Browsing by Author "Essack, Sabiha Yusuf."

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Access to higher education in the health sciences : a policy implementation analysis.
(2014) Orton, Penelope M.; Brysiewicz, Petra.; Essack, Sabiha Yusuf.
Access to health sciences education in South Africa is a challenging and contested area of higher education seeped in politics and history within a context of transformation. There are a large number of students wanting to study health science courses but there are limited places. The first democratically elected government in South Africa issued White Paper 3: A Programme for the Transformation of Higher Education with a vision of transforming the higher education system to one that was more representative of the country`s demographic profile. However in the absence of any guidelines for the implementation of this White Paper 3, higher education in many instances has not been transformed as the government envisaged. The aim of this study was to identify the factors affecting access to health sciences education at universities in South Africa and to develop guidelines to broaden access for social redress. This study was conducted within a pragmatic paradigm using a mixed methods sequential exploratory design in the complementarity genre. Universities offering traditional health science courses` including medicine were included in the study. The research consisted of 3 Phases – Phase 1 reviewed existing policies and practices through the review of relevant documents; Phase 2 assessed existing practices through one-on-one interviews and Policy Delphi and Phase 3 developed policy implementation guidelines and two policy briefs to broaden access using the information gathered from the literature reviewed and data collected from stakeholders. The Policy Delphi questionnaire was developed following the analysis of qualitative data collected in Phase 2 and the instrument was subjected to 2 cycles of item content validity index (I-CVI). The results indicated that achieving equity of access is multi-factorial and has diverse and complex challenges. Some of these challenges are ingrained in South Africa`s apartheid history, some are rooted in the process of access and some in the mind-set of the actors involved in access. The research identified eight categories, promotion of health science disciplines; challenges to transformation; competitiveness; health sciences sets the “bar”; alternative access; reason for choosing a health sciences profession; innovation in teaching and learning and retention and throughput rates which were related to access to health sciences education in universities. The data indicated that the student demographic has changed substantially in Health Science programmes but more could be done. Faculties of Health Sciences need to implement some strategies to reach out to the eligible students in rural and remote areas. Student success in Health science courses is relatively good as would be expected as the selection and admission criteria, is generally higher. Health Sciences at many of the universities are committed to the imperative of transformation for social redress but there are others who are caught between facilitating transformation and overwhelming demand for their programmes. Guidelines for the Implementation of the Access Policy in Health Sciences Education and the Access for Success in Health Sciences Education in Universities Policy briefs were informed by the results. Universities have implemented a number of initiatives to address the past injustice in higher education access however the issue of enabling access for those who are socio-economically disadvantaged is very much more complex and challenging to address. Transformation of health sciences education in universities is essential to the transformation of the health service to reflect a health service that is accessible, available, affordable and agreeable, something that every South African citizen.
Antibiotic resistance in the food chain : a case study of Campylobacter spp. in poultry.
(2013) Bester, Linda Antionette.; Essack, Sabiha Yusuf.
The sub-therapeutic use of antibiotics for growth promotion in food animal production, has engendered substantial debate on the dissemination of antibiotic resistance via the food chain, specifically, the probability of antibiotic use in food production creating a reservoir of resistant bacteria and/or resistance genes that may spread to humans thereby limiting the therapeutic value of antimicrobial drugs. In the absence of any surveillance programme on food-borne bacteria in South Africa, this study focussed on Campylobacter spp. in poultry and encompassed a literature review on the prevailing debate on the dissemination of antibiotic resistance via the food chain, a phenotypic observational study on the prevalence and antibiotic resistance profiles of Campylobacter spp. isolated within and across different poultry farming systems and a genotypic component that covered identification methods, plasmid profile determination and strain typing. Identification methods for Campylobacter spp., viz, biochemical tests and matrix assisted laser desorption ionization- time of flight (MALDI-TOF) mass spectrometry was compared to the PCR which is considered the gold standard as a molecular method of identification. The MALDI-TOF was shown to be superior to the biochemical tests for the identification of C. coli but equivalent to the biochemical tests for C. jejuni. Of the 363 samples collected in total, the frequency of thermophilic Campylobacter was 68 % in rural farms (or informally reared poultry), 47 % in both commercial free-range and industrial broilers and the highest in industrial layers at 94 %. Antibiotic resistance analysis showed that isolates from the rural farming systems were significantly (P < 0.01) more susceptible to ciprofloxacin, tetracycline and erythromycin when compared to the other farming systems. Significant (P < 0.001) antibiotic resistance differences were detected between broilers (5 - 8 week lifespan), and layers (36 - 52 week lifespan) for gentamicin, ciprofioxacin and tetracycline. Plasmids were fonnd be harboured by isolates in all the farming systems; in 84 % of isolates from free-range broilers, 77 % of isolates from industrial broilers, 83 % of isolates from industrial layer hens and 75 % of isolates from the rural farming system. The PFGE genotyping of 42 Campylobacter isolates generated 39 SmaI types. Substantial and substantive genetic diversity was observed between and within farming systems. The lack of correlations amongst the parameters within and between farming systems attested to the diversity and complexity of phenotypes and genotypes and indicated de novo evolution in response to antibiotic selection pressure and animal husbandry practices.
