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. 2021 Apr 28;12(2):4-18.
doi: 10.5365/wpsar.2020.11.1.006. eCollection 2021 Apr-Jun.

Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014

Jeremiah Chilam  1   2 , Silvia Argimón  3   2 , Marilyn T Limas  1 , Melissa L Masim  1 , June M Gayeta  1 , Marietta L Lagrada  1 , Agnettah M Olorosa  1 , Victoria Cohen  3 , Lara T Hernandez  1 , Benjamin Jeffrey  3 , Khalil Abudahab  3 , Charmian M Hufano  1 , Sonia B Sia  1 , Matthew T G Holden  4 , John Stelling  5 , David M Aanensen  3   6   2 , Celia C Carlos  1   2 ; Philippines Antimicrobial Resistance Surveillance Program
Affiliations

Genomic surveillance of Pseudomonas aeruginosa in the Philippines, 2013-2014

Jeremiah Chilam et al. Western Pac Surveill Response J. .

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen that often causes nosocomial infections resistant to treatment. Rates of antimicrobial resistance (AMR) are increasing, as are rates of multidrug-resistant (MDR) and possible extensively drug-resistant (XDR) infections. Our objective was to characterize the molecular epidemiology and AMR mechanisms of this pathogen. We sequenced the whole genome for each of 176 P. aeruginosa isolates collected in the Philippines in 2013-2014; derived the multilocus sequence type (MLST), presence of AMR determinants and relatedness between isolates; and determined concordance between phenotypic and genotypic resistance. Carbapenem resistance was associated with loss of function of the OprD porin and acquisition of the metallo-β-lactamase (MBL) gene bla VIM. Concordance between phenotypic and genotypic resistance was 93.27% overall for six antibiotics in three classes, but varied among aminoglycosides. The population of P. aeruginosa was diverse, with clonal expansions of XDR genomes belonging to MLSTs ST235, ST244, ST309 and ST773. We found evidence of persistence or reintroduction of the predominant clone ST235 in one hospital, and of transfer between hospitals. Most of the ST235 genomes formed a distinct lineage from global genomes, thus raising the possibility that they may be unique to the Philippines. In addition, long-read sequencing of one representative XDR ST235 isolate identified an integron carrying multiple resistance genes (including bla VIM-2), with differences in gene composition and synteny from the P. aeruginosa class 1 integrons described previously. The survey bridges the gap in genomic data from the Western Pacific Region and will be useful for ongoing surveillance; it also highlights the importance of curtailing the spread of ST235 within the Philippines.

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Figures

Figure 1A
Figure 1A
Annual resistance rates to nine antibiotics of P. aeruginosa isolates referred to the ARSP, 2005–December 2014
Figure 1B
Figure 1B
Annual resistance rates to nine antibiotics of P. aeruginosa isolates referred to the ARSP, 2005–December 2014
Figure 1C
Figure 1C
Annual resistance rates to nine antibiotics of P. aeruginosa isolates referred to the ARSP, 2005–December 2014
Figure 1D
Figure 1D
Association between resistance and the origin of infection for 176 P. aeruginosa isolates sequenced in this study
Figure 1E
Figure 1E
Mechanisms of resistance to carbapenems and other β-lactam antibiotics identified in the genomes of 176 isolates grouped by their resistance profilea
Figure 2A
Figure 2A
Genomic surveillance of P. aeruginosa from the Philippines, 2013–2014a
Figure 2B
Figure 2B
Genomic surveillance of P. aeruginosa from the Philippines, 2013–2014a
Figure 2C
Figure 2C
Genomic surveillance of P. aeruginosa from the Philippines, 2013–2014a
Figure 2D
Figure 2D
Genomic surveillance of P. aeruginosa from the Philippines, 2013–2014a
Figure 3A
Figure 3A
P. aeruginosa from the Philippines in the global contexta
Figure 3B
Figure 3B
P. aeruginosa from the Philippines in the global contexta
See this image and copyright information in PMC

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