ABSTRACT
Genomic data on clinically important bacteria species such as Streptococcus pneumoniae and Streptococcus pseudopneumoniae from low- and middle-income countries, including Ghana, are scarce. In this study, we provide data on antimicrobial resistance (AMR) and whole-genome profiles of a collection of streptococci species to support AMR surveillance efforts in the country.
KEYWORDS: Africa, Streptococcus pneumoniae, S. pseudopneumoniae
ANNOUNCEMENT
Streptococci are a major cause of a wide range of diseases including pneumoniae, bacteremia, and meningitis (1). The similarities between Streptococcus pseudopneumoniae and Streptococcus pneumoniae make distinguishing them using traditional typing methods challenging (2, 3). Information on the epidemiology and genomic characteristics of S. pseudopneumoniae is scarce in sub-Saharan countries, including Ghana. Like S. pneumoniae, S. pseudopneumoniae is frequently associated with high rates of antimicrobial resistance, particularly to penicillin, macrolides, co-trimoxazole, and tetracycline (3). This article details the antimicrobial susceptibility and genomic profiles of 10 S. pneumoniae and 3 S. pseudopneumoniae isolates recovered from nasopharyngeal swabs collected from HIV-positive individuals during a cross-sectional study conducted at three hospitals in the Greater Accra Region of Ghana: University of Ghana Hospital, LEKMA Hospital, and Korle Bu Teaching Hospital. The study received approval from the University of Ghana, College of Health Sciences Ethical and Protocol Review Committee (Protocol number: CHS-Et/M.7-P 4.3/2022–2023). The nasopharyngeal swab samples were plated on 5% sheep blood agar (Oxoid) and incubated anaerobically for 24 hours at 37°C. Bacteria identification was done using the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometer. Antimicrobial susceptibility testing was performed on MH agar with 5% sheep blood using seven antibiotics (chloramphenicol, clindamycin, erythromycin, linezolid, tetracycline, trimethoprim-sulfamethoxazole, and vancomycin) in a disk diffusion assay and interpreted according to the Clinical Laboratory Standards Institute guidelines (CLSI, 2023). S. pneumoniae ATCC 49619 strain was used as control.
Following the manufacturer’s instructions, DNA was extracted from pure overnight cultures using the QIAamp DNA Mini Kit (Qiagen, Germany) after suspending the colonies in lysozyme. The extracted DNA was then quantified using the Qubit 4.0 fluorometer and the High Sensitivity dsDNA Assay Kit. Libraries were generated using the Illumina DNA library preparation kit (Illumina Inc., San Diego, CA, USA). The quality and concentration of the libraries were subsequently assessed using the 2100 bioanalyzer system (Agilent) and Qubit 4.0 fluorometer, respectively. The libraries underwent dilution to reach a concentration of 2 nM, subsequently pooled, and subjected to sequencing on the Illumina Miseq platform (Illumina Inc., San Diego, CA) using a 2 × 300 bp chemistry. After sequencing, Trimmomatic v.0.39 (4) was employed in the trimming of adaptors and reads with a quality score below 20. FastQC v.1.0 (https://www.bioinformatics.babraham.ac.uk) was used in the quality control checks of the reads. Unicycler v.0.5.0 (5) was used in the assembly of the trimmed reads and subsequently assessed using Quast v.5.2.0 (6). All genomes had a Q-score greater than 30, a minimum coverage of 40×, less than 300 contigs, and a minimum contig size exceeding 200 bp. Post assembly, KmerFinder v.4.1 (https://cge.food.dtu.dk/services/KmerFinder/) (7) was employed in bacterial species identification. ResFinder v.4.1 (https://cge.food.dtu.dk/services/ResFinder/) (8), CARD v.3.2.9 (https://card.mcmaster.ca/) (9), VirulenceFinder v.2.0 (https://cge.food.dtu.dk/services/VirulenceFinder/) (10), and MLST v.2.0 (https://cge.food.dtu.dk/services/MLST/) (11) were used in the determination of sequence types, resistance, and virulence genes using default settings. The assembled genomes were annotated using Prokka v.1.14.6 (12).
ACKNOWLEDGMENTS
Participant recruitment was funded by HIV Co-morbidities Research Training in Ghana program (HIV-ComRT). Antimicrobial susceptibility testing was supported by CAPREX project (RY89). Culture, identification, and whole-genome sequencing were supported by SeqAfrica (FF RGR2 FF25) project, funded by the Department of Health and Social Care’s Fleming Fund using UK aid.
