Whole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units

Manisha Goyal; Andreu Coello Pelegrin; Magali Jaillard; Yulia Rosa Saharman; Corné H W Klaassen; Henri A Verbrugh; Juliëtte A Severin; Alex van Belkum

doi:10.3389/fmicb.2022.861222

Whole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units

Front Microbiol. 2022 Jul 14:13:861222. doi: 10.3389/fmicb.2022.861222. eCollection 2022.

Authors

Manisha Goyal¹, Andreu Coello Pelegrin¹, Magali Jaillard², Yulia Rosa Saharman^{3

4}, Corné H W Klaassen⁴, Henri A Verbrugh⁴, Juliëtte A Severin⁴, Alex van Belkum¹

Affiliations

¹ bioMérieux Open Innovation and Partnerships, Macry-LÉtoile, France.
² bioMérieux EU Data Science, Macry-LÉtoile, France.
³ Department of Clinical Microbiology, Faculty of Medicine, Dr. Cipto Mangunkusumo General Hospital, Universitas Indonesia, Jakarta, Indonesia.
⁴ Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands.

Abstract

We have previously studied carbapenem non-susceptible Pseudomonas aeruginosa (CNPA) strains from intensive care units (ICUs) in a referral hospital in Jakarta, Indonesia (Pelegrin et al., 2019). We documented that CNPA transmissions and acquisitions among patients were variable over time and that these were not significantly reduced by a set of infection control measures. Three high risk international CNPA clones (sequence type (ST)235, ST823, ST357) dominated, and carbapenem resistance was due to carbapenemase-encoding genes and mutations in the porin OprD. Pelegrin et al. (2019) reported core genome analysis of these strains. We present a more refined and detailed whole genome-based analysis of major clones represented in the same dataset. As per our knowledge, this is the first study reporting Single Nucleotide Polymorphisms (wgSNP) analysis of Pseudomonas strains. With whole genome-based Multi Locus Sequence Typing (wgMLST) of the 3 CNPA clones (ST235, ST357 and ST823), three to eleven subgroups with up to 200 allelic variants were observed for each of the CNPA clones. Furthermore, we analyzed these CNPA clone clusters for the presence of wgSNP to redefine CNPA transmission events during hospitalization. A maximum number 35350 SNPs (including non-informative wgSNPs) and 398 SNPs (ST-specific_informative-wgSNPs) were found in ST235, 34,570 SNPs (including non-informative wgSNPs) and 111 SNPs (ST-specific_informative-wgSNPs) in ST357 and 26,443 SNPs (including non-informative SNPs) and 61 SNPs (ST-specific_informative-wgSNPs) in ST823. ST-specific_Informative-wgSNPs were commonly noticed in sensor-response regulator genes. However, the majority of non-informative wgSNPs was found in conserved hypothetical proteins or in uncharacterized proteins. Of note, antibiotic resistance and virulence genes segregated according to the wgSNP analyses. A total of 8 transmission chains for ST235 strains followed by 9 and 4 possible transmission chains for ST357 and ST823 were traceable on the basis of pairwise distances of informative-wgSNPs (0 to 4 SNPs) among the strains. The present study demonstrates the value of detailed whole genome sequence analysis for highly refined epidemiological analysis of P. aeruginosa.

Keywords: Pseudomonas aeruginosa; genome sequencing; resistome; virulome; wgMLST; wgSNPs.