Staphylococcus aureus remains one of the leading causes of infections worldwide and a common cause of bacteraemia. However, studies documenting the epidemiology of S. aureus in South America using genomics are scarce. We hereby report on the largest genomic epidemiology study to date of both methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in South America, conducted by the StaphNET-SA network. We characterised 404 genomes recovered from a prospective observational study of S. aureus bacteraemia in 58 hospitals from Argentina, Bolivia, Brazil, Paraguay and Uruguay between April and October 2019. We show that a minority of S. aureus isolates are phenotypically multi-drug resistant (5.2%), but more than a quarter are resistant to macrolide–lincosamide–streptogramin B (MLSb). MSSA were more genetically diverse than MRSA. Lower rates of associated antimicrobial resistance in community-associated(CA)-MRSA versus hospital-associated (HA)-MRSA were found in association with three S. aureus genotypes dominating the MRSA population: CC30-MRSA-IVc-t019-lukS/F-PV+, CC5-MRSA-IV-t002-lukS/F-PV- and CC8-MRSA-IVc-t008-lukS/F-PV+-COMER+. These are historically from a CA origin, carry on average fewer antimicrobial resistance determinants, and often lack key virulence genes. Surprisingly, CC398-MSSA-t1451-lukS/F-PV- related to the CC398 human-associated lineage is widely disseminated throughout the region, and is described here for the first time as the most prevalent MSSA lineage in South America. Moreover, CC398 strains carrying ermT (largely responsible for the MLSb resistance rates of MSSA strains: inducible iMLSb phenotype) and sh_fabI (related to triclosan resistance) were recovered from both CA and HA origin. The frequency of MRSA and MSSA lineages differed between countries but the most prevalent S. aureus genotypes are high-risk clones widely distributed in the South American region without a clear country-specific phylogeographical structure. Therefore, our findings underline the need for continuous genomic surveillance by regional networks such as StaphNET-SA. This article contains data hosted by Microreact.

Noroviruses represent one of the leading causes of outbreaks and sporadic acute gastroenteritis (AGE) cases across all age groups. Although the GII.4 norovirus has been identified as the primary cause of most AGE outbreaks, the transient predominance of other genotypes has been reported globally. In this study, we describe a multi-province AGE outbreak caused by a potential new lineage of norovirus GII.17[P17], which has been recently detected at a high incidence in the United States and Europe. An amino acid analysis of the major viral capsid protein revealed several substitutions in the hypervariable region compared to strains circulating in the mid-2010s, which could play a key role in immune evasion. This is the first report of the detection of these viruses in the Southern Hemisphere, underscoring the importance of maintaining active genomic surveillance in the context of increasing numbers of acute gastroenteritis outbreaks.

The rise in prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is of public health concern. In Argentina, several studies documented a shift in the epidemiology of CA-MRSA since 2009, with clonal complex 30 (CC30) and, in particular, sequence type 30 MRSA SCC mec type IV(ST30-MRSA-IV) replacing other clones both in communities and in hospitals and possibly displaying increased virulence.

The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR prediction tools. Although many may implement similar principles, these tools differ significantly in their supported inputs, search algorithms, parameterisation, and underlying reference databases. Each of these tools generates a report of detected AMR genes or variants in a distinct, non-standard, format. This presents a huge barrier to the comparison of results and to the modularity of tools for AMR gene prediction within bioinformatic workflows. In collaboration with 17 public health laboratories across 10 countries, the Public Health Alliance for Genomic Epidemiology (PHA4GE) ( https://pha4ge.org ) data structures working group has developed and piloted a standardized output specification for the bioinformatic detection of AMR from microbial genomes. In this report, we discuss hAMRonization, a python package and command-line utility, which implements PHA4GE’s AMR specification to combine the outputs of disparate antimicrobial resistance gene detection tools into a single unified format. hAMRonization can be easily extended and currently supports 18 different tools (both species-agnostic and species-specific) for the detection of genes and/or variants conferring AMR. The harmonized reports are available in tabular form, JSON format or through an interactive HTML file (e.g., https://maguire-lab.github.io/assets/interactive_report_demo.html ) that can be opened within the browser for navigable data exploration. As of 2024-03-07 hAMRonization has been downloaded ∼12,500 times, incorporated into >9 public bioinformatic tools and workflows, and been internally adopted by several national and international public health groups. The hAMRonization tool and underlying specification are open-source and freely available through PyPI, conda and GitHub ( https://github.com/pha4ge/hAMRonization ).

Introduction: Staphylococcus aureus is considered one of the most important human pathogens, and its levels of resistance to methicillin have increased even in strains isolated from people without nosocomial risk factors. Molecular analysis is essential for understanding the patterns of dissemination. The objective of this study was to identify community-acquired methicillin-resistant S. aureus (CA-MRSA) clones that infected Paraguayan children patients in two periods of time. Methodology: An observational, descriptive study was designed to determine the genetic variability of 115 isolates of CA-MRSA recovered from children who attended four reference centers in Paraguay between 2009-2010 and 2012-2013. Results: The combined use of Pulsed Field Gel Electrophoresis (PFGE), Multi-Locus Sequencing Typing, Multi-Locus Variable Analysis (MLVA) and Spa typing techniques allowed the identification of two dominant clones: ST30-IV-t019 (77%) and ST5-IV-t311 (10%), and the establishment of the former as the leading cause of CA-MRSA infections in children during the study period. Conclusions: This is the first study that provides epidemiological information as well as microbiological and molecular characteristics of CA-MRSA isolates recovered from children from Asunción and the Central Department of Paraguay.