ABSTRACT
Burkholderia cepacia complex (Bcc) are opportunistic and environmental pathogens associated with nosocomial bacteremia, yet data from low-income countries are scarce. Here, we report the draft whole-genome sequences of Bcc from blood cultures of admitted patients (n = 16) and the hospital environment (n = 5) at the Manhiça District Hospital.
KEYWORDS: Burkholderia cepacia complex, bacteremia, nosocomial infection, whole-genome sequencing (WGS), Mozambique, antimicrobial resistance (AMR)
ANNOUNCEMENT
Burkholderia cepacia complex (Bcc) is a group of environmental and opportunistic non-spore-forming gram-negative bacilli comprising more than 20 species, commonly shown to possess resistance to multiple classes of antimicrobials (1–3). Burkholderia cenocepacia, Burkholderia multivorans, Burkholderia dolosa, and Burkholderia contaminans frequently cause nosocomial infections in neonates, immunocompromised individuals, and cystic fibrosis patients, resulting in bacteremia from indwelling catheters, urinary tract infections, septic arthritis, peritonitis, and respiratory tract infections (4–8). Sources for nosocomial infections include taps, medications, suction equipment, and water (7–9). There is scarce information on Bcc in Sub-Saharan Africa. Herein, we announce draft whole-genome sequences of eight B. cenocepacia, seven B. contaminans, and one Burkholderia gladioli isolated from the blood cultures of admitted patients and five B. contaminans from the hospital environment in the Manhiça District Hospital (MDH), Southern Mozambique, between 2020 and 2023.
The draft Bcc genomes described in this report were obtained following the whole-genome sequencing of strains from blood samples collected upon admission of children <2 years or children aged 2–14 years, and adults with axillary temperature ≥39°C or with signs of severe illness within the invasive bacterial disease surveillance at the MDH as previously described (10). We also describe the genomes of strains isolated from hospital environment samples (swabs of surfaces and instruments in the pediatric ward) collected in a nosocomial outbreak investigation. The isolates were typed by multilocus sequence typing (MLST), using the Bcc scheme with the recA gene used for species identification (11, 12). Pure fresh colonies subcultured on Tryptone Soya Agar and incubated at 37°C for 18–24 h were used for genomic DNA extraction using the QIAamp DNA Mini Kit (Qiagen, Germany) and quantified on a Qubit fluorometer using a High Sensitivity dsDNA Assay Kit (Thermo Fisher Scientific, USA). Genomic libraries were prepared using the Nextera XT Library preparation protocol (Illumina) for obtaining 150-bp paired-end reads, followed by sequencing with Illumina MiSeq (B. cenocepacia) or HiSeq (B. contaminans and B. gladioli) instruments. All commercial kits were used following the vendor’s protocols without modifications.
Raw reads were processed using fastp v.0.26.0 (13) and de novo assemblies generated using the shovill v.1.1.0 (https://github.com/tseemann/shovill) pipeline that uses SPAdes v3.15.5 (14) and then evaluated with QUAST v.5.2.0 (15). Genome completeness and contamination were assessed through CheckM v.1.2.2 (16) and MLST confirmed in silico using mlst (https://github.com/tseemann/mlst). Upon submission to the National Center for Biotechnology Information (NCBI), draft genomes were annotated using the Prokaryotic Genome Annotation Pipeline v.6.10 (17). The presence of antimicrobial resistance (AMR) genes was analyzed through ABRicate v1.0.1 (https://github.com/tseemann/abricate) using ncbi, resfinder, and plasmidfinder databases, in addition to NCBI AMRFinder Plus v3.12.8 (18) and ResFinder v4.4.3 (19) command line tools. All software tools were used with default parameters.
Table 1 presents key genome statistics and AMR determinants identified in silico. These genomes provide a valuable resource for comparative genomics and phylogenetic studies of nosocomial infections by Bcc in Mozambique and Sub-Saharan Africa, especially with description of novel STs.
TABLE 1.
