Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia

ABSTRACT Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.

P seudomonas aeruginosa is associated with chronic recurrent pulmonary infections that are responsible for high mortality in children with underlying conditions such as hematology-oncology diseases, extended hospitalization in the intensive care unit (ICU), and prematurity (1).
Two P. aeruginosa strains (Pa1207 and Pa1242) were sequenced. The strains were isolated from children with bacteremia admitted to a pediatric hospital in Mexico City. Strain Pa1207 was resistant to different ␤-lactams (including carbapenems and cephalosporins), amikacin, and tobramycin but was susceptible to gentamicin, polymyxin B, and fluoroquinolones. Strain Pa1242 presented only intermediate resistance to polymyxin B and was susceptible to 19 antimicrobials tested.
The genomic DNA of the strains was purified with the DNeasy blood and tissue kit (Qiagen) and sent to the Yale Center for Genome Analysis for PacBio RS II singlemolecule real-time (SMRT) sequencing. A standard library of 20-kb fragments was prepared and sequenced on two SMRT cells with P4-C2 chemistry. The continuous long reads were assembled using the HGAP/Quiver protocol in SMART Portal v3 (2). The final assemblies had mean coverages of ϳ146ϫ and ϳ181ϫ for Pa1207 and Pa1242, respectively, and consisted of chromosomes of 7,411,863 bp and 7,050,510 bp, with mean GϩC contents of 65.7% and 65.8%, respectively. A total of 7,153 genes were annotated for Pa1207: 7,072 CDSs, 65 tRNAs, 12 rRNAs, 4 noncoding RNAs (ncRNAs), and 247 pseudogenes. For strain Pa1242, 6,735 genes were annotated: 6,654 CDSs, 65 tRNAs, 12 rRNAs, 4 ncRNAs, and 346 pseudogenes.
In both strains, there are three large genomic islands inserted at previously identified loci (7-10) but with different genetic compositions. One island conserved the first 31 open reading frames (ORFs) described in P. aeruginosa genome island 1 (PAGI-1), and the other had only the 4 ORFs described in pathogenicity island 2 (PAPI-2). Strain Pa1207 presents a mobile element shared with Pseudomonas fluorescens, which encodes to dehydrogenases, type VI secretion system components, and hypothetical proteins. Other islands in both strains are hybrids formed for genes from PAPI-1/pKLC-102, where a group of genes of the major pilins are conserved.

ACKNOWLEDGMENTS
We thank José Luis Méndez for performing the antibiotic susceptibility essays and Guilin Wang from the Yale Center for Genome Analysis, Yale University, for skillful PacBio sequencing.
This paper is part of the doctoral research carried out by L.F.E.-C., a doctoral student from Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), who received fellowship 619928 from CONACYT. This work was also supported by DGAPA/PAPIIT-UNAM (IN213816 to R.M.-E.).
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.