Antimicrobial and chemical analyses of selected bulbine species.
(2000) Mocktar, Chunderika.; Essack, Sabiha Yusuf.; Rogers, B. C.; Dangor, Cassim Mahomed.
The use of plant materials for the treatment of various diseases is very common in African countries. As traditional medicine used by the rural people does not always have a proper scientific basis, research programmes have to be undertaken to evaluate their therapeutic efficacy and safety. In traditional African medicine various Bulbine species are used to treat a number of conditions including sexually transmitted diseases, wound infections, dysentery and urinary tract infections. The Bulbine species belong to the family Asphodelaceae. There are over fifty South African Bulbine species and they are mostly herbs. Their leaves are evergreen and succulent in appearance. Bulbine species have thick fleshy tuberous roots, are easy to grow, are able to withstand drought and heat and are able to grow in poor soil. There is very little documented information on the antimicrobial activity and chemical properties of the Bulbine species. Therefore research programmes of this nature have to be undertaken. Various Bulbine species, viz., B. natalensis Bak, B. frutescens Willd (yellow flowers), B. narcissifalia Salm Dyck, B. abyssinica A Rich and B. frutescens Willd (orange flowers) were collected. The plants were washed with tap water, air dried and separated into the different components. Each component was cut into small pieces and immersed in methanol: dichloromethane (1:1, v/v) for extraction. The organic solvent was decanted from the plant material and evaporated under reduced pressure. The resultant crude extracts were stored in glass vials in the freezer. In addition, the roots, stems and leaves of B. natalensis and B. frutescens (yellow flowers) were extracted aqueously. The crude organic and aqueous were subjected to various tests to evaluate their antimicrobial and cytotoxic potential. To evaluate their antibacterial activities, the Disk Diffusion and Bore Well Methods were employed. The crude extracts were tested against various pathogens implicated in wound and urinary tract infections and dysentery. In these experiments the Disk Diffusion Method produced better results than the Bore Well Method. The crude organic and aqueous extracts were found to be effective against many of the bacteria used in this study including K. pneumoniae, S. aureus, S. typhi and S. flexneri which are considered to be troublesome pathogens. The TLC bioassay was employed to evaluate the antifungal potential of the various crude extracts against Aspergillus and Penicillium and the Disk Diffusion and Bore Well methods were used to evaluate the antifungal potential of C. albicans. The Bulbine species displayed no antifungal activity against Penicillium and limited antifungal activity against Aspergillus. The two method used to evaluate the antifungal activity of. C albicans was chosen because C. albicans grows in a similar manner to bacteria on solid and liquid culture media. Only the root extracts of the two B. frutescens varieties were inhibitory to C. albicans. The Brine Shrimp Bioassay was used to ascertain the cytotoxic potential of the crude extracts. The majority of the extracts were cytotoxic at the most concentrated dilution (i.e., dilution 1) but not cytotoxic at the lower dilutions. The only extracts that were not cytotoxic at the most concentrated dilution were the organic extract of the root of B. frutescens (yellow flowers), the organic extract of the root of B. narcissifolia and the organic extract of the leaf of B. abyssinica. TLC and column chromatography was carried out to evaluate the chemical composition of the Bulbine species. The TLC indicate that this technique could be a valuable tool in identifying the different species in the genus Bulbine. Column chromatogram was carried out on the extract which displayed a significant amount of antibacterial activity against the bacteria used in this study. The stem extract of B. natalensis was chosen for further analysis. The stem extract was fractitioned into different fractions but unfortunately none of the chemical component could be identified. According to the results obtained in this study, there is considerable scope for further studies of this genus.
Antimicrobial resistance and antibiotic stewardship: knowledge, attitudes and perceptions amongst final-year undergraduate health professional students in a South African university.
(2016) Singh, Shanay.; Essack, Sabiha Yusuf.
Antimicrobial resistance (AMR) is a major threat to human health. The World Health Organization (WHO) and subsequently the South African Department of Health have developed detailed plans to combat AMR including recommendations to implement Antibiotic Stewardship (ABS) in the curricula of healthcare students. A number of studies have measured the knowledge, attitudes and perceptions (KAP) of healthcare students globally. However, in South Africa, no multidisciplinary studies have been performed. This study thus ascertained KAP on AMR and antibiotic stewardship amongst final year medical, nursing and pharmacy students at a South African university by means of a cross-sectional questionnaire based survey. A total of 132 questionnaires were completed (response rate 33%), with individual response rates of 63% (n=63), 86% (n=46) and 9% (n=23) for pharmacy, nursing and medical students respectively. The mean correct knowledge score was 88.9%, with significantly lower scores seen for nursing students when compared to other two groups. The perceived seriousness of AMR at international, national and local levels was also significantly lower amongst nursing students. Only a third of all students and 45% of nursing students agreed that use of antibiotics contributes to AMR. Large percentages of nursing and medical students prefer to take antibiotics for viral illnesses whilst, 76% of all students consult a doctor before starting an antibiotic. Several knowledge gaps were identified, as well as key differences between the student groups. Curriculum review to educate students about their role in contributing to AMR and antimicrobial stewardship is imperative as sub-optimal KAP are likely to lead to negative patient outcomes.
