Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V

Abstract

Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. IMPORTANCE A. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.

Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes

“…The data reported here confirms that at least four different CCs are circulating in the different hospitals from a single metropolitan area from Northeastern Brazil, with no obvious association found between any of the CCs/STs and variables such as hospitals, collection years or sampling methods. This is in contrast with other studies which usually reports outbreaks of either a single ST or closely related ones (Mosqueda et al, 2013;Wright et al, 2014;Li et al, 2015;Ou et al, 2015), although a recent report from Latin America has also found multiple lineages of MDR A. baumannii coexisting within the same hospital (Graña-Miraglia et al, 2020). Among those CCs founds here, CC1, CC15, and CC113 (ST25) are considered globally spread Acinetobacter clonal complexes, having been isolated from different parts of the world for more than 20 years (Diancourt et al, 2010;Di Nocera et al, 2011;Di Popolo et al, 2011;Karah et al, 2012;Sahl et al, 2015;Gaiarsa et al, 2019).…”

“…Among those CCs founds here, CC1, CC15, and CC113 (ST25) are considered globally spread Acinetobacter clonal complexes, having been isolated from different parts of the world for more than 20 years (Diancourt et al, 2010;Di Nocera et al, 2011;Di Popolo et al, 2011;Karah et al, 2012;Sahl et al, 2015;Gaiarsa et al, 2019). In contrast, CC79 strains have been described mostly from North and South America but also in Europe (Karah et al, 2012;Villalón et al, 2013;Chagas et al, 2014;Wright et al, 2014;Bado et al, 2018;Da Silva et al, 2018;Levy-Blitchtein et al, 2018;Graña-Miraglia et al, 2020), while ST113 (also belonging to CC113) was described originally in the Middle East but has more recently mostly been reported from South America (Bonnin et al, 2013;Clímaco et al, 2013;Girlich et al, 2014). Here, the availability of draft genome sequences from multiple strains from various STs and clonal complexes co-existing in the same environments allowed a large-scale comparison of the multiple elements associated with their antibiotic resistance and virulence.…”

High mortality in an outbreak of multidrug resistant Acinetobacter baumannii infection introduced to an oncological hospital by a patient transferred from a general hospital

“…This lineage emerged rather recently (about 22 years ago) and since then it has spread in many countries in Latin and North America; notably, strains from this lineage are not only carbapenem resistant but also multidrug resistant. In terms of acquired oxacillinases (OXAs), this lineage presents the worldwide-distributed OXA-23-like family but also the less disseminated OXA-40-like family [24].…”

Diversity of carbapenem-resistantAcinetobacter baumanniiand bacteriophage-mediated spread of the Oxa23 carbapenemase

“…Isolates belonging to IC5 are members of CC PAS and are found at particularly high frequency in Latin America (15,57,67,68). The allele profiles of the founder sequence types of CC PAS 158 and CC PAS 79 (ST PAS 158 and ST PAS 79 respectively) are quite different, sharing only 1 of the 7 alleles (rplB allele 4), which at the nucleotide level translates to 13 SNPs.…”