Wales. It was hypothesized that PCV13 is controlling clade Iα and 1β but not clade II, resulting in clade II expansion and ultimately rendering the vaccine ineffective against Spn3. It is imperative to test this hypothesis in other regional contexts given the implications on vaccine design and efficacy. Therefore, our group assessed the dynamics of Spn3 population structure and PCV13 in Portugal. Prevalence of Spn3 clonal complexes before and after the introduction of PCV13 in Portugal Methods We whole-genome sequenced 501 Spn3 strains from Portugal and analyzed over 1400 Spn3 whole genome sequences from published datasets for global comparisons. Phylogenetic tree construction, clade identification, clonal complex typing, and annotation of antimicrobial resistance (AMR) and virulence genes was used to evaluate changes in bacterial genetics. Prevalence of Spn3 clades before and after the introduction of PCV13 in Portugal Results Consistent with previous work, the prevalence of clonal complexes significantly changed before and after the introduction of PCV13 in Portugal (p=4.94-12): CC180 increased from 29% of Spn3 strains to 65%. The prevalence of lineages also changed (p=2.33-13): clade Iα increased from 21% to 54% of Spn3 strains, while clade II was not detected pre-PCV13 but increased to only 5% post-PCV13. This contrasts with studies conducted elsewhere. The phylogenetic distribution of AMR alleles is similar across different regions, so altered antibiotic fitness does not explain the continued success of clade Iα over clade II in Portugal. Conclusion Our data suggests clade II is not the global driver of Spn3 PCV13 vaccine escape as clade Iα remains dominant in Portugal. Current work aims to determine if clade Iα allelic variants augment virulence and thus competitive fitness against clade II in Portugal. Informed vaccine design requires an understanding of the region-specific bacterial population structure and genetic features to optimize efficacy. Disclosures Richard Malley, MD, Amplitude Therapeutics: Board Member|Corner Therapeutics: Board Member|GSK: Advisor/Consultant|Merck: Advisor/Consultant Mario Ramirez, PhD, GSK: Advisor/Consultant|Merck Sharp and Dohme: Advisor/Consultant|Pfizer: Honoraria

Bacterial pathogens deploy diverse virulence factors to subvert host immunity, yet the molecular details of these interactions often remain unresolved. Here, we investigate the structure and host interactome of the Streptococcus pyogenes nuclease A (SpnA). We characterized the structure and dynamics of SpnA using hydrogen-deuterium exchange mass spectrometry and single-particle electron cryo microscopy, yielding the first structural insights to this protein. This allowed us to identify an additional oligonucleotide-binding domain whose flexible structure may play an important function in the nucleolytic activity of SpnA. Affinity-pulldown mass spectrometry identified the complement system membrane attack complex C5b67 components as key interactors in human plasma. Cross-linking mass spectrometry combined with integrative modeling identified the direct binding interfaces between SpnA and C5b67. These interfaces are highly conserved among genetically diverse S. pyogenes strains. The interaction between SpnA and C5b67 is suggested to prevent the assembly of a functional membrane attack complex. Taken together, our findings uncover a novel function of SpnA in complement inhibition and identifies new potential targets to prevent and treat S. pyogenes infections. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2022-03860 Royal Physiographic Society of Lund Stiftelsen Clas Groschinskys Minnesfond, https://ror.org/015kngk22 Åke Wibergs Stiftelse, https://ror.org/03htnqd27 Crafoord Foundation, https://ror.org/02hwwbr17 Alfred Österlunds Stiftelse, https://ror.org/020hnjs91 Fundação para a Ciência e Tecnologia, 2020.08493.BD

Shewanella is an environmentally ubiquitous genus with significant roles in bioelectrochemical applications and human infections. However, identification problems involving Shewanella putrefaciens, Shewanella xiamenensis, and Shewanella seohaensis have been reported, potentially hindering research progress in these areas. In this study, we explored how to discriminate between these species. By comparing the genomes of Shewanella spp. available in public databases with that of the newly sequenced strain DSM9451, we showed that this strain is a member of the species S. seohaensis. Of the eight public genomes associated with this species, only two were correctly identified in public databases. Phenotypic analysis revealed distinct features of S. seohaensis with respect to S. putrefaciens and Shewanella decolorationis. However, only differences in the intensity of biochemical reactions were observed between S. xiamenensis and S. seohaensis. To discriminate between these closely related species and explore their diversity, a whole-genome multilocus sequence typing scheme was developed. The scheme distinguished related species and revealed significant diversity among S. seohaensis and S. xiamenensis isolates, suggesting that both species may harbor isolates with significantly different metabolic properties. These differences are so wide within the clade that they may explain why these two species are difficult to distinguish. The identification of exclusive genes of each species allowed the design of a simple molecular method to differentiate S. seohaensis from closely related species, which will help in clarifying its role in human infections and environmental processes.IMPORTANCEMisidentification within the Shewanella genus, particularly between Shewanella putrefaciens, Shewanella xiamenensis, and Shewanella seohaensis, has been reported and misperceives scientific research on Shewanella spp. in diverse fields, including both biotechnological applications and human infections. Near-complete 16S rRNA gene sequencing fails to correctly classify many Shewanella species, and MALDI-TOF systems used in clinical microbiology laboratories are suboptimal for species-level identification. In this study, we identified phenotypic characteristics that can guide differentiation and classification, and building upon the identification of species-specific genes, we suggest an accurate and cost-effective molecular test as an alternative to genome sequencing. The proposed whole-genome multilocus sequence typing scheme allows the exploration of species and strain diversity, highlighting the limitations of generalizing results from studies of a single strain. As an emergent pathogen and biotechnological candidate, the proper identification by a single molecular test will enhance the insights about these species towards biotechnology development and public health safety.

