The epidemiology of Gram negative bacteraemia at Tygerberg Hospital

Paterson, Lauren Ann (2018-03)

Thesis (MSc)--Stellenbosch University, 2018.

Thesis

Background Escherichia coli and Klebsiella pneumoniae are common causes of Bloodstream Infections (BSI). β-lactam antibiotics, such as cephalosporins and carbapenems, are commonly used to treat these infections. Increasing resistance has been noted, usually due to plasmid mediated β-lactamases such as Extended-Spectrum β-lactamases (ESBLs) and carbapenemases. This study describes the antibiotic resistance profiles, outcomes and epidemiology of Gram negative BSIs in a tertiary hospital in Cape Town, South Africa. Methods Patients with E. coli (n=70) and K. pneumoniae (n=70) bacteraemia identified at Tygerberg Hospital between April 2015 and March 2016 were included. Identification and Antibiotic Susceptibility Testing (AST) were performed as part of routine testing. Patient data was obtained through record review. ESBL and carbapenemase genes were characterised by Polymerase Chain Reaction (PCR) and DNA sequencing. Isolates were typed using rep-PCR and Pulsed Field Gel Electrophoresis (PFGE). Chi-square and Mann-Whitney tests were used to estimate significance of correlation. Results and discussion 45% of patients were male, and 30.7% were paediatric. 66.4% of BSI were hospital-acquired. K. pneumoniae accounted for 61.3% of hospital-acquired isolates; 72.3% of community-acquired isolates were E. coli. 55.7% of K. pneumoniae and 15.7% of E. coli were cephalosporin resistant (presumed ESBL); one K. pneumoniae isolate was carbapenem resistant. Increased antibiotic resistance and ESBL production was seen in hospital-acquired isolates. ESBL genes were harboured in 35.7% of isolates; 50.7% contained β-lactamase genes and 13.6% no β-lactamase genes. Most TEM genes (98%) were β-lactamases; 47.4% of SHV genes were β-lactamases, 7% were ESBLs and 45.6% were SHV genes whose spectrum is uncertain. Isolates containing SHV genes with uncertain spectrum were phenotypically susceptible to cephalosporins, suggesting these enzymes do not have extended-spectrum activity. Multiple β-lactamase genes were present in 60% of K. pneumoniae isolates, and only 5.7% of E. coli isolates. CTX-M genes were the most common ESBL genes, with most (91.3%) of these belonging to group 1. CTX-M genes were found in combination more often than not (84.8%). No carbapenemase genes were detected. Molecular and phenotypic resistance agreed in 95.3% of isolates. The 30-day mortality rate was 30%, with no association between mortality and hospital-acquired infection, or with ESBL production (phenotypic or molecular). Molecular and phenotypic resistance was associated with hospital-acquired isolates (P=0.001, P<0.001). Both strain typing techniques showed substantial diversity among isolates, with minimal clustering; which suggests multiple clones in the hospital, precluding any possibility of assessing associations. Conclusion Increased resistance was observed in hospital-acquired isolates, and the association between hospital-acquired isolates and ESBL presence was significant, which is not unexpected. Isolates were genetically diverse and showed minimal clustering, suggesting that resistance may be due to horizontal transmission. Continuous efforts towards surveillance of the epidemiology and resistance patterns of circulating strains are required to monitor and guide antimicrobial stewardship, infection prevention and control (IPC) practises and empiric therapy.

