Colistin resistance in gram-negative pathogens in the Western Cape, South Africa
| dc.contributor.advisor | Newton-Foot, Mae | en_ZA |
| dc.contributor.advisor | Whitelaw, Andrew Christopher | en_ZA |
| dc.contributor.advisor | Maloba, Motlatji Reratilwe Bonnie | en_ZA |
| dc.contributor.author | Snyman, Yolandi | en_ZA |
| dc.contributor.other | Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Division of Medical Microbiology. | en_ZA |
| dc.date.accessioned | 2021-10-12T12:23:19Z | en_ZA |
| dc.date.accessioned | 2022-02-22T10:24:00Z | en_ZA |
| dc.date.available | 2021-10-12T12:23:19Z | en_ZA |
| dc.date.available | 2022-02-22T10:24:00Z | en_ZA |
| dc.date.issued | 2021-12 | en_ZA |
| dc.description | Thesis (PhD)--Stellenbosch University, 2023. | en_ZA |
| dc.description.abstract | ENGLISH ABSTRACT: Background Antimicrobial resistance is a public health concern and injudicious antibiotic prescribing and inadequate infection control practices have left the global community with untreatable multidrugresistant (MDR) bacteria. Colistin is a last resort antibiotic used to treat infections with MDR Gramnegative bacteria (GNB), especially carbapenem-resistant GNB. Therefore, the emergence of colistin resistance is a serious problem. This study from the Western Cape, South Africa, describes colistin resistance mechanisms in colistin-resistant GNB isolates from clinical specimens from various hospitals, stool samples from healthy children in the community, and river and storm water. Methods Colistin-resistant GNB isolates from clinical specimens from different healthcare facilities were collected from the NHLS microbiology laboratory at Tygerberg Hospital during 2016 and 2017. Fifty stool samples from healthy children (≤ 5 year of age) in the Cape Town metropolitan were collected between November 2017 and August 2018, and three surface water sources and stormwater were collected in 2019 and 2020. Selective media was used to isolate colistin-resistant GNB from the stool and water samples. Colistin resistance was confirmed using broth microdilution (BMD). The mobile colistin resistance genes, mcr-1-9, were detected by PCR and whole-genome sequencing (WGS). In selected mcr-negative isolates chromosomal colistin resistance mutations were identified by WGS. Strain typing was performed by WGS (MLST and SNP analyses) and repPCR. The functionality of mcr genes with unknown colistin resistance profiles was determined by BMD following recombinant expression or plasmid curing. Results mcr-1 was present in 55% (12/22) of Escherichia coli and 71% (5/7) of Klebsiella spp. isolates from patients at various hospitals during 2016-2017. pmrB mutations were identified in 8/10 mcrnegative E. coli and mgrB was disrupted in the two mcr-negative Klebsiella spp. isolates. Most colistin-resistant GNB isolated from hospitalised patients in 2016 and 2017 were unrelated, however, some clonal relatedness was observed in the 2017 E. coli population and a clonal expansion of an emerging colistin-resistant MDR Acinetobacter baumannii strain was noted among isolates from 2017. No previously described colistin resistance mechanism was detected in the A. baumannii isolates, but a possible novel mechanism was described. mcr-4.3 was detected in a Stellenbosch University https://scholar.sun.ac.za iii single Acinetobacter nosocomialis isolate, although recombinant mcr-4.3 did not confer colistin resistance in E. coli, plasmid curing of the mcr-4.3-containing plasmid restored colistin susceptibility. Colistin-resistant E. coli were isolated from the stools of two healthy children from the community (4%, 2/50) during 2017-2018; however, mcr genes were not detected. Colistin-resistant GNB, mainly Aeromonas spp., and mcr-5.1 and/or various mcr-3 variants were detected in the Plankenburg river, Eerste river, and Berg river and stormwater from Muizenberg and Fish Hoek in 2019 and 2020. Of the colistin-resistant Aeromonas spp. isolated from the Berg river, 25% (6/24) contained five novel mcr-3 variants, which were confirmed to confer colistin resistance. Conclusion The emergence of colistin resistance mechanisms in diverse strains obtained from hospital patients, with the limited gastrointestinal carriage of colistin-resistant Enterobacterales in community children and the disparate colistin-resistant species and mechanisms in the environment, suggest that selective pressure, and not community transmission, is the main driver of colistin resistance in clinical settings. | en_ZA |