Beta-lactamase mediated resistance in Escherichia Coli isolated from state hospitals in KwaZulu-Natal.
(2008) Mocktar, Chunderika.; Essack, Sabiha Yusuf.; Sturm, Adriaan Willem.
Escherichia coli, one of the most common pathogens causing urinary tract infections, has shown increased resistance to commonly used antibiotics. In this study we analyzed the β-lactamase profiles of 38 inhibitor-resistant E. coli isolates obtained from public hospitals at three different levels of healthcare in KwaZulu-Natal, selected on the basis of their resistance profiles to the three antibiotic/inhibitor combinations, viz., amoxicillin/clavulanate, ampicillin/ sulbactam and piperacillin/ tazobactam. The isolates were subjected to MIC determinations, IEF analysis, plasmid profile analysis, PCR of the different β-lactamase genes and sequencing thereof to detect the possible mechanism/s of resistance. A range of β-lactamases including two novel inhibitor-resistant TEM β-lactamases, TEM-145 and TEM-146 were detected in two isolates whilst a novel plasmid-mediated AmpC-type β-lactamase, CMY-20 was detected in three isolates. Other β-lactamases included OXA-1, TEM-55, SHV-2, CTX-M-l and TEM-1. Changes were detected in the chromosomal AmpC promoter/attenuator regions in one isolate. Diverse β-lactamase genes and plasmid profiles inferred extensive mobilization of β-lactamase genes causing the concern of limited therapeutic options in the face of increasing resistance.
Beta-lactamase mediated resistance in Salmonella spp. at a tertiary hospital in KwaZulu-Natal.
(2008) Govinden, Usha.; Essack, Sabiha Yusuf.; Sturm, Adriaan Willem.; Moodley, Prashini.
Extended spectrum (3-lactamases (ESBLs) were characterized in Salmonella spp. isolates from a pediatric ward of a hospital in Durban. Forty one Salmonella spp. were subjected to serotyping, antibiotic susceptibility testing, E-Tests for ESBL detection, iso-electric focusing, polymerase chain reaction for detection of genes and sequencing. Isolates were screened for the presence of WaTEM, WaSHV, WaCTX-M, WaOXA , WaCMY, WaDHA and WaACC genes. The most common serotype was Salmonella Typhimurium. Isolates were multi-drug resistant with 100% susceptibility only to meropenem and ciprofloxacin. Tazobactam was the most effective inhibitor. Forty-one percent of the isolates were resistant to ceftriaxone, thus limiting therapeutic options for Salmonella infections.TEM-1 was the most predominant (3-lactamase found in 51% of isolates while SHV-12 found in 39 % was the most common ESBL. TEM-63 was evident in 29 %, TEM-116 in 10 % and TEM-131 was found in one isolate. The high ceftazidime MICs of isolates expressing only TEM-63 were indicative of R164S substitution which widens the binding cavity to accommodate the bulky side chains of oxyiminoaminothiazolyl cephalosporins. The identification of TEM-131 which differs from TEM-63 by 1 amino acid reiterates the evolutionary potential of the TEM-type plactamase. Other ESBLs identified included SHV-2, CTX-M-3, CTX-M-15 and CTX-M-37. CMY-2 and the OXA-1 p-lactamase were also detected. This is the first report of TEM-116, CTX-M-3, -15 and -37 in Salmonella spp. in South Africa. All isolates with nalidixic acid MICs > 48 ug/ml had the mutation D87N, or D87G in the QRDR of the gyrA gene. This study showed that Salmonella spp. may be multi-drug resistant with the propensity to harbour p-lactamases in unique combinations. The diversity of ESBLs and the co-expression of quinolone resistance suggests that their incidence in salmonellae needs to be monitored.
The demographic and microbiological profile of cystic fibrosis in public and private sectors in KwaZulu-Natal.
Mhlongo, Nonhlanhla.; Essack, Sabiha Yusuf.; Govinden, Usha.
Abstract available in hard copy.
Dynamics of drug resistance in environmental bacteria within an aquatic ecosystem.
(2023) Chukwu, Kelechi Benedict.; Akebe, Luther King Abia.; Essack, Sabiha Yusuf.