The views expressed in this publication are those of the authors and not necessarily those of the UK Department.
Contributor Information
Beverly Egyir, Email: beverlyegyir@gmail.com, begyir@noguchi.ug.edu.gh.
Catherine Putonti, Loyola University Chicago, Chicago, Illinois, USA.
DATA AVAILABILITY
The genomes were deposited in the National Center for Biotechnology Information database with BioProject number PRJNA952500. Table 1 summarizes the antibiotic profile and genomic characteristics of the isolates.
TABLE 1.
Antimicrobial resistance profiles and genomic characteristics of isolatesa
| Isolate ID | Strain | Hospital | Genome accession no. | SRA accession no. | Biosample accession no. | Antibiotic resistance profile | Resistance genes | Virulence genes | Sequence type | Coverage (×) | Genome size (bp) | No. of contigs | N50 (bp) | GC content (%) | No. of reads | No. of CDS | No. of genes | No. of rRNA | No. of tRNA | No. of tmRNA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S. pneumoniae | ||||||||||||||||||||
| HRV-23–022 | SA1 | LEKMA | JARUNO000000000 | SRR24071752 | SAMN34074645 | ERY, CLI, TE, and SXT | erm(B), mef(A), msr(D), tet(M), patA, patB, pmrA, and VanY | cbpD, cbpG, lytA, lytB, lytC, pce/cbpE, pspA, pspC/cbpA, pavA, lmb, srtA, rrgA, plr/gapA, rrgB, rrgC, srtB, srtC, srtD, hysA, nanA, eno, piaA, piuA, psaA, cppA, iga, htrA/degP, tig/ropA, zmpB, and ply | ST320 | 84 | 2,048,242 | 77 | 71,641 | 39.7 | 1,102,816 | 1,994 | 2,033 | 3 | 35 | 1 |
| HRV-23-D44 | SA3 | LEKMA | JARUNM000000000 | SRR24071750 | SAMN34074647 | SXT | patA, patB, pmrA, and VanY | cbpD, cbpG, lytB, lytC, pce/cbpE, pspA, pspC/cbpA, pavA, lmb, srtA, slrA, plr/gapA, cla, nanA, eno, piaA, piuA, psaA, cppA, iga, htrA/degP, tig/ropA, zmpB, and ply | ST17228 | 104 | 2,149,241 | 75 | 89,076 | 39.4 | 1,448,104 | 2,127 | 2,167 | 3 | 36 | 1 |
| HRV-23–111 | SA4 | KBTH | JBBKAG000000000 | SRR28419022 | SAMN40566640 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cps4A, cps4B, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST172 | 47 | 2,135,800 | 82 | 52,858 | 39.5 | 498,944 | 2,110 | 2,149 | 3 | 35 | 1 |
| HRV-23–147 | SA5 | LEKMA | JBBKAF000000000 | SRR28419021 | SAMN40566641 | TE | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18370 | 67 | 2,025,352 | 137 | 44,799 | 39.7 | 616,808 | 1,955 | 1,989 | 3 | 30 | 1 |
| HRV-23–148 | SA6 | LEKMA | JBBKAE000000000 | SRR28419019 | SAMN40566642 | C, TE, and SXT | patA, patB, pmrA, cat(pC194), and tet(M) | cbpD, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, ply, psaA, rrgA, rrgC, srtC-1/srtB, srtC-2/srtC, and srtC-3/srtD | ST802 | 94 | 2,160,343 | 68 | 77,187 | 39.4 | 971,194 | 2,150 | 2,191 | 3 | 37 | 1 |
| HRV-23–167 | SA7 | KBTH | JBBKAD000000000 | SRR28419018 | SAMN40566643 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18372 | 40 | 2,050,151 | 104 | 42,645 | 39.6 | 435,710 | 2,024 | 2,060 | 3 | 32 | 1 |
| HRV-23–33 | SA8 | LEKMA | JBBKAC000000000 | SRR28419017 | SAMN40566644 | C, TE, and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18370 | 98 | 2,052,594 | 79 | 90,420 | 39.7 | 881,934 | 2,003 | 2,055 | 3 | 37 | 1 |