NCBI accession numbers, assembly metrics, and detected antimicrobial resistance (AMR) genes for each isolate analyzed in this study
| Isolate (source sample type) | SRA accession (BioSample); genome assembly accessiona | Species | Sequence type |
Nr of reads (Nr. of bases) | Genome size, bp (GC, %) |
Genome coveraged | Number of contigs (>500 bp) | N50, bp (L50) | Completeness, % (contamination, %)f |
Nr of genes (coding) | Antimicrobial resistance genes |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1785371_2 (blood) | SRR28968521 (SAMN41266729); JBWJFE000000000 | B. cenocepacia | 1890 (novelb) | 5294662 (693751230) | 8009678 (67) | 91× | 554 (473) | 29699 (78) | 99.26 (2.16) | 7597 (7413) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacEΔ1 |
| 1785313_2 (blood) | SRR28968535 (SAMN41266726); JBWJFD000000000 | B. cenocepacia | 1890 (novelb) | 4612626 (609612607) | 8003196 (67) | 81× | 580 (483) | 29671 (80) | 99.57 (1.58) | 7598 (7412) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacEΔ1 |
| 1785322_4 (blood) | SRR28968534 (SAMN41266727https://www.ncbi.nlm.nih.gov/biosample/SAMN41266727https://www.ncbi.nlm.nih.gov/biosample/SAMN41266727); JBWJFC000000000 | B. cenocepacia | 1890 (novelb) | 4226696 (559149139) | 7983685 (66.97) | 76× | 788 (689) | 22158 (102) | 99.58 (2.38) | 7719 (7521) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacEΔ1 |
| 1808361_3 (blood) | SRR28968519 (SAMN41266731); JBWJFB000000000 | B. cenocepacia | 1890 (novelb) | 2873396 (376978074) | 7996005 (66.98) | 55× | 796 (691) | 20958 (108) | 99.41 (1.99) | 7709 (7510) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacEΔ1 |
| 1785344_6 (blood) | SRR28968523 (SAMN41266728https://www.ncbi.nlm.nih.gov/biosample/SAMN41266728); JBWJFA000000000 | B. cenocepacia | 1890 (novelb) | 3568564 (469419805) | 7999258 (66.99) | 64× | 649 (537) | 25888 (89) | 99.26 (1.58) | 7609 (7419) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacE |
| 1785380_4 (blood) | SRR28968520 (SAMN41266730); JBWJEZ000000000 | B. cenocepacia | 1890 (novelb) | 4733844 (614457751) | 8021377 (67.02) | 80× | 429 (347) | 44166 (60) | 99.78 (1.58) | 7536 (7369) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacE |
| 1830240_0 (blood) | SRR28968517 (SAMN41266733); JBWJEY000000000 | B. cenocepacia | 1890 (novelb) | 2717916 (353238156) | 7856499 (66.83) | 57× | 1513 (1393) | 9151 (222) | 97.52 (2.79) | 8083 (7857) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacE |
| 1808391_0 (blood) | SRR28968518 (SAMN41266732); JBWJEX000000000 | B. cenocepacia | 1890 (novelb) | 3458624 (451801050) | 7917807 (66.98) | 66× | 1346 (1236) | 10680 (186) | 97.95 (2.59) | 8030 (7807) | blaOXA-1043, blaPEN-B1, dfrA5, sul1, ere(A), tet(64), qacE |
| 2086484_2 (blood) | SRR28968530 (SAMN41266739); JBWJEW000000000 | B. contaminans | 102 | 20962280 (3.100253 G) | 8917882 (66.12) | 348×e | 160 (101) | 237857 (9) | 100 (0.42) | 8191 (7794) | blaPEN-BCC, tet(64) |
| 2086461_3 (blood) | SRR28968531 (SAMN41266738); JBWJEV000000000 | B. contaminans | 102 | 20132794 (2.943245 G) | 8924256 (66.12) | 330×e | 143 (83) | 270770 (9) | 100 (0.42) | 8181 (7980) | blaPEN-BCC, tet(64) |
| 2085810_0 (blood) | SRR28968532 (SAMN41266737); JBWJEU000000000 | B. contaminans | 102 | 20971638 (3.102135 G) | 8924884 (66.12) | 348×e | 150 (83) | 280843 (8) | 100 (0.42) | 8185 (7982) | blaPEN-BCC, tet(64) |
| 2086498_9 (blood) | SRR28968529 (SAMN41266740); JBWJET000000000 | B. contaminans | 102 | 21229698 (3.144416 G) | 8925105 (66.12) | 353×e | 144 (85) | 270770 (9) | 100 (0.42) | 8180 (7978) | blaPEN-BCC, tet(64) |
| 2085750_9 (blood) | SRR28968533 (SAMN41266736); JBWJES000000000 | B. contaminans | 102 | 20243470 (2.982369 G) | 8925635 (66.12) | 334×e | 135 (82) | 280843 (10) | 100 (0.42) | 8175 (7975) | blaPEN-BCC, tet(64) |
| 2040454_3 (blood) | SRR28968515 (SAMN41266735); JBWJER000000000 | B. contaminans | 102 | 19335790 (2.846366 G) | 8925287 (66.12) | 319×e | 154 (84) | 280843 (8) | 100 (0.42) | 8184 (7983) | blaPEN-BCC, tet(64) |
| 2040452_9 (blood) | SRR28968516 (SAMN41266734); JBWJEQ000000000 | B. contaminans | 102 | 20079232 (2.956453 G) | 8925586 (66.12) | 332×e | 144 (81) | 296109 (8) | 100 (0.42) | 8176 (7975) | blaPEN-BCC, tet(64) |
| Z-28 (saline solution) | SRR28968526 (SAMN41266743); JBWJEP000000000 | B. contaminans | 102 | 19417104 (2.870609 G) | 8928984 (66.12) | 322×e | 180 (89) | 223985 (10) | 100 (0.42) | 8191 (7994) | blaPEN-BCC, tet(64) |
