Molecular Characterization and Antimicrobial Resistance of Uropathogenic Bacteria Among Elderly Residents of Nursing Care Homes in Accra, Ghana

Technical Summary: Molecular Characterization and Antimicrobial Resistance of Uropathogenic Bacteria Among Elderly Residents of Nursing Care Homes in Accra, Ghana

Problem Statement
Urinary tract infections (UTIs) represent a significant health burden among the elderly, particularly those residing in institutional care settings. In developing nations like Ghana, the burden of antimicrobial resistance (AMR) is exacerbated by limited treatment options and the indiscriminate use of antimicrobial agents. While Escherichia coli is the primary etiological agent in both community and nosocomial UTIs, there is a growing concern regarding the emergence of multidrug-resistant (MDR) uropathogens and Extended-Spectrum Beta-Lactamase (ESBL)-producing strains. Conventional microbiological methods often lack the precision to differentiate between phenotypically identical bacteria or to fully characterize the genetic diversity and resistance mechanisms of these pathogens. This study addresses the need for molecular characterization of uropathogens and the assessment of their resistance profiles among elderly residents in nursing care homes in Accra, Ghana.

Methodology
The study was conducted between December 2022 and December 2024 involving 118 elderly residents (aged 55–100 years) from five nursing care homes in Accra.

• Sample Collection and Diagnosis: Early morning mid-stream urine samples were collected and analyzed using dipstick testing (leukocyte esterase and nitrite) and microscopy. UTI was confirmed via culture on CLED, MacConkey, and Blood Agar plates, with significant growth defined as $\ge 10^5$ CFU/mL.
• Pathogen Identification: Isolates were identified using biochemical tests, MALDI-TOF mass spectrometry, and 16S rRNA gene sequencing. Sequences were aligned and phylogenetic trees were constructed using the maximum likelihood method (Tamura-Nei model) in MEGA XI software.
• Molecular Characterization:
  • Virulence and Phylogeny: E. coli isolates were screened via multiplex PCR for virulence genes (papE, sfa, sfas, afa, allele II) and phylogenetic grouping (Groups A, B1, B2, D) using triplex PCR.
  • ESBL Detection: All bacterial isolates were screened for 10 specific ESBL genes (blaTEM, blaSHV, blaMA, blaCTX-M-825, blaCTX-M-914, blaCMY-1, blaCMY-2, blaOXA-1, blaOXA-2, and CF) via PCR.
• Antimicrobial Susceptibility Testing (AST): The Kirby-Bauer disc diffusion method was employed following 2023 CLSI guidelines to test resistance against 10 antibiotics, including carbapenems, cephalosporins, fluoroquinolones, and aminoglycosides.

Key Results

• Prevalence and Pathogen Distribution: Out of 118 samples, 34 (28.8%) tested positive for UTI. The predominant pathogens were Gram-negative bacteria: E. coli (38.2%), Klebsiella pneumoniae (20.6%), Proteus mirabilis (20.6%), and Enterobacter cloacae (11.8%). Gram-positive isolates included Acinetobacter junii (5.9%) and Bacillus cereus (2.9%).
• Genetic Diversity: 16S rRNA sequencing revealed varying degrees of genetic relatedness. E. coli isolates showed close clustering with NCBI reference strains (bootstrap values 80–100), though some exhibited unique evolutionary divergence. P. mirabilis and B. cereus demonstrated high genetic conservation, while K. pneumoniae isolates displayed complex phylogeny with longer branch lengths, indicating intra-species diversity and local adaptation.
• Virulence and Phylogeny of E. coli: Among E. coli isolates, the sfas gene was the most prevalent virulence factor (40.8%), followed by sfa (25.9%), papE (18.5%), afa (11.1%), and allele II (3.7%). Phylogenetic analysis placed the majority of isolates in Group B2 (38.4%) and Group D (30.8%), which are associated with extraintestinal pathogenic E. coli (ExPEC).
• Antimicrobial Resistance: High resistance rates were observed across multiple classes.
  • E. coli showed high resistance to cefepime (84.6%) and azithromycin (76.9%).
  • K. pneumoniae exhibited 100% resistance to imipenem and high resistance to ertapenem and cefepime (85.7%).
  • P. mirabilis and E. cloacae also demonstrated significant resistance to carbapenems and cephalosporins.
  • A. junii and B. cereus showed total resistance to several tested antibiotics, including ertapenem and cefepime.
• ESBL Carriage: A total of 189 ESBL genes were detected across the isolates. The most prevalent genes were blaTEM and blaCTX-M-825 (16 detections each), followed by blaSHV (15) and blaCMY-1 (13). E. coli harbored all 10 screened ESBL genes, while K. pneumoniae and P. mirabilis lacked only blaMA.

Significance and Claims
The authors claim that this study highlights the critical significance of routine molecular surveillance of uropathogens within home care settings in Accra. The research provides critical insights into the molecular epidemiology of these pathogens, revealing a high prevalence of multidrug-resistant organisms and diverse resistance mechanisms, particularly among Gram-negative uropathogens.

The study asserts that the observed resistance patterns, including resistance to last-resort carbapenems (imipenem) and the widespread presence of ESBL genes, indicate an alarming incidence of highly resistant strains in this vulnerable population. The authors conclude that these findings necessitate an urgent need for population-specific surveillance data to inform evidence-based treatment guidelines. They recommend the implementation of antimicrobial stewardship programs and enhanced infection prevention and control measures to improve health outcomes for the elderly in institutional care. The paper does not propose new experimental applications but rather calls for policy and clinical interventions based on the documented molecular and resistance profiles.