Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings

Abstract

Antibiotic resistance and virulence profiles of <i>Enterococcus faecium</i>, <i>Klebsiella pneumoniae</i>, and <i>Pseudomonas aeruginosa</i>, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical <i>P. aeruginosa</i> (PAO1) and one clinical <i>K. pneumoniae</i> (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical <i>E. faecium</i> Ef CD1 was extensively drug resistant (XDR); all <i>K. pneumoniae</i> isolates (<i>n</i> = 12) (except <i>K. pneumoniae</i> ATCC 13883) were multidrug resistant (MDR), while the <i>P. aeruginosa</i> (<i>n</i> = 16) isolates exhibited higher susceptibility profiles. The <i>tetM</i> gene (tetracycline resistance) was identified in 47.4 % (<i>n</i> = 6 environmental; <i>n</i> = 3 clinical) of the <i>E. faecium</i> isolates, while the <i>bla</i>_<i>KPC</i> gene (carbapenem resistance) was detected in 52.6 % (<i>n</i> = 7 environmental; <i>n</i> = 3 clinical) and 15.4 % (<i>n</i> = 2 environmental) of the <i>E. faecium</i> and <i>K. pneumoniae</i> isolates, respectively. The <i>E. faecium</i> isolates were predominantly poor biofilm formers, the <i>K. pneumoniae</i> isolates were moderate biofilm formers, while the <i>P. aeruginosa</i> isolates were strong biofilm formers. All <i>E. faecium</i> and <i>K. pneumoniae</i> isolates were gamma (γ)-haemolytic, non-gelatinase producing (<i>E. faecium</i> only), and non-hypermucoviscous (<i>K. pneumoniae</i> only), while the <i>P. aeruginosa</i> isolates exhibited beta (β)-haemolysis and produced gelatinase. The <i>fimH</i> (type 1 fimbriae adhesion) and <i>ugE</i> (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the <i>K. pneumoniae</i> isolates, while the <i>P. aeruginosa</i> isolates possessed the <i>phzM</i> (phenazine production) and <i>algD</i> (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical <i>E. faecium</i>, <i>K. pneumoniae</i>, and <i>P. aeruginosa</i>, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.