BACKGROUND:Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn) causing disease among children and adults worldwide. The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal to conduct our population genomics and molecular epidemiology comparative study. METHODS:We performed whole-genome sequencing (WGS) of 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999 and 2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics. FINDINGS:Relative to strains from all other lineages, CC180 Clades I, II, III, IV, and VI strains trend towards a decreased association with invasive disease cases compared to non-invasive pneumonia cases (binomial logistic regression, odds ratio or OR = 0.59, 95% confidence interval or CI = [0.34, 0.98], P = 0.046) and adult patients compared to paediatric patients (binomial logistic regression, OR = 0.34, 95% CI = [0.098, 0.92], P = 0.054). The serotype 3 CCs shifted post-PCV13 such that Clades I-VI comprise the majority of post-PCV13 lineages (binomial logistic regression, OR = 7.33, 95% CI = 4.36, 12.80, P < 0.0001), with Clade I representing 54% (220/404) of all post-PCV13 strains. As observed elsewhere, Clade I strains from Portugal are largely antibiotic-sensitive and carry the ΦOXC141 prophage. However, strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins. INTERPRETATION:Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The additional accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape. FUNDING:National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.

AbstractNucleic acid amplification tests (NAATs) greatly enhance the capacity to identify the etiology of pediatric complicated pneumonia. However, the use of pneumococcal conjugate vaccines could reduce the importance of Streptococcus pneumoniae in pediatric complicated pneumonia with the potential emergence of other bacterial agents. Using an expanded NAAT in culture negative pleural fluid or empyema samples collected in 2010–2024 (n = 554) in Portugal, we show that S. pneumoniae remains the most frequent agent despite decades of pneumococcal conjugate vaccine use and the COVID-19 pandemic. A rebound in pediatric complicated pneumonia occurred post-pandemic, including a rise in cases by Streptococcus pyogenes and Haemophilus influenzae. Empiric therapy of pediatric complicated pneumonia should still consider S. pneumoniae as the most likely cause, even in countries where the pneumococcal conjugate vaccine is in the national immunization program with a high uptake.

Increases in macrolide resistance occurred recently among Streptococcus pyogenes (Group A Streptococcus, GAS) in some countries. While the importance of monitoring the clinical and molecular epidemiology of non-invasive GAS is increasingly recognized, most surveillance focuses on invasive infections, since culture is rarely performed in tonsillo-pharyngitis. We determined the antimicrobial susceptibility and characterized the macrolide-resistant lineages of 2,002 pharyngeal isolates recovered in a Portuguese hospital in 2014-2019. There were seasonal variations in the numbers of recovered isolates, with peaks shifting between March-July and October-December, but consistently low numbers in August and September. Macrolide-resistant and macrolide-susceptible GAS presented independent seasonal and clonal dynamics, with resistant isolates showing lower genetic diversity and minimal overlap with susceptible lineages. Overall, 84 (4%), 77 (4%), and 52 (3%) isolates were resistant to erythromycin, clindamycin, and tetracycline, respectively. Until 2018, macrolide resistance was mainly due to an internationally disseminated emm77-ST63 lineage carrying erm(A) and tet(O) in ICESp2905 and an emm75-ST49 lineage carrying mef(A)-msr(D) in a novel ɸ1207.3 variant. In 2019, resistance peaked at 9% due to the rapid expansion of mef(A)-msr(D)-positive emm2-ST55 isolates, replacing previous lineages. Other minor resistant lineages carried mostly erm(B) in a diversity of mobile genetic elements, including emm75-ST150, emm9-ST75, emm11-ST403, emm12-ST36, emm76-ST50, and emm77-ST399 [erm(T)]. Tetracycline resistance was associated with the genes tet(M) and tet(O), in most cases co-located in the same genetic elements as the erm genes. This study reveals clonal changes among macrolide-resistant GAS driving fluctuations in macrolide resistance and associated phenotypes.