| dc.description.abstract | AFRIKAANS OPSOMMING: Agtergrond Weerstandigheid teen antibiotika is 'n enorme stryd vir openbare gesondheid. Antibiotika wat onoordeelkundig voorgeskryf word, sowel as onvoldoende infeksiebeheerpraktyke laat die wêreldwye gemeenskap met onbehandelbare multi-dwelm-weerstandige (MDW) bakterieë. Kolistien is geklassifiseer as „n laaste uitweg antibiotika wat slegs toegedien word om infeksies met MDW Gram-negatiewe bakterieë (GNB) te behandel, veral karbapenem-weerstandige GNB, en daarom is kolistien-weerstandigheid 'n ernstige probleem. Hierdie studie vanuit die Wes-Kaap, Suid-Afrika, beskryf kolistien-weerstandigheidsmeganismes in kolistien-weerstandige GNB-isolate van kliniese monsters vanaf verskeie gesondheidsorgfasiliteite, stoelgangmonsters van gesonde kinders in die gemeenskap, en rivier- en stormwater. Metodes Kolistien-weerstandige GNB-isolate van kliniese monsters vanaf verskeie gesondheidsorgfasiliteite is deur die NHLS-mikrobiologielaboratorium in Tygerberg hospitaal gedurende 2016 en 2017 gekollekteer. Vyftig stoelgangmonsters van gesonde kinders (≤ 5 jaar oud) in die Kaapse metropool is gekollekteer tussen November 2017 en Augustus 2018. Watermonsters van drie riviere en twee stormwaterpunte is gekollekteer in 2019 en/of 2020. Kolistien-weerstandige GNB-isolate in die stoelgang- en water-monsters is met selektiewe media geïsoleer. Kolistien-weerstandigheid is bevestig met antibiotiese-mikroverdunning (AMV). Die mobiele kolistien-weerstandigheidsgene, mcr-1-9, is met „n polimerase kettingreaksie (PKR), asook heelgenoom-volgordebepaling (HGV) opgespoor. Chromosomale kolistien-weerstandigheidsmutasies is met behulp van HGV in geselekteerde mcr-negatiewe isolate geïdentifiseer. Stamtipering is uitgevoer deur gebruik te maak van HGV (MLST en SNP ontleding) en rep-PKR. Die funksionaliteit van mcr-gene met onbekende kolistien-weerstandigheidsprofiele was met AMV bepaal, nadat rekombinante uitdrukking van plasmied-genesing plaasgevind het. Resultate mcr-1 was teenwoordig in 55% (12/22) Escherichia coli en 71% (5/7) Klebsiella spp. isolate van pasiënte in verskeie hospitale tydens 2016-2017. pmrB mutasies is in 8/10 mcr-negatiewe E. coli geïdentifiseer en die mgrB geen is in beide mcr-negatiewe Klebsiella spp. isolate ontwrig. Die Stellenbosch University https://scholar.sun.ac.za v meeste geïsoleerde kolistien-weerstandige GNB vanaf pasiënte in gesondheidsorgfasiliteite tydens 2016 en 2017 was nie verwant nie. Daar is egter 'n mate van klonale verwantskap in die 2017 E. coli populasie waargeneem, asook 'n klonale uitbreiding van 'n opkomende kolistienweerstandige MDW Acinetobacter baumannii stam in isolate van 2017. Geen voorheen beskryfde kolistien-weerstandigheidsmeganismes is in die A. baumannii isolate waargeneem nie, maar 'n moontlike nuwe meganisme is wel beskryf. mcr-4.3 is waargeneem in 'n enkele Acinetobacter nosocomialis isolaat en, alhoewel die rekombinante mcr-4.3 nie kolistienweerstandigheid in E. coli verleen nie, het plasmied-genesing van die mcr-4.3-bevattende plasmied kolistien-vatbaarheid herstel. Kolistien-weerstandige E. coli is uit die stoelgangmonsters van twee gesonde kinders in die gemeenskap gedurende 2017-2018 geïsoleer (4%, 2/50); mcr-gene is egter nie opgespoor nie. Kolistien-weerstandige GNB, veral Aeromonas spp., en mcr-5.1 en/of verskillende mcr-3-variante is in die Plankenburg-, Eerster- en Bergrivier en stormwater van Muisenberg en Vishoek in 2019 en 2020 waargeneem. In die Bergrivier is 25% (6/24) kolistien-weerstandige Aeromonas spp. geïsoleer, waarvan vyf nuwe mcr-3-variante is. Kolistien-weerstandigheid van hierdie variante is bevestig. Afsluiting Die opkoms van kolistien-weerstandigheidsmeganismes in verskeie bakteriële stamme vanuit hospitaal pasiënte, asook die beperkte gastro-intestinale inhoud van kolistien-weerstandige Enterobacterales in gemeenskapskinders en die verskillende kolistien-weerstandige spesies en meganismes in die omgewing, dui daarop dat selektiewe druk die hoof drywer van kolistienweerstandigheid in kliniese omgewings is en dat gemeenskapsoordrag na die kliniese omgewings hoogs onwaarskynlik is. | af_ZA |
| dc.description.version | Doctorate | en_ZA |
| dc.embargo.terms | 2022-09-10 | en_ZA |
| dc.format.extent | xiii, 161 pages : illustrations | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/10019.1/124299 | en_ZA |
| dc.language.iso | en_ZA | en_ZA |
| dc.publisher | Stellenbosch : Stellenbosch University | en_ZA |
| dc.rights.holder | Stellenbosch University | en_ZA |
| dc.subject.lcsh | Gram-negative bacteria | en_ZA |
| dc.subject.lcsh | Pathogenic microorganisms | en_ZA |
| dc.subject.lcsh | Anti-infective agents | en_ZA |
| dc.subject.lcsh | Multidrug resistance | en_ZA |
| dc.title | Colistin resistance in gram-negative pathogens in the Western Cape, South Africa | en_ZA |
| dc.type | Thesis | en_ZA |