Initial Assessment of the Molecular Epidemiology of bla _NDM-1 in Colombia

Abstract

fWe report complete genome sequences of four bla NDM-1 -harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. The bla NDM-1 genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates belong to sequence type 10 (ST10) (Escherichia coli), ST392 (Klebsiella pneumoniae), and ST322 and ST464 (Acinetobacter baumannii and Acinetobacter nosocomialis, respectively). Our analysis identified that the Inc A/C2 plasmid in E. coli contained a novel complex transposon (Tn125 and Tn5393 with three copies of bla NDM-1 ) and a recombination "hot spot" for the acquisition of new resistance determinants.A t this time, bla NDM is recognized as a major global health threat. Guatemala and Colombia reported the first cases of bla NDM-1 -harboring isolates in Latin America (1, 2). In both instances, bla NDM-1 was discovered in hospital-acquired, clonally related Klebsiella pneumoniae isolates that were recovered from patients who had not travelled recently. The molecular epidemiology of bla NDM carbapenemases in South America has been investigated only in a limited fashion, and data in Colombia are very scarce. In order to understand the dissemination of bla NDM-1 in Colombia, we performed a genomic analysis of four sentinel isolates, Acinetobacter baumannii, Acinetobacter nosocomialis, Escherichia coli, and K. pneumoniae collected in 2012, shortly after the first reported outbreak (1).

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

“…These observations of the 19Aba78 isolate and the E. coli transconjugant C19-78 thus contribute further evidence of dissemination of closely related pNDM-BJ01-like plasmids among unrelated Acinetobacter spp. isolates, as has been reported in Asia and Latin America ( Hu et al 2012 ; Sun et al 2013 ; Waterman et al 2013 ; Zhang et al 2013 ; Wang et al 2014 ; Brovedan et al 2015 ; Espinal et al 2015 ; Feng et al 2015 ; Jones et al 2015 ; Li et al 2015 ; Rojas et al 2016 ), and also its capability to transfer to Enterobacteriaceae .…”

“…Two other NDM-1-positive strains of Acinetobacter spp., isolated from other Colombian cities (Neiva and Pasto, 520 km away from each other, and 320 and 390 km away from Cali, respectively) were recently reported ( Rojas et al 2016 ). The bla NDM-1 -positive plasmids from these strains, p6200-47kb and p6411-9kb were also found to be pNDM-BJ01-like, each with 99% nucleotide identity over 100% of the pNDM-BJ01 length ( fig.…”

“…In contrast to the similarity between the bla NDM-1 -positive plasmids found in the three Colombian NDM-1-positive strains of Acinetobacter spp., the strains themselves were of different, unrelated sequence type (ST). The Neiva A. baumannii (harboring p6200-47kb) was ST322 and the Pasto A. nosocomialis (harboring p6411-9kb) was ST464 ( Rojas et al 2016 ), but the Cali A. baumannii isolate 19Aba78 belongs to ST239, as determined by the Pasteur MLST scheme for A. baumannii ( Diancourt et al 2010 ). These observations of the 19Aba78 isolate and the E. coli transconjugant C19-78 thus contribute further evidence of dissemination of closely related pNDM-BJ01-like plasmids among unrelated Acinetobacter spp.…”

“… Plasmid Size (bp) Inc Group Host Resistance Gene Profile GenBank Accesion No Reference pNDM-BJ01 47,274 Not assigned Acinetobacter spp. aph(3 ′ )-VIa , bla NDM-1 NC_019268 Hu et al (2012) p6234-178kb 178,193 IncA/C2 K. pneumoniae aph(3 ′ )-VIa , aacA29 , aadA2 , bla NDM-1 , bla CARB-2 , mph(E) , msr(E) , catB3 , cmlA1 , sul2 , sul1 NZ_CP010391 Rojas et al (2016) p16Pre36-NDM 244,116 Not assigned P. rettgeri aadA1 , aph(3 ′ )-Ia , bla NDM-1 , sul2 , sul1 , tet(B) , dfrA1 KX832927 This study p16Pre36-2 43,191 Not assigned P. rettgeri aac(3)-IIa , bla TEM-1B KX832926 This study pRB151-NDM 108,417 Not assigned P. rettgeri bla NDM-1 CP017672 Marquez-Ortiz et al (2017) p06-1619-NDM 54,712 Not assigned P. rettgeri <...>…”

Genomic Insights into Colistin-Resistant Klebsiella pneumoniae from a Tunisian Teaching Hospital

“…ST101, ST15, ST11, and ST147 have been described worldwide, as well as in Tunisia, and are associated with the carbapenemases OXA-48, KPC, OXA-204, and NDM and the extended-spectrum beta-lactamase (ESBL) CTX-M-15 (21)(22)(23)(24)(25). The single ST392 strain has never been described in Tunisia but was sporadically observed in three distinct countries related to KPC-2 in China (26), to NDM in Colombia (27), and to OXA-244 in Spain (28). In our study, ST-2 was associated with CTX-M-15 but not any carbapenemase.…”