Recently there has been a rapid increase in the incidence and prevalence of drug-resistant bacteria and antimicrobial resistance genes in the environment, largely attributed to selection pressure from the environmental presence of antimicrobials such as antibiotics, biocides, and heavy metals, as well as other physicochemical stressors. such as Poly aromatic hydrocarbons, pH, temperature, and reactive oxygen. However, the concentrations at which these antimicrobials could elicit resistance are poorly understood. Such lack of information could hamper the development of standards for the environmental surveillance of antmicrobials with potential adverse effects on human, animal and environmental health. In this study, Water samples were collected from all the points that impact the environment directly around the Darvill wastewater treatment plant, namely the treatment plant effluent discharge point, the upstream and downstream from the effluent discharge point. Antibiotics, heavy metals, and biocides were identified and quantified from the water samples, and we ascertained the effect of environmental concentrations of some of these selected stressors on the antibiotic resistance in previously susceptible Escherichia coli. Heavy metals concentrations were determined using the United States Environmental Protection Agency (US EPA) method 200.7. Biocide and antibiotic residue concentrations were determined using validated ultra-high-performance liquid chromatography with tandem mass spectrometry-based methods. E. coli was identified and quantified using the Colilert-18TM system from IDEXX, while antimicrobial susceptibility was performed using the disc diffusion method according to the Clinical and Laboratory Standards Institute guidelines. The concentration of antibiotics observed ranged from sulfamethoxazole (286.180 μg/L) to penicillin (2.2 μg/L); for metals, sodium (27.734 mg/L) to iron (0.001 mg/L); and for biocides, benzalkonium chloride (BAC) 12 (7.805 μg/L) to BenthEZ (0.035 μg/L). There was observed increase in the pollutant concentrations in the effluent and downstream samples compared to the upstream samples, suggesting that the WWTP might be a potential source of interest, indicating that these pollutants, were not completely removed at the WWTP. Thirty days' exposure of wholly susceptible E. coli ATCC 25922 strains, to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC 12 and DADMAC 10 was conducted but could not trigger phenotypic resistance. Genotypic analysis of the WGS on the exposed isolates, found only the macrolide resistance mdf (A) gene (which was also present in the control) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes compared to the control. Only one resistance gene was detected, robA, a member of the ArcC/XylS family, that regulates the ArcAB-TolC multi-drug efflux, that contributes to multi-drug resistance. The other 18 genes we detected were tolerance conferring genes, acnB, cusA, degQ, epmA, hsmP, mlc, purH, queG, srlE, tsaB, yddh and yqhH genes, in all the exposed isolates. filA genes in only the oxytetracycline and BAC 12-exposed isolates, mutM gene in zinc exposed isolates, nudK gene in all the exposed isolates except the DADMAC 10 exposed isolates, ptsG gene in only the oxytetracycline-exposed isolates, and ompD in only DADMAC 12-exposed isolates. All the genes detected in the exposed isolates were also detected in the environmental isolates, except the robA gene. These genes detected encode for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations. In addition, we observed that the 30-days exposed isolates developed increased tolerance to high (25 x MIC) concentrations of ampicillin by 30 to 50% when compared to unexposed control. BAC 12-exposed isolates had the highest tolerance increase. The increased tolerance seems to emanate from multi gene induced persister cells formations, as well as tolerance gene expressions. The MSW of the exposed isolates to ampicillin and amoxicillin, also slightly increased compared to the control indicating the amplification of persister cells during the 30-day exposure but the MSW remained same to oxytetracycline. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues, as observed in the aquatic environment, cannot induce phenotypic resistance but can encode for genes responsible for the development of persistence and tolerance in bacteria, which seems to be the pathway towards eventual antimicrobial resistance in environmental bacteria.
Effect of rifampicin and efavirenz on moxifloxacin concentrations when co-administered in patients with drug-susceptible TB.
(Oxford University Press., 2017) Naidoo, Anushka.; Chirehwa, Maxwell.; McIlleron, Helen.; Naidoo, Kogieleum.; Essack, Sabiha Yusuf.; Yende-Zuma, Fortunate Nonhlanhla.; Kimba-Phongi, Eddy.; Adamson, John.; Govender, Katya.; Padayatchi, Nesri.; Denti, Paolo.
Abstract available in pdf.
Enterococcus sp. contamination surveillance in different levels of healthcare in eThekwini District, KwaZulu-Natal (KZN) South Africa.
(2021) Shobo, Christiana Omowunmi.; Bester, Linda Antionette.; Essack, Sabiha Yusuf.