| HRV-23–443 | SA9 | LEKMA | JBBKAB000000000 | SRR28419016 | SAMN40566645 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, hysA, lytA, lytB, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST700 | 101 | 2,057,773 | 69 | 82,415 | 39.5 | 970,696 | 2,016 | 2,055 | 3 | 35 | 1 |
| HRV-23–66 | SA10 | LEKMA | JBBKAA000000000 | SRR28419015 | SAMN40566646 | C, TE, and SXT | patA, patB, pmrA, cat(pC194), and tet(M) | cbpD, cbpG, hysA, lytA, lytC, nanB, pce, pfbA, ply, psaA, and pspC/cbpA | ST13456 | 47 | 2,052,751 | 84 | 39,511 | 39.6 | 464,844 | 2,001 | 2,035 | 3 | 30 | 1 |
| HRV-23–71 | SA11 | LEKMA | JBBJZZ000000000 | SRR28419014 | SAMN40566647 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytB, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18376 | 84 | 2,115,087 | 90 | 64,833 | 39.5 | 847,416 | 2,083 | 2,120 | 3 | 33 | 1 |
| S. pseudopneumoniae | ||||||||||||||||||||
| HRV-23–029 | SA12 | LEKMA | JBBJZY000000000 | SRR28419013 | SAMN40566648 | ERY, CLI, and SXT | patB | cbpD, lytA, lytC, pavA, pce, ply, and psaA | UNK | 46 | 1,941,672 | 47 | 75,591 | 40.3 | 387,928 | 1,769 | 1,795 | 2 | 25 | 1 |
| HRV-23–34 | SA13 | LEKMA | JBBJZX000000000 | SRR28419012 | SAMN40566649 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, hysA, lytC, pavA, pce, and psaA | UNK | 91 | 2,155,673 | 292 | 20,469 | 39.9 | 918,962 | 1,983 | 1,999 | 2 | 13 | 1 |
| HRV-23–36 | SA14 | LEKMA | JBBJZW000000000 | SRR28419020 | SAMN40566650 | TE and SXT | hysA, lytA, lytC, pavA, pce, ply, and psaA | patA, patB, pmrA, and tet(M) | UNK | 135 | 2,057,522 | 45 | 131,504 | 40.0 | 1,208,424 | 1,876 | 1,917 | 2 | 38 | 1 |
ERY, erythromycin; CLI, clindamycin; TE, tetracycline; SXT, trimethoprim-sulfamethoxazole; C, chloramphenicol; UKN, unknown; LEKMA, LEKMA Hospital; KBTH, Korle Bu Teaching Hospital.
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Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genomes were deposited in the National Center for Biotechnology Information database with BioProject number PRJNA952500. Table 1 summarizes the antibiotic profile and genomic characteristics of the isolates.
TABLE 1.
Antimicrobial resistance profiles and genomic characteristics of isolatesa
| Isolate ID | Strain | Hospital | Genome accession no. | SRA accession no. | Biosample accession no. | Antibiotic resistance profile | Resistance genes | Virulence genes | Sequence type | Coverage (×) | Genome size (bp) | No. of contigs | N50 (bp) | GC content (%) | No. of reads | No. of CDS | No. of genes | No. of rRNA | No. of tRNA | No. of tmRNA |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S. pneumoniae | ||||||||||||||||||||
| HRV-23–022 | SA1 | LEKMA | JARUNO000000000 | SRR24071752 | SAMN34074645 | ERY, CLI, TE, and SXT | erm(B), mef(A), msr(D), tet(M), patA, patB, pmrA, and VanY | cbpD, cbpG, lytA, lytB, lytC, pce/cbpE, pspA, pspC/cbpA, pavA, lmb, srtA, rrgA, plr/gapA, rrgB, rrgC, srtB, srtC, srtD, hysA, nanA, eno, piaA, piuA, psaA, cppA, iga, htrA/degP, tig/ropA, zmpB, and ply | ST320 | 84 | 2,048,242 | 77 | 71,641 | 39.7 | 1,102,816 | 1,994 | 2,033 | 3 | 35 | 1 |
| HRV-23-D44 | SA3 | LEKMA | JARUNM000000000 | SRR24071750 | SAMN34074647 | SXT | patA, patB, pmrA, and VanY | cbpD, cbpG, lytB, lytC, pce/cbpE, pspA, pspC/cbpA, pavA, lmb, srtA, slrA, plr/gapA, cla, nanA, eno, piaA, piuA, psaA, cppA, iga, htrA/degP, tig/ropA, zmpB, and ply | ST17228 | 104 | 2,149,241 | 75 | 89,076 | 39.4 | 1,448,104 | 2,127 | 2,167 | 3 | 36 | 1 |
