First report of abdominal sepsis caused by a recently described species: Chimaeribacter arupi.

We present a case of a 34-year-old patient with abdominal sepsis caused by an infrequent species: Chimaeribacter arupi. Genomic analysis confirmed the identification which is difficult to achieve by other methods so far. To our knowledge, this represents the first case of infection by this species reported in Argentina.

Phytobacter spp: the emergence of a new genus of healthcare-associated Enterobacterales encoding carbapenemases in Argentina: a case series.

Members of the genus Phytobacter (order Enterobacterales) are isolated from the natural environment and clinical settings. Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories. In this study we describe the first three clinical cases associated with Phytobacter spp. reported in Argentina. We describe the identification, the molecular analysis using whole genome sequencing and the potential clinical relevance.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.

The SARS-CoV-2 genome occupies a unique place in infection biology - it is the most highly sequenced genome on earth (making up over 20% of public sequencing datasets) with fine scale information on sampling date and geography, and has been subject to unprecedented intense analysis. As a result, these phylogenetic data are an incredibly valuable resource for science and public health. However, the vast majority of the data was sequenced by tiling amplicons across the full genome, with amplicon schemes that changed over the pandemic as mutations in the viral genome interacted with primer binding sites. In combination with the disparate set of genome assembly workflows and lack of consistent quality control (QC) processes, the current genomes have many systematic errors that have evolved with the virus and amplicon schemes. These errors have significant impacts on the phylogeny, and therefore over the last few years, many thousands of hours of researchers time has been spent in "eyeballing" trees, looking for artefacts, and then patching the tree. Given the huge value of this dataset, we therefore set out to reprocess the complete set of public raw sequence data in a rigorous amplicon-aware manner, and build a cleaner phylogeny. Here we provide a global tree of 3,960,704 samples, built from a consistently assembled set of high quality consensus sequences from all available public data as of March 2023, viewable at https://viridian.taxonium.org. Each genome was constructed using a novel assembly tool called Viridian (https://github.com/iqbal-lab-org/viridian), developed specifically to process amplicon sequence data, eliminating artefactual errors and mask the genome at low quality positions. We provide simulation and empirical validation of the methodology, and quantify the improvement in the phylogeny. Phase 2 of our project will address the fact that the data in the public archives is heavily geographically biased towards the Global North. We therefore have contributed new raw data to ENA/SRA from many countries including Ghana, Thailand, Laos, Sri Lanka, India, Argentina and Singapore. We will incorporate these, along with all public raw data submitted between March 2023 and the current day, into an updated set of assemblies, and phylogeny. We hope the tree, consensus sequences and Viridian will be a valuable resource for researchers.

Bactericidal killing of meningococcal W strains isolated in Argentina by the sera of adolescents and infants immunized with 4-component meningococcal serogroup B vaccine (4CMenB).

Invasive meningococcal disease (IMD) is a life-threatening disease caused by meningococcal serogroups A, B, C, W, X, and Y, of which B and W are most common in Argentina. The 4-component meningococcal serogroup B (4CMenB) vaccine contains three purified recombinant protein antigens (Neisseria adhesin A [NadA], factor H binding protein [fHbp], and Neisserial Heparin Binding Antigen [NHBA]) and outer membrane vesicles (OMV), which is derived from the New Zealand epidemic strain and contains Porin A 1.4. These antigens are present and conserved in strains that belong to other serogroups. In this study, we show that 10/11 (91%) meningococcal serogroup W (MenW) strains selected to be representative of MenW isolates that caused IMD in Argentina during 2010-2011 were killed in bactericidal assays by the sera of adolescents and infants who had been immunized with the 4CMenB vaccine. We also show that MenW strains that caused IMD in Argentina during 2018-2021 were genetically similar to the earlier strains, indicating that the 4CMenB vaccine would likely still provide protection against current MenW strains. These data highlight the potential of 4CMenB vaccination to protect adolescents and infants against MenW strains that are endemic in Argentina.

Plasmidic resistance to colistin mediated by mcr-1 gene in Escherichia coli clinical isolates in Argentina: A retrospective study, 2012–2018