Hospital-acquired infections (HAIs) have been identified as long-standing setbacks affecting hospitals' quality of health care. While one of the major challenges related to HAIs is controlling cross-transmission, the role and significance of the inanimate hospital environment chain of transmission are yet to be unequivocally elucidated. Therefore, this study investigated the functional profile and diverseness of bacteria from various inanimate environmental sources, from two different wards in public hospitals at various healthcare levels in eThekwini District, KwaZulu-Natal, South Africa. True to the study focus on investigating the dissemination of bacteria from equipment within the hospital, the study further used Enterococcus as well-known HAI as target bacteria and described the molecular and genomic profiles of this specie isolated from the hospital environments. Samples were collected for a period of three months (September – November 2017) from the four levels of healthcare in eThekwini district, KwaZulu-Natal. The intensive care unit and peadiatic ward were employed in this study. An overall of 620 swabs were collected from areas frequently touched by healthcare workers (HCWs) and patients. These sites include the occupied bed linen, unoccupied bed linen, drip stands, patient files, ward phones, ventilators, nurses' tables, blood pressure apparatus, sinks, linen room door handle and mops. Swabs were placed in Amies transport medium and transported in a cooler box to the laboratory facility to be processed within four hours. The collected swabs (n=620) were pooled and incubated in tryptone soya broth containing 6.5% NaCl at 36.5oC for 24 hrs and subsequently plated on enterococci chromogenic media. The microbial diversity and functional profiles from the sites were identified using 16S rRNA metagenomics. Positive colonies were sub-cultured on bile esculin azide agar, and screened using standard microbiological methods, including haemolytic, oxidase and catalase, and API. Identifications were confirmed with polymerase chain reaction (PCR) with the added genus-specific tuf-gene and species-specific sodA-gene. Antibiotic resistance patterns in the Enterococcus spp. isolates were determined by the Kirby-Bauer disk diffusion method against 14 antibiotics as recommended by the Clinical and Laboratory Standard Institute (CLSI) guidelines. Thirty-seven samples from E. faecalis showed intermediate Resistance to vancomycin and were further analyzed using molecular tools viz. whole-genome sequencing (WGS) and bioinformatics analyses. This enabled determining the resistome, mobile genetic elements (MGEs), and clonal lineages circulating across the sites, wards, and hospitals. Metagenomics identified a total of 288 species, 190 genera, 105 families, 50 orders, 29 classes and 11 phyla from the samples analyzed. The dominant functional metabolic pathways implicated in causing human infection discovered were the signal transduction mechanisms, citrate cycle (TCA), transcription-factor bisphenol degradation, tyrosine metabolism. A total of 295 Enterococcus spp. isolates were recovered from the hospitals` environmental sites, 83% (n=245) were identified as Enterococcus faecium, 13% (n=38) as Enterococcus faecalis, 2% (n=6) Enterococcus gallinarum and another 2% (n=6) Enterococcus casseliflavus. Notably, the pediatric wards had the highest isolation rate compared to ICU, 64% and 36%, respectively. Overall, the sites with the highest isolation rate were occupied beds and mops (to clean ward floors) with 14.9% (n=44) each. The tertiary hospital were the most affected. The most prominent MDR antibiogram for E. faecium was CIP-RIF-NIT-TET-ERY and for WGS analysis of the E. faecalis samples confirmed that the tet(M) and erm(C) genes were the prevalent antibiotic resistance genes found in hospitals. The isolates harboured mobile genetic elements consisting of plasmids (n =11) and prophages (n=14), predominantly clonally specific. The 37 isolates analyzed consisted of 15 clonal lineages with six major sequence types (ST). Phylogenomic analysis showed that major lineages were mostly conserved within specific hospital environments. This study highlighted the inanimate hospital environment as a possible source of opportunistic nosocomial pathogens using Enterococcus as an illustrative example and emphasized the urgent necessity to optimize infection prevention and control measures to intercept/moderate the spread of bacteria in the hospital environments.
Exploring trends in antibiotic use and resistance in a district, regional and tertiary hospital in the uMgungundlovu District.
(2017) Desai, Ayesha.; Essack, Sabiha Yusuf.; Suleman, Fatima.
Antibiotics play an important role in overcoming life-threatening bacterial infections. However, the increasing rate of antibiotic resistance is a serious threat to public health. Undoubtedly the indiscriminate use of antibiotics plays a role in the emergence of resistance. The objective of this study was to identify the trends in antibiotic use and resistance at three public sector hospitals at three different levels of healthcare in the uMgungundlovu district, i.e., a district hospital, a regional hospital and a tertiary hospital. The antibiotics indicated for the treatment of infections caused by Escherichia coli (Gram-negative bacteria) and Staphylococcus aureus (Gram-positive bacteria) were investigated. Yearly antibiotic consumption data was calculated as Defined Daily Dose (DDD) per 1 000 inhabitants and percentage susceptibility was analysed based on susceptible and non-susceptible isolates for each antibiotic. There was a general trend of reduced antibiotic susceptibility as the levels of healthcare increased attributed to the fact that more severe and complex infections are treated at the higher levels of healthcare and require greater quantities of and/or broader spectrum antibiotics. For treatment of infections caused by S. aureus antibiotic use generally increased as the level of healthcare increased. Azithromycin was the most frequently used while linezolid was the least used antibiotic and showed the highest levels of susceptibility across all levels of healthcare. S. aureus showed the lowest level of susceptibility to cloxacillin across all the levels of healthcare and was indicative of the prevalence of methicillin-resistant S. aureus (MRSA). When antibiotic use was correlated with resistance, cloxacillin displayed a downward trend in use from 2014 to 2016 while cloxacillin resistance increased from 2014 to 2015 followed by a decrease in resistance in 2016 indicating that resistance is a function of time and use and that the lag time between the decrease in use and a corresponding decrease in resistance is not predictable and varies for different antibiotics in different healthcare settings. In contrast, azithromycin showed a steady decline in resistance although use increased over the three years (2014-2016). In the case of the treatment of infections caused by E. coli there was a general trend of the greater use of narrow spectrum antibiotics at the lower district and regional levels while the broad-spectrum antibiotics were used more frequently at a tertiary level. Trimethoprim-sulphamethoxazole was used the most, whereas colistin was used the least. Contrary to expectations, there were higher susceptibility levels to third and fourth generation cephalosporins and meropenem at a tertiary level than regional level. E. coli showed lowest levels of susceptibility to ampicillin and highest level of susceptibility to levofloxacin across all levels of healthcare. When antibiotic use was correlated with resistance, antibiotics that were used frequently however resistance remained high. The same trend was observed with amoxicillin clavulanic acid and ampicillin use and resistance indicating possible co-selection of resistance by the use of other classes of antibiotics. This study added to the body of knowledge that there exists a link between the use of antibiotics and resistance, albeit not a direct causal one. Quantifying antibiotic use and identifying trends in resistance associated with antibiotic consumption assists prescribers and policy makers to improve antibiotic use, guide antibiotic stewardship programmes and optimise antibiotic policies and guidelines.(sulphamethoxazole-trimethoprim, amoxicillin clavulanic acid and ampicillin) displayed high levels of resistance over the three years. Trimethoprim-sulphamethoxazole use decreased slightly over the years however resistance remained high. The same trend was observed with amoxicillin clavulanic acid and ampicillin use and resistance indicating possible co-selection of resistance by the use of other classes of antibiotics. This study added to the body of knowledge that there exists a link between the use of antibiotics and resistance, albeit not a direct causal one. Quantifying antibiotic use and identifying trends in resistance associated with antibiotic consumption assists prescribers and policy makers to improve antibiotic use, guide antibiotic stewardship programmes and optimise antibiotic policies and guidelines.