Agtergrond Escherichia coli en Klebsiella pneumoniae is alombekend om bloedstroominfeksies (BSI) te veroorsaak. Hierdie infeksies word grotendeels behandel met β-laktam antibiotika, soos kefalosporiene en “carbapenems”, Verhoogde β-laktam antibiotika weerstandigheid word toegeskryf aan plasmied-gemedieërde β-laktamases soos die “Extended-Spectrum β-lactamases” (ESBLs) en “carbapenemases”. Hierdie studie beskryf die antibiotiese weerstandsprofiele, uitkomste en epidemiologie van Gram negatiewe BSI’s in ‘n tersiêre hospitaal in Kaapstad, Suid-Afrika. Metodes E. coli (n=70) en K. pneumoniae (n=70) bakterieë vanaf kliniese monsters van Tygerberg Hospitaal tussen April 2015 en Maart 2016 was ingesluit. Spesie-identifikasie en antibiotiese-vatbaarheidstoetse was uigevoer as deel van roetine toetse. Pasiënt data was deur middel van mediese rekords verkry. ESBL en carbapenemase gene is met polimerasekettingreaksie (PKR) en DNA-volgordebepaling gekarakteriseer. Isolate is getipeer met rep-PKR en “Pulsed Field Gel Electrophoresis” (PFGE). Chi-kwadraat en Mann-Whitney toetse was toegepas om die statistiese betekenisvolheid van korrelasie te skat. Resultate en bespreking 45% van pasiënte was manlik en 31.4% was pediatries. 66.4% van BSI was hospitaal-geassosieerd. 61.3% van die hospitaal-geassosieerd isolate was K. pneumoniae; 72.3% van die gemeenskaps-geassosieerde isolate was E. coli. 55.7% van K. pneumoniae en 15.7% van E. coli was kefalosporien-weerstandig (veronderstelde ESBL); een K. pneumoniae isolaat was carbapenem-weerstandig. ‘n Toename in antibiotiese weerstandiheid en ESBL-produksie was waargeneem in die hospitaal-geassosieerd isolate. ESBL gene was teenwoordig in 35.7% van die isolate; 50.7% bevat β-laktamase gene en 13.6% bevat geen β-laktamase gene nie. TEM gene (98%) was grotendeels β-laktamases; 47.4% van die SHV gene was β-laktamases, 7% was ESBL en 45.6% was SHV gene waarvan die spektrum onbekend was. Isolate met SHV gene met onbekende spektrums was fenotipies vatbaar vir kefalosporiene, wat voorstel dat hierdie ensieme nie uitgebreide spektrum aktiwiteit gehad het nie. Verskeie β-laktamase gene was teenwoordig in 60% van K. pneumoniae isolate en 5.7% E. coli isolate respektiewelik. CTX-M gene was die mees algemeen ESBL gene en die meerderheid (91.3%) behoort aan groep 1, wat die wêreldbekende CTX-M (CTX-M-15) bevat. CTX-M gene was grotendeels waargeneem in kombinasie (84.8%). Geen carbapenemase gene was gevind nie. Molekulêre en fenotipiese weerstandigheid het in 95.3% van die isolate ooreengestem. Die 30-dag mortaliteit was 30%, met geen assosiasie tussen hospitaal-geassosieerde infeksie, of met ESBL produksie (molekulêr of fenotipies) nie. Molekulêre en fenotipiese weerstandigheid was geassosieer met hospitaal-geassosieerde isolate (P=0.001; P<0.001). Beide tiperingstegnieke het aansienlike diversiteit bevestig tussen die isolate met minimale groepering. Dit dui daarop dat verskeie klone voorkom in die hospitaal, en dat enige moontlikheid om die assosiasies tussen tipe, weerstands-fenotipe of -genotipe of uitkoms bepaal kan word. Gevolgtrekking ‘n Toename in weerstandigheid was waargeneem in alle hospitaal-geasosieerde isolate. Die assosiasie tussen hospitaal geasosieerde islolate en die teenwoordigheid van ESBL’s was statisties relevant. Isolate was geneties divers en het minimale groepering in identiteit vertoon, dit stel voor dat die verspreing horisontaal plaas kon gevind het. Verdere navorsing in epidemiologie en weerstandigheids patrone van verspreidende stamme is noodsaaklik om antimikrobiese verhoudings, infeksie beheer en empiriese terapie te kan bevorder.

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