Carbapenemase-Producing Extraintestinal Pathogenic Escherichia coli From Argentina: Clonal Diversity and Predominance of Hyperepidemic Clones CC10 and CC131

Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) causes infections outside the intestine. Particular ExPEC clones, such as clonal complex (CC)/sequence type (ST)131, have been known to sequentially accumulate antimicrobial resistance that starts with chromosomal mutations against fluoroquinolones, followed with the acquisition of blaCTX–M–15 and, more recently, carbapenemases. Here we aimed to investigate the distribution of global epidemic clones of carbapenemase-producing ExPEC from Argentina in representative clinical isolates recovered between July 2008 and March 2017. Carbapenemase-producing ExPEC (n = 160) were referred to the Argentinean reference laboratory. Of these, 71 were selected for genome sequencing. Phenotypic and microbiological studies confirmed the presence of carbapenemases confirmed as KPC-2 (n = 52), NDM-1 (n = 16), IMP-8 (n = 2), and VIM-1 (n = 1) producers. The isolates had been recovered mainly from urine, blood, and abdominal fluids among others, and some were from screening samples. After analyzing the virulence gene content, 76% of the isolates were considered ExPEC, although non-ExPEC isolates were also obtained from extraintestinal sites. Pan-genome phylogeny and clonal analysis showed great clonal diversity, although the first phylogroup in abundance was phylogroup A, harboring CC10 isolates, followed by phylogroup B2 with CC/ST131, mostly H30Rx, the subclone co-producing CTX-M-15. Phylogroups D, B1, C, F, and E were also detected with fewer strains. CC10 and CC/ST131 were found throughout the country. In addition, CC10 nucleated most metalloenzymes, such as NDM-1. Other relevant international clones were identified, such as CC/ST38, CC155, CC14/ST1193, and CC23. Two isolates co-produced KPC-2 and OXA-163 or OXA-439, a point mutation variant of OXA-163, and three isolates co-produced MCR-1 among other resistance genes. To conclude, in this work, we described the molecular epidemiology of carbapenemase-producing ExPEC in Argentina. Further studies are necessary to determine the plasmid families disseminating carbapenemases in ExPEC in this region.

Emergence and Dissemination of Extraintestinal Pathogenic High-Risk International Clones of Escherichia coli

“…However, subclade C1 presents bla CTX-M-14 or bla CTX-M-27 ESBL genes, while on the other hand, subclade C2, which has a single nucleotide polymorphism (SNP) at fimH30, is mainly associated with bla CTX-M-15 . The bla CTX-M-27 positive subset of C1, referred to as subclade C1-M27, recently became prominent in Japan, Canada, Germany and China [20,46,[80][81][82]. In Iran, a comparative study on MDR ST131 and non-ST-131 clones reported that both were associated with bla TEM , bla SHV , bla CTX-M , bla OXA-48 genes, as well as with plasmid-mediated quinolone resistance (PMQR) determinants (bifunctional aminoglycoside acetyltransferase-Ib-cr [aac6 -Ib-cr] and Qnr protective proteins [qnrB, qnrS] [83].…”

“…As an interesting result, a strain referenced as ECO14 of ST131 exhibited resistance to colistin (MIC ≥ 4 µg/mL), but it lacked mcr. It developed colistin resistance due to seven chromosomal mutations in the pmrB and pmrA genes (phosphoetanolamin transferase coding genes) [20].…”

“…In total, 87 of 169 studies describe this clone for the period 1995-2018. ST69 is characterised by the presence of bla KPC-2 , bla NDM-1 [40], co-carriage of bla NDM-1 with bla CMY-6 , [20], bla CTX-M-1,-14,-15,-27 [100], mcr-1 [105], fosA3 [106] and gyrA, parC mutations, leading to fluoroquinolone resistance [107]. During other studies in Italy, this clone has also been identified from various origins, including dairy products, the diaphragms of wild boars, poultry, mussels, clams, and human stool.…”

“…On the other hand, the ST617 clone exhibited the co-existence of bla KPC-2 , bla CTX-M-14 and bla CTX-M-27 . The nucleotide sequence information was submitted in GenBank under the BioProject accession number PRJNA784589 [20] (Table 1). In addition to β-lactam resistance, CC10 has also been marked by fluoroquinolone-resistance determinants (e.g., qnrS1, aac(6 )-Ib-cr) and the mcr-1 colistin-resistance gene [7,60,111,112].…”

“…The most frequently detected ESBLs in E. coli clinical isolates are mainly CTX-M-type enzymes [10,11]; however, transferable genetic elements harbouring carbapenemase genes have also been described, namely, bla NDM (New Delhi metallo-β-lactamase), bla KPC (Klebsiella pneumoniae carbapenemase) and bla OXA-48 (OXA-48 carbapenemase) [12][13][14][15][16][17]. Further antibiotic resistance genes have also been reported in E. coli clinical isolates, namely, fluoroquinolone-, aminoglycosideand colistin-resistance determinants [18][19][20]. Carbapenem-and third-generation cephalosporin-resistant Enterobacteriaceae are grouped into the 'critical' category on the priority list of the World Health Organisation (WHO); therefore, there is an urgent need for effective antibiotics against this pathogen [21].…”