Extended spectrum B-lactamase and plasmid mediated AmpC resistance in clinical isolates of escherichia coli from the central hospital of Maputo, Mozambique.
(2016) Estaleva, Calvina Ernesto Langa.; Sundsfjord, Arnfinn Staale.; Essack, Sabiha Yusuf.; Zimba, Tomas Francisco.
Antibiotic resistance is one of the main public health problems worldwide, reducing treatment options and increasing morbidity and mortality. The production of extendedspectrum β-lactamases (ESBLs), plasmid mediated (pAmpC) β-lactamases are the most important resistance mechanisms that hamper antimicrobial treatment of infections caused by Enterobacteriaceae. This study describes the detection and characterization of pAmpC- and/or ESBL-producing clinical isolates of Escherichia coli (n=230) from urine and blood samples at the Central Hospital of Maputo, Mozambique from midAugust to mid-November 2015. Antimicrobial susceptibility testing was performed by the disc diffusion method. Isolates with reduced susceptibility to cefotaxime and/ or ceftazidime (n=75) were subjected to phenotypic AmpC- and/or ESBL testing as well as PCR-detection of blaCTX-M, blaTEM, blaSHV, blaCMY, blaMOX, blaFOX and blaDHA. A total of 75/230 (32.6 %) isolates were ESBL positive, and twenty-five of these were pAmpC positive. The most prevalent ESBL and pAmpC were CTX-M (77%) and FOX (32%), respectively. Most CTX-M negative ESBL-strains were blaSHV positive indicating a SHV-ESBL-type. The presence of co-resistance (R and I) to clinically important antibiotics were also frequent; blood ciprofloxacin (CIP; n= 12/17: 70.6%), gentamicin (GEN; n= 8/17: 47.1 %) and trimethoprim-sulfamethoxazole (SXT; n= 17/17; 100%) and urine CIP (n=40/58; 68.9%), GEN (n= 27/58; 46.5 %) and SXT (n= 55/58; 94.8%). Multidrug resistance was observed in 17/17 (100 %) and 58/58 (100 %) blood and urinary isolates, respectively. ERIC-PCR analysis revealed a large genetic diversity of strains with some minor clusters indicating intra hospital spread. The study has shown that: (i) a large proportion of clinical isolates of E. coli from the urinary tract and blood cultures from the Central Hospital are pAmpC and/or ESBLproducing. (ii) CTX-Ms and FOX were the dominant ESBL- and pAmpC-types, respectively. (iii) All ESBL- and pAmpC-producing strains were MDR-strains only susceptible to antibiotics that are not easily available in the current location. The overall findings strongly support the urgent need for strengthened and rapid diagnostic services to guide correct treatment of serious life-threatening infections and improved infection control measurements.
Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella spp. in Mozambican students.
(2017) Chirindze, Lourenço Marcos Junior.; Essack, Sabiha Yusuf.; Simonsen, Gunnar Skov.; Zimba, Tomas Francisco.
In recent years, the world has seen a surge in extended-spectrum β-lactamase (ESBL)-producing bacteria. Among antibiotic resistance mechanisms, the production of β-lactamase is the most rapidly developing and clinically significant in Gram-negative bacteria. In the present study, a total of 275 stool samples were collected from students of both sexes in three student residencies of Eduardo Mondlane UniversityMozambique from January to February 2016. All samples were cultured on MacConkey agar with ceftriaxone (1mg/L) and without ceftriaxone. The isolates were biochemically identified with API20E test. Confirmed E. coli and Klebsiella spp. isolates were subjected to antimicrobial susceptibility testing by the disc diffusion method and ESBL strains were confirmed with the disc approximation method. From these samples, 56 ESBL positive E. coli(n=35) and Klebsiella spp. (n=21) strains were isolated. Among the ESBL-positive isolates, 39.3% (22/56) were cefoxitin resistant and none were confirmed as carbapenemase producers. The frequency of ESBL colonization in both sex were similar for E. coli and Klebsiella spp. Among the ESBL-positive isolates, 50% (28/56) of the isolates only contained class A ESBLs, 5.4% (3/56) only class C ESBLs, and 44.6% (25/56) both class A and C ESBLs. Among the E. coli strains, 100% were resistance to ampicillin, and both E. coli and Klebsiella spp. demonstrated69.6% resistance to tetracycline and cotrimoxazole, 62.5% to ceftazidime, 33.9% to ciprofloxacin, and 34.8% to cefoxitin. None of the isolates showed resistance to meropenem. In total, 78.6 % of ESBL strains were defined as multi-resistant. The ERIC-PCR demonstrated low similarity among the strains. This study demonstrated that the carriage rates and the diversity of ESBL genes among the students are high.
