Background: Whole genome sequencing analysis (WGSA) provides the best resolution for typing of bacterial isolates and has the potential for identification of transmission pathways. The aim of the study was to apply WGSA to elucidate the possible transmission events involved in two suspected Staphylococcus aureus hospital outbreaks in Ghana and describe genomic features of the S. aureus isolates sampled in the outbreaks. Methods: The study was carried out at Korle-Bu Teaching Hospital and Lekma Hospital where the suspected outbreaks occurred in 2012 and 2015, respectively. The S. aureus isolates collected from the two hospitals were from three sources including carriage, invasive disease, and the environment. Whole genome sequencing of the S. aureus isolates was performed and the sequence reads were mapped to the S. aureus reference genome of strain USA300_FPR3757. A maximum-likelihood phylogenetic tree was reconstructed. Multilocus sequence typing together with the analysis of antimicrobial resistance and virulence genes were performed by short read mapping using the SRST2. Results: The S. aureus isolates belonged to diverse sequence types (STs) with ST15 and ST152 most common. All isolates carried the blaZ gene, with low prevalence of tetK and dfrG genes also observed. All isolates were mecA negative. The pvl genes were common and observed in distinct lineages that revealed diverse Sa2int phages. At Korle-Bu Teaching Hospital, the genomics data indicated several transmission events of S. aureus ST15 involving contamination of various surfaces in the pediatric emergency ward where the outbreak occurred. Conclusion: The pattern of dissemination of the ST15 clone in the emergency ward of Korle-Bu Teaching Hospital highlights a basic problem with disinfection of environmental surfaces at the hospital. Diverse phage population rather than a single highly transmissible phage type likely mediates the high prevalence of pvl genes among the S. aureus isolates.

In 2012, Ghana introduced PCV13 into its childhood immunization program. To monitor the pneumococcus after PCV13 vaccination, we analyzed serotypes, antibiotic resistance, and virulence genes of pneumococcal carriage isolates among children under five years of age. We obtained nasopharyngeal swabs from 513 children from kindergartens and immunization centers in Cape Coast, Ghana. Pneumococcal serotypes were determined by multiplex-PCR and Quellung reaction. Antibiotic resistance and virulence genes prevalence were determined by disc diffusion and PCR respectively. Overall, carriage prevalence was 29.4% and PCV13 coverage was 38.4%. Over 60% of the isolates were non-PCV13 serotypes and serotype 23B was the most prevalent. One isolate showed full resistance to penicillin, while 35% showed intermediate resistance. Resistance to erythromycin and clindamycin remained low, while susceptibility to ceftriaxone, levofloxacin and vancomycin remained high. Penicillin resistance was associated with PCV13 serotypes. Forty-three (28.5%) strains were multidrug-resistant. Virulence genes pavB, pcpA, psrP, pilus-1, and pilus-2 were detected in 100%, 87%, 62.9%, 11.9%, and 6.6% of the strains, respectively. The pilus islets were associated with PCV13 and multidrug-resistant serotypes. PCV13 vaccination had impacted on pneumococcal carriage with a significant increase in non-PCV13 serotypes and lower penicillin resistance. Including PcpA and PsrP in pneumococcal protein-based vaccines could be beneficial to Ghanaian children.

Antibiotic resistance in pneumococci contributes to the high pneumococcal deaths in children. We assessed the molecular characteristics of multidrug-resistant (MDR) pneumococci isolated from healthy vaccinated children under five years of age in Cape Coast, Ghana. A total of 43 MDR isolates were selected from 151 pneumococcal strains obtained from nasopharyngeal carriage. All isolates were previously serotyped by multiplex PCR and Quellung reaction. Susceptibility testing was performed using either the E-test or disk diffusion method. Virulence and antibiotic resistance genes were identified by PCR. Molecular epidemiology was analyzed using multilocus sequence typing (MLST). Vaccine-serotypes 23F and 19F were predominant. The lytA and pavB virulence genes were present in all isolates, whiles 14–86% of the isolates carried pilus-islets 1 and 2, pcpA, and psrP genes. Penicillin, tetracycline, and cotrimoxazole resistance were evident in >90% of the isolates. The ermB, mefA, and tetM genes were detected in (n = 7, 16.3%), (n = 4, 9.3%) and (n = 43, 100%) of the isolates, respectively. However, >60% showed alteration in the pbp2b gene. MLST revealed five novel and six known sequence types (STs). ST156 (Spain^9V-3) and ST802 were identified as international antibiotic-resistant clones. The emergence of international-MDR clones in Ghana requires continuous monitoring of the pneumococcus through a robust surveillance system.