BACKGROUND:Streptococcus pneumoniae (Sp) is the leading bacterial pathogen causing complicated pneumonia, that is, with parapneumonic effusion/pleural empyema (PPE/PE). In 2022, there was a rise in group A Streptococcus (GAS)-complicated pneumonias in children. METHODS:We reviewed the clinical characteristics of Sp- or GAS-complicated pneumonias admitted to 4 Portuguese tertiary hospitals, in 2018-2023. RESULTS:Of the 128 cases, 107 were by Sp and 21 by GAS, with a rise in PPE/PE in 2023. Pathogens were identified by molecular methods (89.8%) or culture (16.4%) from pleural fluid or blood. The mean age was 3.8 years (standard deviation 2.9) and 52.3% were male. Children with GAS PPE/PE were more likely to have rash (57.1% vs. 3.8%, P < 0.001), pharyngitis (52.4% vs. 19.8%, P = 0.004), septic shock (28.6% vs. 0.9%, p <0.001), higher procalcitonin (PCT) (80 vs. 2.13 ng/mL, P = 0.005), higher rates of admission to the intensive care unit (81.0% vs. 55.1%, P = 0.030) and of invasive mechanical ventilation (38.1% vs. 11.2%, P = 0.005). Fatality rate was similar in both groups (4.8% vs. 0%, P = 0.164). Among cases where genotyping was possible, 4/7 GAS were emm 1 (3/4 M1 UK sublineage, all in 2023) and 64/88 Sp were serotype 3. CONCLUSIONS:Sp serotype 3 remains the leading cause of PPE/PE in children in Portugal. The increase in GAS PPE/PE cases in 2023 followed an expansion of the M1 UK sublineage in Portugal. GAS should be considered, especially in children presenting with rash, pharyngitis or higher PCT levels. Adequate antimicrobial and clinical management of GAS PPE/PE could be crucial to improve outcomes.

In Portugal, after a decline in the proportion of adult invasive pneumococcal disease (IPD) associated with serotypes included in PCV7 and PCV13 attributed to their use in children, we observed a stabilization in the number of IPD episodes caused by serotypes included in conjugate vaccines, suggesting that no further benefit could be expected from pediatric vaccination. Worldwide, the COVID-19 pandemic and the measures adopted to contain viral transmission had major impacts on other respiratory transmissible pathogens, including pneumococcal infections. Many countries reported a decline in IPD cases, followed by an increase, coinciding with the relaxation of those measures. In Portugal, between 2018 and 2023, we found a pronounced decrease in the number of IPD samples in 2019-2021 (76% reduction in 2020-2021 relative to 2018-2019). Although we observed an increase in the following years, the annual number of IPD cases did not exceed the pre-pandemic levels, contrary to what was already reported for children in Portugal. Despite the fluctuations in the number of IPD cases, there were no major changes in serotype distribution, when compared to the pre-pandemic period. Serotypes 8 and 3 continue to be the dominant serotypes, together accounting for approximately 40% of all cases, although there was an increase in serotype 3, and a decrease in serotype 8 samples. An increase in serotype 4 IPD was found, in line with other countries. Despite more than two decades of conjugate vaccine use, a considerable proportion of IPD cases could have been potentially prevented by vaccination. Because higher valency conjugate vaccines such as PCV20 or PCV21 showed a very high coverage in Portugal (74% and 80% respectively), the direct vaccination of adults with these vaccines could have a profound effect on the burden of disease and serotype distribution.

Objectives: The COVID-19 pandemic led to the institution of public health measures in many countries which reduced respiratory infections. We aimed to identify and characterize changes in pediatric (< 18 years) invasive pneumococcal disease (pIPD) in Portugal in 2018-2023. Methods: pIPD cases were identified by culture and molecular methods and stratified by age and serotype. When available the susceptibility of the isolates to antimicrobials was evaluated. Results: pIPD cases were markedly reduced in the last trimester of 2019-2020 and the entire 2020-2021 season. While 2021-2022 was in line with pre-pandemic seasons, in 2022-2023, the number of pIPD cases exceeded those found pre-pandemic. Molecular tests were responsible for identifying and serotyping 30% of cases, highlighting their importance in evaluating pIPD. Among the 316 pIPD cases, 37 different serotypes were detected, of which serotypes 3 (n = 85, 26.9%), 8 (n = 25, 7.9%), 10A (n = 21, 6.6%) and 24F (n = 20, 6.3%) were the most frequent. The post-pandemic serotype distribution reflected mostly pre-pandemic trends and the rebound was not driven by particular serotypes. We identified many vaccine failures, most (n = 37) representing serotype 3 infections. Penicillin non-susceptibility increased from 14% pre-pandemic to 29%, with serotype 24F becoming particularly significant. Conclusions: The higher number of cases of pIPD post-COVID-19 in Portugal raises the possibility of a higher burden of pneumococcal disease in Europe post-pandemic. The relatively stable serotype distribution and the current availability of the higher valency conjugate vaccines PCV15 and PCV20, potentially preventing a large proportion of pIPD (43% and 67%, respectively), offer an opportunity to control this increase. (c) 2024 The Author(s). Published by Elsevier Ltd on behalf of The British Infection Association. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

