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Draft genome sequences of three NDM-1-producing Enterobacteriaceae species isolated from Brazil

The emergence of multidrug-resistant Enterobacteriaceae strains producing carbapenemases, such as NDM-1, has become a major public health issue due to a high dissemination capacity and limited treatment options. Here we describe the draft genome of three NDM-1-producing isolates: Providencia rettgeri (CCBH11880), Enterobacter hormaechei subsp. oharae (CCBH10892) and Klebsiella pneumoniae (CCBH13327), isolated in Brazil. Besides blaNDM-1, resistance genes to aminoglycosides [aadA1, aadA2, aac(6’)-Ib-cr] and quinolones (qnrA1, qnrB4) were observed which contributed to the multidrug resistance profile. The element ISAba125 was found associated to the blaNDM-1 gene in all strains.

The emergence of carbapenemase-producing Enterobacteriaceae has become a major public health issue worldwide due to a high dissemination capacity and limited treatment options (Nordaman et al. 2011). NDM is a metallo-beta-lactamase first reported in 2009 (Yong et al. 2009) and, now, it has already been detected in several countries worldwide. In Brazil, this carbapenemase was first described in a Providencia rettgeri isolate from the city of Porto Alegre, state of Rio Grande do Sul (RS) (South Region of Brazil), in 2013 (Carvalho-Assef et al. 2013). Then, the detection of six clonally related NDM-producing Enterobacter hormaechei subsp. oharae isolates was reported from the same public hospital . After that, nine NDM-1-producing Enterobacter cloacae complex isolates and two Morganella morgannii were also recovered from three different hospitals in Porto Alegre (Rozales et al. 2014). Recently, NDM-1-producing bacteria have been described in the state of Rio de Janeiro (RJ) (Southeast Region of Brazil) . In 2014, a NDM-1-producing Acinetobacter baumannii was also detected in Londrina, state of Paraná (South Region of Brazil) (Pillonetto et al. 2014).
Here, we aim to announce the draft genome of three NDM-1-producing isolates: P. rettgeri (CCBH11880), isolated from a surgical wound of a patient from RS, E. hormaechei subsp. oharae (CCBH10892), isolated from a rectal swab of another patient in RS, and Klebsiella pneumoniae (CCBH13327), isolated from a rectal swab of a patient in the city of Rio de Janeiro, RJ.
Initially all of the strains were tested against different antimicrobial drugs and showed multidrug resistance profiles. Genomic DNA of all strains was extracted using QIAamp DNA Blood Mini Kit (Qiagen, Germany). Whole genome shotgun libraries from each strain were prepared with the Nextera XT DNA Sample Prep kit (Illumina Inc, USA), according to the manufacturer's instructions, and sequenced on an Illumina MiSeq system with the MiSeq Reagent v.2 500 cycles kit. Sequence reads were then trimmed and filtered using a Phred score >20. The software Geneious v.6.1.7 (Biomatters Ltd, New Zealand) was used to perform de novo assembling. Rapid Annotation using System Technology v.2.0 server was used for genome annotation. Acquired resistance genes were analysed using the ResFinder platform (genomicepidemiology.org). The detailed features of all isolates can be found on Table. For the P. rettgeri isolate (CCBH11880) we obtained 656,560 paired end reads of 250 base pairs (bp), which were assembled into 80 contigs. The G+C content for this strain was 41%, considered common for this species. The estimated genome size, comprising all contigs, was 4,999,177 bp. Overall, 4,670 protein coding sequences were found and 89 RNAs were annotated (79 tRNA and 10 rRNA). Acquired resistance genes were searched using the ResFinder platform and different resistance genes were observed such as: aadA1 (GenBank JSEQ01000006.1;199,767-200,555 816-1,325 bp). Overall, we observed that these NDM-1-producing Enterobacteriaceae strains carry resistance genes to different antimicrobial classes, which can explain the multidrug resistant profile observed.
In P. rettgeri CCBH 11880, the bla NDM-1 was found inside the Tn125 transposon, which is composed of two copies of ISAba125 (Carvalho-Assef et al. 2013) (data not shown).
In the E. hormaechei ) (Gen-Bank acession NG041719) and K. pneumoniae isolates, the bla NDM-1 gene was found flanked by only one copy of ISA-ba125 (truncated) at the right boundary (data not shown).
The announcement of the whole-genome sequence of the three NDM-1-producing Enterobacteriaceae strains also provides basis for other studies, which will certainly increase our understanding of the role of this species in the drug resistance scenario. Nucleotide sequence accessions -These Whole Genome Shotgun project have been deposited in DDBJ/ ENA/GenBank under the accessions JSEQ00000000, JSBO00000000 and JSER00000000 for P. rettgerii (CCBH11880), E. hormaechei (CCBH10892) and K. pneumoniae (CCBH13327), respectively. The versions described in this paper are the first version (JSEQ00000000, JSBO00000000 and JSER00000000).