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Masters Degrees (Medical Microbiology)

Permanent URI for this collectionhttps://hdl.handle.net/10413/9620

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Browsing Masters Degrees (Medical Microbiology) by Subject "Antibiotics."

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    Defining the role of high-dose isoniazid in the treatment of multi-drug resistance tuberculosis: isoniazid resistant profiling.
    (2021) Ngema, Senamile Lale.; Dookie, Navisha.; Naidoo, Kogieleum.
    Background: High-dose isoniazid is recommended in short-course regimens for multidrug-resistant tuberculosis (MDR-TB). However, there is no substantial evidence supporting its use in the presence of INH resistant mutations. Therefore, this study aimed to establish the efficacy of INH in the presence INH resistance associated mutations. Methods: We selected 94 clinical isolates obtained from 65 patients from the IndEX (CAP020) study specimen biorepository. Isolates were selected based on whole genome sequencing results showing evidence of INH resistant conferring mutations. Twenty-one isolates had inhA promoter gene and/ inhA coding region mutations, 35 had katG mutations, and 20 had both inhA promoter and/ inhA coding region plus katG mutations. Additionally, 18 INH susceptible clinical isolates were included in this analysis. Minimum inhibitory concentrations (MICs) were done in different concentration ranges depending on the mutation present. INH susceptible and H37Rv (0.016-0.256) μg/ml, inhA (0.256-4.0) μg/ml, katG (1.0-16.0) μg/ml and inhA plus katG (4.0-16) μg/ml. Results: Among 94 isolates, 36 were excluded: 11 MPT64 antigen negative, 23 non-growers and two were contaminated. Fifty-eight isolates from 55 patients were left for analysis. Eleven isolates had inhA mutations, 23 katG mutations, 12 had double mutations in inhA and katG, and 12 were INH susceptible. MICs obtained varied within isolates ranging from 0.016 to >64.0 μg/ml. InhA, katG, inhA plus katG mutations and INH susceptible isolates had median INH MIC of 8.0 (4.0-64.0), 4.0 (95% CI, 4.0-8.0), 64.0 (95% CI, 64.0-64.0), and 0.48 (95% CI, 0.32-1.0) μg/ml, respectively, confirming the association between INH MICs and genotypic profile. The MDR-TB and pre/XDR-TB had median INH MIC of 8.0 (95% CI, 8.0-32.0) and 48.0 (4.0-64.0) μg/ml, respectively. We found association between cavitary disease and increase in INH MICs for inhA mutants, median of 64.0 (64.0-64.0) μg/ml, and previous TB history and increased INH MICs (8.0[95% CI, 8.0-64]. Conclusion: This study demonstrated highly variable MIC range with significant overlap in MIC range among the mutant groups. Furthermore, inhA mutants demonstrated unexpectedly high MICs raising a concern for the ongoing use of the high-dose INH in our setting. Our findings suggest that the current one-size-fits all approach to MDR-TB short-course regimen requires urgent review.
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    Molecular characterization of antibiotic-resistant Staphylococcus aureus in an intensive pig production system in KwaZulu-Natal, South Africa.
    (2021) Sineke, Ncomeka.; Amoako, Daniel Gyamfi.; Abia, Akebe Luther King.; Essack, Sabiha Yusuf.; Bester, Linda Antionette.
    The increase in antibiotic resistance in food animals and food of animal origin has been attributed to the extensive use of antibiotics during animal husbandry giving rise to multidrug-resistant bacteria. Staphylococcus aureus is a major threat in veterinary medicine, the agricultural sector and public health because of its zoonotic potential. Despite significant research on S. aureus in food animals in other parts of the world, in-depth studies outside healthcare facilities are limited in South Africa. This study characterized the molecular epidemiology of antibiotic resistant S. aureus from farm-to-fork in an intensive pig production chain in the uMgungundlovu district, Kwa-Zulu Natal, South Africa. A total of 333 samples collected along a pig production chain on the farm (faecal, litter and slurry samples) during transport (truck samples) and at the abattoir (caeca, carcass swabs, carcass rinsate and retail meat samples) were investigated for the presence S. aureus using selective media and biochemical tests. Confirmation was done by using PCR targeting the nucA gene. Antibiotic susceptibility patterns were investigated by the Kirby Bauer disk diffusion according to CLSI guidelines against the WHO-AGISAR recommended panel of antibiotics. Selected resistance and virulence genes were detected using PCR. REPPCR was used to evaluate the molecular relatedness of isolates across the pig production chain. Of the 333 samples, 141 (43%) yielded staphylococci isolates. After molecular confirmation, 97(69%) isolates were confirmed S. aureus and 44(31%) as other staphylococcal species. Isolates displayed resistance to erythromycin (85%), clindamycin (85%), penicillin-G (81%), tetracycline (79%), doxycycline (77%), vancomycin (69%), ampicillin (61%), trimethoprim/sulfamethoxazole (57%), rifampicin (57%), teicoplanin (52%), linezolid (51%), chloramphenicol (51%), nitrofurantoin (47%), moxifloxacin (33%), cefoxitin (20%), ciprofloxacin (15%), tigecycline (10%), levofloxacin (8%), gentamicin (8%), and amikacin (2%). Multidrug resistance (MDR) was recorded in 84% (80/97) of isolates with 56 different antibiograms. Resistance genes ermC, blaZ, tetK, tetM, msrA, aac’6, mecA were evident in 82%, 73%, 58%, 28%, 15%, 5%, and 