Genomic Analysis of Multidrug-Resistant Hypervirulent (Hypermucoviscous) Klebsiella pneumoniae Strain Lacking the Hypermucoviscous Regulators (rmpA/rmpA2)

Abstract

Hypervirulent K. pneumoniae (hvKP) strains possess distinct characteristics such as hypermucoviscosity, unique serotypes, and virulence factors associated with high pathogenicity. To better understand the genomic characteristics and virulence profile of the isolated hvKP strain, genomic data were compared to the genomes of the hypervirulent and typical K. pneumoniae strains. The K. pneumoniae strain was isolated from a patient with a recurrent urinary tract infection, and then the string test was used for the detection of the hypermucoviscosity phenotype. Whole-genome sequencing was conducted using Illumina, and bioinformatics analysis was performed for the prediction of the isolate resistome, virulome, and phylogenetic analysis. The isolate was identified as hypermucoviscous, type 2 (K2) capsular polysaccharide, ST14, and multidrug-resistant (MDR), showing resistance to ciprofloxacin, ceftazidime, cefotaxime, trimethoprim-sulfamethoxazole, cephalexin, and nitrofurantoin. The isolate possessed four antimicrobial resistance plasmids (pKPN3-307_type B, pECW602, pMDR, and p3K157) that carried antimicrobial resistance genes (ARGs) (blaOXA-1,blaCTX-M-15, sul2, APH(3″)-Ib, APH(6)-Id, and AAC(6′)-Ib-cr6). Moreover, two chromosomally mediated ARGs (fosA6 and SHV-28) were identified. Virulome prediction revealed the presence of 19 fimbrial proteins, one aerobactin (iutA) and two salmochelin (iroE and iroN). Four secretion systems (T6SS-I (13), T6SS-II (9), T6SS-III (12), and Sci-I T6SS (1)) were identified. Interestingly, the isolate lacked the known hypermucoviscous regulators (rmpA/rmpA2) but showed the presence of other RcsAB capsule regulators (rcsA and rcsB). This study documented the presence of a rare MDR hvKP with hypermucoviscous regulators and lacking the common capsule regulators, which needs more focus to highlight their epidemiological role.

Infection Sources and Klebsiella pneumoniae Antibiotic Susceptibilities in Endogenous Klebsiella Endophthalmitis

“…However, the details of antibiotic susceptibility testing results are lacking in patients with EKE. Amidst growing concern over the emergence of multidrug-resistant (MDR) bacteria, selecting appropriate antibiotics for infection treatment has become a critical issue [ 14 , 15 ]. Common variants of MDR K. pneumoniae include extended-spectrum β-lactamase (ESBL)-producing and carbapenemase-producing K. pneumoniae [ 14 , 15 , 16 ].…”

“…Amidst growing concern over the emergence of multidrug-resistant (MDR) bacteria, selecting appropriate antibiotics for infection treatment has become a critical issue [ 14 , 15 ]. Common variants of MDR K. pneumoniae include extended-spectrum β-lactamase (ESBL)-producing and carbapenemase-producing K. pneumoniae [ 14 , 15 , 16 ]. Although most isolates causing ocular infections are not caused by MDR bacteria, antibiotic susceptibility testing may reveal antibiotic susceptibility and resistance trends.…”

Genomic Study of Chromosomally and Plasmid-Mediated Multidrug Resistance and Virulence Determinants in Klebsiella Pneumoniae Isolates Obtained from a Tertiary Hospital in Al-Kharj, KSA

“…KP has evolved and become resistant to third-generation cephalosporins and carbapenems, which has led to narrow treatment options for MDR KP, and in some settings, entirely removed [ 17 ]. However, there is a continuous surge in the prevalence of MDR KP strains; hypermucoviscous and hypervirulent KP strains have also been acknowledged and described [ 18 ].…”

Genomic Analysis of Antibiotics Resistance in Pathogens

“…This collection also gathers papers on antibiotic resistance of some of the major emerging infections pathogens such as Mycobacteroides abscessus [ 3 ], Klebsiella pneumoniae [ 4 , 5 ], Salmonella sp. [ 6 , 7 ], Francisella tularensis [ 8 ], Acinetobacter baumannii [ 9 , 10 ], or Pseudomonas aeruginosa [ 11 ] and other human pathogens such as Neisseria gonorrhoea [ 12 ], Staphylococcus aureus [ 13 ], or Escherichia coli [ 14 ].…”

“…Altayb et al studied and isolated a K. pneumoniae isolate from a patient with recurrent urinary tract infection, identified as hypermucoviscent, type 2 (K2) capsular polysaccharide, ST14, and multidrug-resistant. The authors performed genomic analysis and demonstrated that it harbors four plasmids, several virulence factors, and antibiotic resistance encoding genes, which are worth studying in more detail [ 5 ].…”