| Z-18 (10% dextrose solution) | SRR28968528 (SAMN41266741); JBWJEO000000000 | B. contaminans | 102 | 19263906 (2.836790 G) | 8924982 (66.12) | 318×e | 127 (76) | 280843 (8) | 100 (0.42) | 8172 (7971) | blaPEN-BCC, tet(64) |
| Z-19 (syringe for solution preparation) | SRR28968527 (SAMN41266742); JBWJEN000000000 | B. contaminans | 102 | 18960470 (2.804278 G) | 8924242 (66.12) | 315×e | 151 (80) | 390653 (7) | 100 (0.42) | 8184 (7986) | blaPEN-BCC, tet(64) |
| Z-57 (10% dextrose solution) | SRR28968525 (SAMN41266744); JBWJEM000000000 | B. contaminans | 102 | 19867398 (2.945530 G) | 8929891 (66.12) | 331×e | 113 (73) | 433656 (7) | 100 (0.42) | 8202 (7988) | blaPEN-BCC, tet(64) |
| Z-58 (glucose solution) | SRR28968524 (SAMN41266745); JBWJEL000000000 | B. contaminans | 102 | 19654256 (2.895199 G) | 8925695 (66.12) | 324×e | 136 (79) | 270770 (9) | 100 (0.42) | 8177 (7977) | blaPEN-BCC, tet(64) |
| 2085882_7 (blood) | SRR28968522 (SAMN41266746); JBWJEK000000000https://www.ncbi.nlm.nih.gov/wgs_batch/JBWJEK000000000 | B. gladioli | 2349 (novelc) | 19283476 (2.851013 G) | 8614985 (68.14) | 332×e | 115 (58) | 388591 (7) | 100 (1,66) | 7612 (7454) | bla PEN-N |
Draft genome assemblies submitted were trimmed to remove adapter sequences and other potential contaminants; only contigs >200 bp were included in the sequences submitted to NCBI Genomes database.
ST1890, a single locus variant of ST817.
ST2349, a double locus variant of ST1622.
Estimated by shovill v.1.1.0.
Downsampled to ~150× for genome assembly with shovill.
Estimated by CheckM v.1.2.2.
ACKNOWLEDGMENTS
This study was partly supported by funds from PATH through to the pneumonia and pneumococcus surveillance study (GAT.770-790-01350-LPS), the Bill & Melinda Gates Foundation through the Center for Vaccine Development, University of Maryland School of Medicine, the United States Agency for International Development mission in Mozambique through Fixed Obligation grant no. AID-656-F-12-00001, under RFA-656-12-000003, and the “Child Health and Mortality Prevention Surveillance-CHAMPS” through Bill & Melinda Gates Foundation under grant OPP1126780, subcontract SC00003286. The funders played no role in study design, implementation, preparation of the article, or the decision to publish. CISM is supported by the Government of Mozambique and the Agencia Española de Cooperación Internacional para el Desarrollo. ISGlobal authors acknowledge support from grant CEX2023-0001290-S funded by MCIN/AEI/10.13039/501100011033 and support from the Generalitat de Catalunya through the CERCA Program.
The authors express their gratitude to Dr. Nadia Boisen (Statens Serum Institute, Copenhagen, Denmark) for kindly providing the resources for sequencing part of the isolates in this study. They acknowledge the participants and their parents or guardians for participating in Invasive Bacterial Disease Surveillance. They also thank the Manhiça District Hospital and Centro de Investigação em Saúde de Manhiça (CISM) staff for collecting and processing samples and data included in this publication, as well as all the authorities for their collaboration in the research activities.
Contributor Information
Augusto Messa, Jr., Email: augusto.junior@manhica.net.
Inácio Mandomando, Email: inacio.mandomando@manhica.net.
Silvia T. Cardona, University of Manitoba, Winnipeg, Canada
DATA AVAILABILITY
The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under BioProject accession PRJNA1109395. Sequence Read Archive, BioSample, and Genome assemblies accessions are listed and hyperlinked in Table 1 for each genome.
ETHICS APPROVAL
The Bcc strains reported in this announcement were isolated in the scope of a morbidity surveillance system established as part of the Centro de Investigação em Saúde de Manhiça (CISM) Health and Demographic Surveillance System approved by the Institutional Bioethics Committee for Health at CISM (CIBS-CISM), and by the National Bioethics Committee for Health (CNBS–IRB00002657). All residents of the Manhiça district have signed an individual informed consent to become part of the surveillance.
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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 Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under BioProject accession PRJNA1109395. Sequence Read Archive, BioSample, and Genome assemblies accessions are listed and hyperlinked in Table 1 for each genome.