53% respectively and not all resistance phenotypes were genotypically confirmed. The hla (39%), hld (23%), seb (3%), sed (2%), etb (1%), LukS/F-PV (30%) and tst (11%) virulence genes encoding hemolysin, cytotoxins, staphylococcal enterotoxins (sea and seb), exfoliative toxins, PVL pore-forming toxin and toxic shock syndrome toxin-1 were detected. Genetic fingerprinting revealed the diversity of MRSA isolates in the pig production chain with the major REP-types constituting isolates from different sources within the farm, suggesting transmission within the farm environment with no evidence of transmission across the production chain. This study highlights the phenotypic and genotypic diversity of the virulence and resistance profiles of S. aureus isolated across the pig production chain. Resistance to antibiotics used as growth promoters was evident and the high prevalence of MDR isolates with elevated MAR index values >0.2, specifically at farm level indicates exposure to environments of high antibiotic use, necessitating antibiotic stewardship and proper infection control measures in pig husbandry and intensive pig production.
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    Molecular epidemiology of antibiotic resistant Escherichia coli from intensively-produced poultry in a farm-to-fork continuum in KwaZulu-Natal, South Africa.
    (2020) McIver, Katherine Susan.; Essack, Sabiha Yusuf.; Bester, Linda Antionette.; Abia, Akebe Luther King.
    The increased use of antibiotics in intensively produced food animals has resulted in the selection of drug-resistant bacteria across the farm-to-fork continuum. There is a risk of transfer of this resistance to humans and as such a public health risk. The aim of this study was to investigate the molecular epidemiology of antibiotic resistant Escherichia coli from intensively produced poultry in the uMgungundlovu district of Kwa-Zulu Natal, South Africa. This was a longitudinal descriptive study with the aim to determine the epidemiology of antibiotic resistance of E.coli from hatching through to the final retail product from an intensive poultry farm house. The farm reported the use of zinc bacitracin and Salinomycin included in the feed, but no therapeutic antibiotics used in this batch of chickens. However, the following antibiotics were used on the farm in the previous 12 months: Doxycycline, Sulfadiazine and Trimethoprim, Enrofloxacin, Ceva olaquindox 10%, Avilamycin, Tylosin 10% and Kitasamycin tartate. During the first five weeks, ten samples from litter and faeces were collected. During transfer from the house to abattoir ten swabs from transport trucks and transport crates were taken. At the abattoir ten samples from carcass wash were collected. After slaughter and dressing ten caecums, whole chickens, thighs and necks were collected. Again, during house washing, ten samples were collected. E.coli was putatively identified using Eosin Methylene Blue agar followed by Sorbitol MacConkey agar and confirmed by identification of the uidA gene by polymerase chain reaction. Susceptibility to a panel of antibiotics recommended by the World Health Organization Advisory Group on the Integrated Surveillance of Antimicrobial Resistance (WHO-AGISAR) was ascertained by the Kirby-Bauer disk diffusion method for 20 antibiotics according to CLSI guidelines. Realtime PCR was used to test for resistance genes tetA, tetB, qnrB, qnrS, aac(6)-lb-cr, sul1, sul2, sul3, blaSHV, blaCTX-M, blaTEM conferring resistance to tetracyclines, quinolones, sulphonamides and cephalosporin antibiotics. Clonal similarities were investigated using ERIC-PCR. A total of 266 E.coli isolates constituted the sample size with a non-susceptibility profile of ampicillin 48.1%, tetracycline 27.4%, nalidixic acid 20.3%, trimethoprim-sulphamethoxazole 13.9%, chloramphenicol 11.7%, cefalexin 4.5%, ciprofloxacin 4.1%, amoxycillin-clavulanic acid 3.4%, gentamicin 1.9%, cefoxitin 1.1%, cefepime 1.1%, cefotaxime 1.1%, amikacin 1.1%, ceftriaxone 0.8% and azithromycin 0.8%. Isolates were fully susceptible to ceftazidime, imipenem, meropenem and tigecycline. Of the 266 isolates 6.4% were multidrug resistant (resistant to one or more antibiotics in three or more distinct antibiotic classes). The most frequently observed resistance genes were blaCTX-M (100%), sul1(80%), tetA(77%), tetB(71%). Using ERIC-PCR the isolates were grouped into 27 clusters with a 75% similarity. Eight clusters comprised of isolates from only one sample. xiv There was an increase in MDR and resistance genes over the farm to fork continuum with lowest and highest levels seen in transport and waste-water samples respectively. ERIC-PCR did not indicate the transmission of clones across the farm-to-fork continuum. There instead appeared to be de novo or evolution of resistance genes or the introduction of plasmids over the time period. As the only antimicrobials used in this flock were salinomycin and zinc bacitracin it is postulated that the resistance observed could be attributed to the co-selection of resistance genes and/or horizontal gene transfer from the environment, insects, chicken food and workers. Overall resistance levels were low over the six weeks of the study, MDR and the prevalence of resistance genes increased over time. The diverse clonality shown by the ERIC PCR results did not support the transmission of clones across the farm-tofork continuum but indicated a de novo evolution of resistance genes and/or the loss or gain of plasmids over the time period.