Genomic Characterisation of Virulence and AntimicrobialResistance Genes in Pseudomonas aeruginosa Isolatesfrom Northern Tanzania

Abstract

Background: Pseudomonas aeruginosa is a common cause of hospital-acquired infections and is classified as a World Health Organization (WHO) critical-priority pathogen because of its increasing resistance to key antibiotics, including carbapenems. In Tanzania, several studies that documented P. aeruginosa resistance profiles have relied on phenotypic or targeted Polymerase Chain Reaction (PCR) methods, limiting information on comprehensive antimicrobial resistance and virulence profiles. This study aimed to characterize genomic features of P. aeruginosa from a tertiary care hospital in northern Tanzania, focusing on antimicrobial resistance genes, virulence genes, sequence type and genetic relatedness.

Materials and Methods: A total of 16 isolates initially identified as Pseudomonas species were selected for whole genome sequencing analysis, of which 12 isolates were sequenced using Illumina NextSeq 550 and 4 with existing genomic data. Genomic species identification was confirmed using KmerFinder v3.2. Antimicrobial resistance and virulence genes were identified using ABRicate v1.0.1. Mobile genetic elements were identified using MobileElementFinder software v1.0.3 and database v1.0.2 from the Center for Genomic Epidemiology. Analysis of Inter-strain whole genome SingleNucleotide Polymorphisms (SNPs) was performed using CSI Phylogeny v1.4.

Results: Of the 16 isolates, 13 were confirmed as Pseudomonas species by genomic analysis. Antimicrobial susceptibility testing showed the highest susceptibility to meropenem 11(84.6%) followed by gentamicin and ceftazidime 10(76.9%). Genome assemblies ranged from 6.4 to 6.9 Mb: MLST analysis revealed substantial genetic heterogeneity, including the presence of the high-risk ST235. All isolates carried intrinsic resistance genes, including blaPAO, blaOXA variants,

catB7, fosA, aph(3′)-IIb. Acquired resistance genes included sul1/2, aadA2/6, ant(2″)-Ia, blaCARB-2, tet(G) and the carbapenemase gene blaDIM-1. The tmexC3/D3-TOprJ3 efflux system was detected. Mobile genetic elements (insertion sequences and transposons) were detected and co-localized with resistance genes. The highest proportion of resistance genes were observed among urine isolates 19(34.5%). Virulence genes associated with adhesion, secretion, biofilm, and toxin production were widely distributed. Phylogenetic analysis revealed genomic diversity ranging from 199 to 54,448 SNPs.

Conclusion: This study showed that multidrug-resistant P. aeruginosa from a tertiary hospital in Tanzania carried a wide range of resistance determinants, virulence factors, and high-risk clones. These preliminary findings support the need for strengthened antimicrobial stewardship and genomic surveillance to support clinical management and infection control