Isolation and characterisation of extended spectrum B-lactamases in South African Klebsiella pneumonia isolates.
(2012) Naidoo, Yashini.; Essack, Sabiha Yusuf.
The use of antibiotics and antimicrobial drugs has played a large role in the elimination of many infectious diseases, however the wide spread use of such drugs has given rise to the phenomenon of antimicrobial resistance and has rendered antibiotics ineffective to a broad range of bacteria. The aim of the study was to ascertain the differences if any in the phenotypic and genotypic resistance profiles of K. pneumoniae isolated from a single tertiary hospital in two surveillance studies undertaken at different times, viz., 2001 and 2007 with special emphasis on ESBLs. A correlation with antibiotic use was also undertaken. ESBL positives were identified and phenotypic resistance profiles were generated based on the resistance profiles of individual isolates by means of their MIC data. The molecular detection of ESBLs was carried out using representative isolates and sequencing was based on the phenotypic expression of the most common ESBL genes. The data was summarized using median values and interquartile ranges. Antibiotic use and susceptibility in 2000 was compared to that in 2007 using a Wilcoxon signed rank test for paired data since the same drugs were tested in both years. Of the isolates that were tested, sequencing revealed that TEM – 1 was identified in all isolates and SHV-1 and SHV-2 were identified in 60 % in the isolates collected in 2000 and 77 % and 11 % respectively in the isolates collected in 2007. SHV – 11 was present in 67% of isolates from 2007 and 55% of those were in combination with SHV – 1. Sequencing also revealed CTXM-15 present in one of the isolates collected in 2007. There was 100% susceptibility to cefoxitin and only one isolate in 2007 showing an intermediate result to imipenem. No novel β-lactamases were identified in this study; however the decrease in susceptibility over time is proof of bacterial evolution. The variety of β-lactamases and diversity of plasmid profiles in these two small populations provides proof to the claim that dissemination of resistance in Klebsiella pneumonia is effortless. Statistical analysis showed an increase in resistance from the year 2000 to 2007 however the correlation between overall antibiotic use and the increase in resistance did not reach statistical significance. It was observed that resistance increased despite only a slight increase in the use of a few antibiotics to which we attributed co-carriage of resistance genes.
Knowledge, attitudes and practices of veterinarians on antibiotic use, resistance and its containment in South Africa.
(2021) Maruve, Simbai Allen.; Essack, Sabiha Yusuf.; Nlooto, Manimbulu.
The inappropriate use of antibiotics in the veterinary sector has led to antibiotic resistance (ABR), which negatively impacts animal health and welfare and indirectly on human health. Understanding the knowledge, attitudes, and practices on antibiotic use, ABR, and its containment amongst veterinarians is critical to optimize antibiotic use and contain resistance. A quantitative questionnaire based online survey was conducted amongst members of professional veterinary associations. The questionnaire consisted of four sections focusing on socio-demographic characteristics, knowledge, attitudes, and practices (KAP) of participants on antibiotic use, ABR, and its containment in the South African veterinary sector. The Independent t-test, analysis of variance (ANOVA), and Chi-square test were used to establish associations among selected socio-demographic variables and selected KAP parameters. A total of 130 responses were received from 2178 animal health professionals, yielding a response rate of 6 %, with 102 complete responses constituting the final sample size. Self-reported knowledge on antibiotic stewardship, antibiotic resistance mechanisms, and pharmacology was good at 96 (94.1%), 91 (89.2%), and 70 (68.6%), respectively. More than half the respondents (60 [58.8%]) were confident that the veterinary training they received prepared them quite a bit/very much on rational antibiotic use. Most respondents (81 [79.4%]) believed that antibiotics were sometimes prescribed for suspected but not confirmed infections. The majority of the respondents (77 [75.5%]) were quite concerned/very concerned about antibiotic resistant infections, compared to 19 (18.7%) of clients expressing the same concern. Veterinary guidelines for appropriate use of antibiotics were sometimes read by respondents (45 [44.1%]). A little more than half of the veterinarians (54 [52.9%]) often/always discussed antibiotic resistance with their clients. Most respondents identified broadspectrum antibiotics such as amoxicillin-clavulanate and metronidazole as first-line treatment at 62 (60.8%) and 64 (62.7%) respectively. Notably, most of the veterinarians (61 [59.8%]) also lacked an antibiotic stewardship programme at their practice. The cost of diagnostics (90 [88.2%]), time to results of diagnostics (83 [81.4%]), and client expectations of receiving antibiotics (74 [72.5%]) were cited amongst barriers to the implementation of an antibiotic stewardship programme. Place of practice was significantly associated (p=0.004) with possession of knowledge about antibiotic resistance. Veterinarians in urban practice were more knowledgeable about antibiotic resistance than those in rural practice. Place of practice was also significantly associated (p=0.035) with discussions on antibiotic resistance with clients. More veterinarians in rural practice frequently carried out such discussions than their urban counterparts. There is a need for education and training to address gaps in KAP. There is also a need for the development and implementation of antibiotic stewardship programmes in veterinary practice. Cost effective diagnostic tests with shorter turnaround time might assist in achieving such. The programmes might encourage microbiology informed therapy and the use of guidelines for appropriate antibiotic use.
