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A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought
Background Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in P. aeruginosa clinical isolates in Cape Town, South Africa during a severe drought. Methods Cases were defined as P. aeruginosa isolated from any clinical sample, and “...
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| Format: | Thesis |
| Language: | English |
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Department of Clinical Laboratory Sciences
2022
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| _version_ | 1867613249793425408 |
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| access_status_str | Open Access |
| author | Opperman, Christoffel Johannes |
| author2 | Centner, Chad M |
| author_browse | Centner, Chad M Opperman, Christoffel Johannes |
| author_facet | Centner, Chad M Opperman, Christoffel Johannes |
| author_sort | Opperman, Christoffel Johannes |
| collection | Thesis |
| description | Background Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in P. aeruginosa clinical isolates in Cape Town, South Africa during a severe drought. Methods Cases were defined as P. aeruginosa isolated from any clinical sample, and “wild-type” as susceptibility to all antibiotics tested. Residential addresses of community-acquired wild-type cases were mapped. Whole genome sequencing and multi-locus sequence typing were used to determine clonality and identify virulence genes. A modified case-control study in a subset of patients with bloodstream infection compared demographic and clinical characteristics between sequence types. Results The outbreak lasted 10 months from December, 2016 to September, 2017 with 3,321 documented cases. At the peak, cases reached 2.3-fold baseline and the city's dams reached a nadir of 19% capacity. Cases were distributed widely across the city. Multi-locus sequence type (ST) 303 was found in 27 of 42 (64%) blood culture isolates of P. aeruginosa during the outbreak, one of 19 (5%) before, and none of 11 after. ST303 infection was independently associated with younger age, but not with co-morbidities nor increased mortality. Fifty-one virulence genes were differentially present in ST303 compared with other sequence types, including genes involved in biofilm formation, iron uptake, and gut penetration. Conclusion The investigation confirmed a citywide outbreak of P. aeruginosa coinciding with and potentially related to a severe drought. We identified a predominant outbreak-associated clone, ST303, which harboured genes that could contribute to virulence and survival in drought-related conditions. Enhanced surveillance for P. aeruginosa during periods of drought is recommended. |
| format | Thesis |
| id | oai:open.uct.ac.za:11427/35998 |
| institution | University of Cape Town (South Africa) |
| language | eng |
| last_indexed | 2026-06-10T12:33:08.525Z |
| license_str | Not specified — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from UCTD — University of Cape Town Open Access Repository |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Department of Clinical Laboratory Sciences |
| publisherStr | Department of Clinical Laboratory Sciences |
| record_format | dspace |
| source_str | UCTD — University of Cape Town Open Access Repository |
| spelling | oai:open.uct.ac.za:11427/35998 A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought Opperman, Christoffel Johannes Centner, Chad M Nicol , Mark P Moodley, Clinton Laboratory Sciences Background Outbreaks of community-acquired Pseudomonas aeruginosa are typically small and localized. We investigated an increase in P. aeruginosa clinical isolates in Cape Town, South Africa during a severe drought. Methods Cases were defined as P. aeruginosa isolated from any clinical sample, and “wild-type” as susceptibility to all antibiotics tested. Residential addresses of community-acquired wild-type cases were mapped. Whole genome sequencing and multi-locus sequence typing were used to determine clonality and identify virulence genes. A modified case-control study in a subset of patients with bloodstream infection compared demographic and clinical characteristics between sequence types. Results The outbreak lasted 10 months from December, 2016 to September, 2017 with 3,321 documented cases. At the peak, cases reached 2.3-fold baseline and the city's dams reached a nadir of 19% capacity. Cases were distributed widely across the city. Multi-locus sequence type (ST) 303 was found in 27 of 42 (64%) blood culture isolates of P. aeruginosa during the outbreak, one of 19 (5%) before, and none of 11 after. ST303 infection was independently associated with younger age, but not with co-morbidities nor increased mortality. Fifty-one virulence genes were differentially present in ST303 compared with other sequence types, including genes involved in biofilm formation, iron uptake, and gut penetration. Conclusion The investigation confirmed a citywide outbreak of P. aeruginosa coinciding with and potentially related to a severe drought. We identified a predominant outbreak-associated clone, ST303, which harboured genes that could contribute to virulence and survival in drought-related conditions. Enhanced surveillance for P. aeruginosa during periods of drought is recommended. 2022-03-08T10:40:21Z 2022-03-08T10:40:21Z 2021 2022-03-08T10:35:28Z Master Thesis Masters MMed http://hdl.handle.net/11427/35998 eng application/pdf Department of Clinical Laboratory Sciences Faculty of Health Sciences |
| spellingShingle | Laboratory Sciences Opperman, Christoffel Johannes A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| thesis_degree_str | Master's |
| title | A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| title_full | A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| title_fullStr | A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| title_full_unstemmed | A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| title_short | A citywide, clonal outbreak of Pseudomonas aeruginosa during a drought |
| title_sort | citywide clonal outbreak of pseudomonas aeruginosa during a drought |
| topic | Laboratory Sciences |
| url | http://hdl.handle.net/11427/35998 |
| work_keys_str_mv | AT oppermanchristoffeljohannes acitywideclonaloutbreakofpseudomonasaeruginosaduringadrought AT oppermanchristoffeljohannes citywideclonaloutbreakofpseudomonasaeruginosaduringadrought |