Carbapenem-resistant Klebsiella pneumoniae complex (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal CR-KP rate has increased steeply, but the factors associated to this expansion are poorly explored.To address this question we compared, by phylogenetic and resistome analysis, the draft genomes of 200 CR-KP isolates collected in 2017-2019 from five hospitals in the Lisbon region, Portugal.We found that CR-KP belonged mainly to ST13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by KPC-3 (74%) or OXA-181 (18%) presence, which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multidrug resistant harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infection isolates were highly related and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified, by cgMLST data analysis (<5 alleles), 41 occurred between different hospitals and 130 within the same hospital.Our results suggest that CR-KP dissemination in the Lisbon region result from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients and transmission of CR-KP within and between hospitals.Our data reinforces that the prudent use of carbapenems, patients screening at hospital entrance, and improvement of infection control will be needed to decrease the burden of CR-KP infection in Portugal.

Whole genome sequencing (WGS) has become a vital tool in clinical microbiology, playing an important role in outbreak investigations, molecular surveillance, and identification of bacterial species, resistance mechanisms and virulence factors. However, the complexity of WGS data presents challenges in interpretation and reporting, requiring tailored strategies to enhance efficiency and impact. This study explores the diverse needs of key stakeholders in healthcare, including clinical management, laboratory work, public surveillance and epidemiology, infection prevention and control, and academic research, regarding WGS-based reporting of clinically relevant bacterial species. In order to determine preferences regarding WGS reports, human-centered design approach was employed, involving an online survey and a subsequent workshop with stakeholders. The survey gathered responses from 64 participants representing the above mentioned healthcare sectors across geographical regions. Key findings include the identification of barriers related to data accessibility, integration with patient records, and the complexity of interpreting WGS results. As the participants designed their ideal report using nine pre-defined sections of a typical WGS report, differences in needs regarding report structure and content across stakeholders became evident. The workshop discussions further highlighted the need to feature critical findings and quality metrics prominently in reports, as well as the demand for flexible report designs. Commonalities were observed across stakeholder-specific reporting templates, such as the uniform ranking of certain report sections, but preferences regarding the depth of content within these sections varied. Using these findings, we suggest stakeholder-specific structures which should be considered when designing customized reporting templates. In conclusion, this study underscores the importance of tailoring WGS-based reports of clinically relevant bacteria to meet the distinct needs of diverse healthcare stakeholders. The evolving landscape of digital reporting increases the opportunities with respect to WGS reporting and its utility in managing infectious diseases and public health surveillance.

Phylogenetic analysis, which allow to understand the evolution of bacterial and viral epidemics, requires large quantities of data to be analysed and processed for knowledge extraction. One of the major challenges consists on the integration of the results from typing and phylogenetic inference methods with epidemiological data, namely in what concerns their integrated and simultaneous analysis and visualization. Numerous approaches to support phylogenetic analysis have been proposed, varying from standalone tools to integrative web applications that include tools and/or algorithms for executing the common analysis tasks for this kind of data. However, most of them lack the capacity to integrate epidemiological data. Others provide the ability for visualizing and analyzing such data, allowing the integration of epidemiological data but they do not scale for large data analysis and visualization. Namely, most of them run inference and/or visualization optimization tasks on the client side, which becomes often unfeasible for large amounts of data, usually implying transferring data from existing databases in order to be analysed. Moreover, the results and optimizations are not stored for reuse. We propose the PHYLOViZ Web Platform, a cloud based tool for phylogenetic analysis, that not only unifies the features of both existing versions of PHYLOViZ, but also supports structured and customized workflows for executing data processing and analyses tasks, and promotes the reproducibility of previous phylogenetic analyses. This platform supports large scale analyses by relying on a workflow system that enables the distribution of parallel computations on cloud and HPC environments. Moreover, it has a modular architecture, allowing easy integration of new methods and tools, as well as customized workflows, making it flexible and extensible.

Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes . Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes . More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.

AbstractStreptococcus dysgalactiaesubsp.equisimilis(SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species,Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE andS. pyogenes.More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were found across species. Assessing potential cross-protection from leadingS. pyogenesvaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.