[ABSTRACT]. Objective. To describe the resistance profile and the genetic characteristics of Escherichia coli isolates that harbor the mobilizable colistin resistance gene mcr-1 in Argentina. Methods. This was a retrospective study of 192 E. coli isolates positive for mcr-1 obtained from 69 hospitals of Buenos Aires City and 14 Argentinean provinces in 2012 – 2018. The antimicrobial susceptibility was performed by agar diffusion, broth macrodilution, and/or agar dilution. Standard polymerase chain reaction (PCR) was performed to detect resistance genes and incompatibility groups; specific PCR was applied to discriminate between blaCTX-M allelic groups and mcr-1.5 variant. The genetic relatedness among isolates was evaluated by XbaI-pulsed field gel electrophoresis and multilocus sequence typing in a subset of isolates. Results. All E. coli isolates showed minimal inhibitory concentrations to colistin ≥ 4μg/mL; nearly 50% were resistant to third-generation cephalosporins, with CTX-M-2 being the main extended-spectrum β-lactamase detected. Five E. coli were carbapenemase-producers (3 NDM, 2 KPC). The mcr-1.5 variant was detected in 13.5% of the isolates. No genetic relationship was observed among the mcr-1-positive E. coli clinical isolates, but a high proportion (164/192; 85.4%) of IncI2 plasmids was detected. Conclusions. The presence of IncI2 plasmids among highly diverse E. coli clones suggests that the mcr-1 gene’s wide distribution in Argentina may be driven by the horizontal transmission of IncI2 plasmids.

[RESUMEN]. Objetivo. Describir el perfil de resistencia y las características genéticas de aislamientos clínicos de Escherichia coli que portan el gen movilizable de resistencia a colistina mcr-1 en Argentina. Métodos. Se realizó un estudio retrospectivo para analizar 192 aislamientos de E. coli mcr-1 positivo, obtenidos en 69 hospitales de la Ciudad de Buenos Aires y 14 provincias de Argentina entre 2012 y 2018. La sensibilidad a los antimicrobianos se analizó mediante los métodos de difusión en agar, macrodilución en caldo y/o dilución en agar. Se aplicó la técnica estándar de reacción en cadena de la polimerasa (PCR) para detectar genes de resistencia y grupos de incompatibilidad; se aplicó PCR específica para distinguir entre variantes alélicas del gen blaCTX-M y la variante mcr-1.5. La relación genética entre los aislamientos fue evaluada mediante la técnica de electroforesis en gel de campo pulsado usando la enzima Xbal y la tipificación por secuencias de múltiples locus en un subconjunto de aislamientos. Resultados. Todos los aislamientos de E. coli mostraron concentraciones inhibitorias mínimas de colistina ≥ 4μg/mL. Casi el 50% mostró resistencia a las cefalosporinas de tercera generación y CTX-M-2 fue la β-lactamasa de espectro extendido que más se detectó. Cinco aislamientos de E. coli mostraron ser productoras de carbapenemasas (3 NDM, 2 KPC). La variante mcr-1.5 se detectó en 13,5% de las cepas aisladas. No se observó relación genética entre los aislamientos clínicos estudiados de E. coli positivas para mcr-1, aunque sí se detectó una proporción elevada (164/192; 85,4%) de plásmidos Incl2. Conclusiones. La elevada ocurrencia de plásmidos IncI2 en un grupo altamente diverso de clones de E. coli podría indicar que la amplia difusión del gen mcr-1 en Argentina estaría asociada a la transmisión horizontal de plásmidos IncI2.

[RESUMO]. Objetivo. Descrever o perfil de resistência e as características genéticas de isolados clínicos de Escherichia coli que carregam o gene mobilizábel de resistência à colistina mcr-1 na Argentina. Métodos. Neste estudo retrospectivo, foram analizados 192 isolados de E. coli positivos para mcr-1 obtidos em 69 hospitais da Cidade de Buenos Aires e 14 províncias da Argentina, entre 2012 e 2018. A sensibilidade aos antimicrobianos foi examinada usando métodos de difusão em ágar, macrodiluição em caldo e/ou diluição em ágar. A técnica padrão de reação em cadeia da polimerase (PCR) foi aplicada para detectar genes de resistência e grupos de incompatibilidade; a PCR específica foi aplicada para discriminar entre variantes alélicas do gene blaCTX-M e a variante mcr-1.5. A relação genética entre os isolados foi avaliada por eletroforese em gel de campo pulsado usando a enzima XbaI e a tipagem por sequências de múltiplos lócus, em um subconjunto de isolados. Resultados. Todos os isolados de E. coli apresentaram concentrações inibitórias mínimas de colistina ≥4μg/ mL. Quase 50% foram resistentes às cefalosporinas de terceira geração, e CTX-M-2 foi a β-lactamase de espectro estendido mais detectada. Cinco isolados de E. coli foram produtores de carbapenemase (3 NDM, 2 KPC). A variante mcr-1.5 foi detectada em 13,5% dos isolados. Não foi observada relação genética entre os isolados clínicos de E. coli positivos para mcr-1, mas foi detectada uma alta proporção (164/192; 85,4%) de plasmídeos IncI2. Conclusões. A alta ocorrência de plasmídeos IncI2 em um grupo altamente diverso de clones de E. coli sugere que a ampla distribuição do gene mcr-1 na Argentina estaria associada a transmissão horizontal de plasmídeos IncI2.