| HRV-23–111 | SA4 | KBTH | JBBKAG000000000 | SRR28419022 | SAMN40566640 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cps4A, cps4B, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST172 | 47 | 2,135,800 | 82 | 52,858 | 39.5 | 498,944 | 2,110 | 2,149 | 3 | 35 | 1 |
| HRV-23–147 | SA5 | LEKMA | JBBKAF000000000 | SRR28419021 | SAMN40566641 | TE | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18370 | 67 | 2,025,352 | 137 | 44,799 | 39.7 | 616,808 | 1,955 | 1,989 | 3 | 30 | 1 |
| HRV-23–148 | SA6 | LEKMA | JBBKAE000000000 | SRR28419019 | SAMN40566642 | C, TE, and SXT | patA, patB, pmrA, cat(pC194), and tet(M) | cbpD, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, ply, psaA, rrgA, rrgC, srtC-1/srtB, srtC-2/srtC, and srtC-3/srtD | ST802 | 94 | 2,160,343 | 68 | 77,187 | 39.4 | 971,194 | 2,150 | 2,191 | 3 | 37 | 1 |
| HRV-23–167 | SA7 | KBTH | JBBKAD000000000 | SRR28419018 | SAMN40566643 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18372 | 40 | 2,050,151 | 104 | 42,645 | 39.6 | 435,710 | 2,024 | 2,060 | 3 | 32 | 1 |
| HRV-23–33 | SA8 | LEKMA | JBBKAC000000000 | SRR28419017 | SAMN40566644 | C, TE, and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18370 | 98 | 2,052,594 | 79 | 90,420 | 39.7 | 881,934 | 2,003 | 2,055 | 3 | 37 | 1 |
| HRV-23–443 | SA9 | LEKMA | JBBKAB000000000 | SRR28419016 | SAMN40566645 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, hysA, lytA, lytB, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST700 | 101 | 2,057,773 | 69 | 82,415 | 39.5 | 970,696 | 2,016 | 2,055 | 3 | 35 | 1 |
| HRV-23–66 | SA10 | LEKMA | JBBKAA000000000 | SRR28419015 | SAMN40566646 | C, TE, and SXT | patA, patB, pmrA, cat(pC194), and tet(M) | cbpD, cbpG, hysA, lytA, lytC, nanB, pce, pfbA, ply, psaA, and pspC/cbpA | ST13456 | 47 | 2,052,751 | 84 | 39,511 | 39.6 | 464,844 | 2,001 | 2,035 | 3 | 30 | 1 |
| HRV-23–71 | SA11 | LEKMA | JBBJZZ000000000 | SRR28419014 | SAMN40566647 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, cbpG, cps4A, cps4B, cps4C, cps4D, hysA, lytA, lytB, lytC, nanB, pavA, pce, pfbA, ply, and psaA | ST18376 | 84 | 2,115,087 | 90 | 64,833 | 39.5 | 847,416 | 2,083 | 2,120 | 3 | 33 | 1 |
| S. pseudopneumoniae | ||||||||||||||||||||
| HRV-23–029 | SA12 | LEKMA | JBBJZY000000000 | SRR28419013 | SAMN40566648 | ERY, CLI, and SXT | patB | cbpD, lytA, lytC, pavA, pce, ply, and psaA | UNK | 46 | 1,941,672 | 47 | 75,591 | 40.3 | 387,928 | 1,769 | 1,795 | 2 | 25 | 1 |
| HRV-23–34 | SA13 | LEKMA | JBBJZX000000000 | SRR28419012 | SAMN40566649 | TE and SXT | patA, patB, pmrA, and tet(M) | cbpD, hysA, lytC, pavA, pce, and psaA | UNK | 91 | 2,155,673 | 292 | 20,469 | 39.9 | 918,962 | 1,983 | 1,999 | 2 | 13 | 1 |
| HRV-23–36 | SA14 | LEKMA | JBBJZW000000000 | SRR28419020 | SAMN40566650 | TE and SXT | hysA, lytA, lytC, pavA, pce, ply, and psaA | patA, patB, pmrA, and tet(M) | UNK | 135 | 2,057,522 | 45 | 131,504 | 40.0 | 1,208,424 | 1,876 | 1,917 | 2 | 38 | 1 |
ERY, erythromycin; CLI, clindamycin; TE, tetracycline; SXT, trimethoprim-sulfamethoxazole; C, chloramphenicol; UKN, unknown; LEKMA, LEKMA Hospital; KBTH, Korle Bu Teaching Hospital.