Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections.

BACKGROUND: Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes. METHODS: A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses. RESULTS: In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020). CONCLUSIONS: This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections.

Emergence of a VIM-2-producing extensively drug-resistant (XDR) Pseudomonas aeruginosa ST309 in South America: a comparative genomic analysis.

Pseudomonas aeruginosa is considered a top priority pathogen associated with elevated morbidity and mortality. Worldwide outbreaks have been associated with a few high-risk epidemic P. aeruginosa lineages. However, the biological features involved in the persistence and spread of such lineages in clinical settings remain to be unravelled. This study reports the emergence of an extensively drug-resistant (XDR) sequence type 309 (ST309) P. aeruginosa in South America (Brazil), specifically in the Amazon region. Genomic analyses were performed with 42 complete and draft ST309 genomes, giving insights into its epidemiology, resistome and mobilome. A heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes was observed, which included blaVIM-2, blaIMP-15 and qnrVC1, all associated with class 1 integrons. Mobilome mining showed the presence of integrative and conjugative elements (ICEs), transposons and genomic islands (GIs) harbouring a huge arsenal of heavy metal resistance determinants, which probably provided adaptive advantages to the ST309 lineage.

Emergence of extensively drug-resistant international clone IC-6 Acinetobacter baumannii carrying blaOXA-72 and blaCTX-M-115 in the Brazilian Amazon region.

OBJECTIVES: The extensively drug-resistant (XDR) Acinetobacter baumannii international clone VI (IC-6) has been identified worldwide since 2006. This study reports the emergence of IC-6 in the Brazilian Amazon region and reveals the particular genomic features considering its mobilome and resistome. METHODS: A total of 32 carbapenem-resistant A. baumannii strains recovered from Boa Vista city (Roraima, Brazil) in 2016 were characterised by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The whole genome sequences of the Brazilian IC-6 strains were obtained. The mobilome and resistome were assessed by in silico analyses. RESULTS: PFGE and MLST demonstrated that the 32 A. baumannii strains belonged to four clones. One XDR clone corresponded to the high-risk pandemic IC-6 lineage from ST944Oxf/78Pas. The IC-6 resistome was composed of aadA5, aac(3'')-IIa, aph(3')-Ia, armA, aadB, msrE, blaTEM-1, IS15DIV-blaCTX-M-115-IS15DIV, blaOXA-90, ISAba1-blaADC-152, blaOXA-72, qacEΔ1 and sul1. Mobilome prediction revealed that blaOXA-72 was embedded in a 15.5-kb plasmid and that it was flanked by putative XerC/D-binding sites, possibly involved in blaOXA-72 mobilisation. Several resistance genes were in a 48-kb multidrug resistance genomic island inserted in the chromosome, which also harboured genes involved in host pathogenicity and adaptive traits. Interestingly, the Brazilian strains shared the blaOXA-72 and blaCTX-M-115 with IC-6/ST944Oxf/78Pas recovered in a distinct spatiotemporal context, pointing to an epidemiological link among them. CONCLUSION: This study highlights the importance of surveillance of XDR A. baumannii strains, even outside of densely populated cosmopolitan regions, to reveal the epidemiology of pandemic lineages, stressing their threat to public health.