Preventive strategies involving the use of pneumococcal conjugate vaccines (PCVs) are known to drastically reduce pneumococcal disease. However, PCV vaccination has been plagued with serotype replacement by non-PCV serotypes. In this study, we describe the prevalence and molecular characteristics of non-PCV13 serotypes (non-vaccine serotypes, NVTs) from pneumococcal carriage isolates obtained from children < 5 years old in Cape Coast, Ghana, after PCV introduction. The isolates were subjected to antibiotic susceptibility testing and multilocus sequence typing (MLST), and molecular techniques were used to detect the presence of virulence genes. Serotypes 11A, 13, 15B, 23B, and 34 formed the top five of the 93 NVT isolates. As such, 20 (21.5%), 49 (48.4%), and 70 (74.3%) isolates were non-susceptible to penicillin, tetracycline, and cotrimoxazole, respectively. Sixteen (17.2%) multidrug-resistant isolates were identified. However, non-susceptibility to ceftriaxone and erythromycin was low and all isolates were fully susceptible to levofloxacin, linezolid, and vancomycin. Whereas pcpA, pavB, lytA, and psrP genes were detected in nearly all serotypes, pilus islet genes were limited to serotypes 11A, 13, and 23B. MLST for predominant serotype 23B isolates revealed three known and seven novel sequence types (STs). ST172 and novel ST15111 were the most dominant and both STs were related to PMEN clone Columbia^23F-26 (ST338). In conclusion, non-PCV13 serotype 23B was the most prevalent, with characteristics of rapid clonal expansion of ST172 and ST15111, which are related to international clones of the pneumococcus. Continuous monitoring of NVTs in Ghana is, therefore, essential, as they have the potential to cause invasive disease, show high antibiotic resistance, and attenuate the effects of PCV vaccination.

Increasing antimicrobial resistance (AMR) levels in Enterobacterales from pigs in Ghana prompted us to investigate farm feed, pig slurry, and farm water for Enterobacterales isolates, their antimicrobial resistance patterns, and antimicrobial residues. Between August and November 2024, we collected one sample each of feed, slurry, and water from 14 pig farms for microbiological analysis. Out of 42 samples, Enterobacterales (E. coli and Enterobacter spp.) were isolated from 30 (71.4%) samples, with the highest prevalence found in feed (85.7%), followed by slurry (78.6%) and water (50.0%). The prevalence of AMR to tetracyclines, trimethoprim-sulfamethoxazole, and ampicillin was high, with over 50% of isolates from slurry and water and 40% from feed exhibiting tetracycline resistance. Multi-drug resistance (MDR) was identified in nine (27.3%) isolates of Enterobacterales, with the highest prevalence found in feed (38.5%), then slurry (23.1%), and water (14.3%). Among 42 farm samples screened for colistin-resistant Enterobacterales, 10 (23.8%) exhibited phenotypic colistin resistance. No antimicrobial residues were detected. Risk factors associated with MDR included large farms with high pig turnover (p < 0.05) and the channelling of slurry into both covered and uncovered pits on the farm (p < 0.05). These high resistance levels underscore the urgent need for improved hygiene in feed, water, and slurry management, stricter antibiotic stewardship with veterinary oversight, and better enforcement of existing antibiotic use regulations on pig farms.

Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana is scarce. This study sequenced 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana, predominantly from paediatric patients under five years (67/103, 65%), with the majority collected from urine (32/103, 31%) and blood (25/103, 24%) cultures. We employed Pathogenwatch for genotyping via Kaptive (K/O antigens) and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome multilocus sequence typing (cgMLST). Among the 44 distinct sequence types (STs) detected, ST133 was the most common, comprising 23% of isolates (n=23/103). We discovered 27 different capsular (K) locus antigens and seven lipopolysaccharide (O) types; KL116 (28/103, 27%) and O1 (66/103, 64%) were the most prevalent. Single-linkage clustering highlighted the global spread of multidrug-resistant clones such as ST15, ST307, ST17, ST11, ST101, and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, several isolates (n=17) constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103, 85%) carried resistance genes for three or more antibiotic classes, with the bla _CTXM-15 gene present in 78% (n=80/103). Carbapenem resistance, predominantly due to bla _OXA-181 and bla _NDM-1 genes, was found in 10% (n=10/103) of the isolates. Yersiniabactin was the predominant acquired virulence trait, identified in 70% (n=72/103) of the isolates. Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.