Molecular and genomic analysis of clinical multidrug-resistant coagulase-negative staphylococci from the uMgungundlovu District in the KwaZulu-Natal Province, South Africa.
(2020) Asante, Jonathan.; Essack, Sabiha Yusuf.; Amoako, Daniel Gyamfi.; Abia, Akebe Luther King.
Coagulase-negative staphylococci (CoNS) are among the most commonly recovered bacteria in clinical specimens. They are usually colonisers (commensals) of the skin and nasal passages and considered contaminants of microbial cultures. However, they have been recognised as emerging pathogens, frequently causing opportunistic infections. The frequent use of indwelling medical devices and long-term hospitalisation present an increased risk of exposure to CoNS, resulting in infections usually caused by multidrug-resistant pathogens. Few studies focus on CoNS, including characterisation of their mechanisms of resistance, virulence, and persistence. Therefore, this study describes the molecular and genomic profiles of clinical CoNS from public sector hospitals in the uMgungundlovu District in KwaZulu-Natal, South Africa. Eighty-nine clinical CoNS isolates collected from three hospitals within the uMgungundlovu District between October 2019 and February 2020, constituted the sample. Isolates were speciated using the Vitek 2 system. Antibiotic susceptibility testing was done against a panel of 20 antibiotics according to Clinical and Laboratory Standards Institute (CLSI) guidelines using the Kirby-Bauer disk-diffusion method and minimum inhibitory concentration (MIC) was determined using the broth microdilution method for penicillin G, cefoxitin, ceftaroline, ciprofloxacin, moxifloxacin, azithromycin, erythromycin, gentamicin, amikacin, chloramphenicol, tetracycline, doxycycline, teicoplanin, tigecycline, linezolid, clindamycin, rifampicin, sulphamethoxazole/trimethoprim, nitrofurantoin and vancomycin. PCR was used to detect the presence of the mecA gene to confirm phenotypic methicillin resistance. Based on their resistance profiles, a sub-sample of isolates were subjected to wholegenome sequencing (Illumina MiSeq) to ascertain the resistome, virulome, mobilome, clonality and phylogenomic relationships using bioinformatic tools. The SPAdes software was used for the assembly of the raw reads. ResFinder 4.1 and CARD were used to identify antibiotic resistance genes in the isolates, while the virulence factor database (VFDB), Center for Genomic Epidemiology‘s MLST 2.0 server and MobileElementFinder v1.0.3 were used to identify virulence genes, sequence types and mobile genetic elements, respectively. Mutations in fluoroquinolone and rifampicin resistance genes were identified by manual curation using BLASTn alignment which was also used to determine the genetic environment of the resistance genes.S. epidermidis was the most abundant CoNS species isolated. Phenotypic methicillinresistance was detected in 76.4% (n=68) of isolates, 92.6% (n=63) of which were genotypically confirmed by PCR. Multidrug resistance (MDR) was observed in 76.4% (n=68) of isolates, with 51 antibiograms observed. The resistance genes mecA, blaZ, erm(A), erm(B), erm(C), msr(A), aac(6')-aph(2'') and fosB, among others, were detected and corroborated the observed phenotypes. Molecular mechanisms of resistance to tigecycline, teicoplanin, linezolid and nitrofurantoin were not detected even though some isolates were resistant to them. There was no association between ARG type and hospital/department. The ica operon known to facilitate biofilm formation was detected in 7/16 isolates sequenced. Known and putatively novel mutations in the gyrA, parC, parE and rpoB genes were also detected for fluoroquinolone- and rifampicin-resistant isolates. Prediction of isolates’ pathogenicity towards human hosts yielded a high average probability score (Pscore ≈ 0.936), which, together with the several virulence genes detected (including atl, ebh, clfA, ebp, icaA, icaB,icaC), support their pathogenic potential to humans. Seven MLST types were found, while the community-acquired SCCmec type IV was the most common SCCmec type detected. Mobile genetic elements (MGEs) haboured by isolates included plasmid replicon Rep10 and insertion sequence IS256. Defense systems such as arginine catabolic mobile element (type I and III), CRISPR system (16), and the restriction-modification system (type II) were detected. Genetic analysis showed that resistance genes were frequently bracketed by MGEs such as transposons (such as Tn554) and insertion sequences (such as IS257 and IS1182) that facilitated their mobility. Phylogenetic studies showed that the distribution of genes did not coincide with the phylogenetic clades. Despite the relatedness of isolates (clades A and B), there is still considerable variation within individual strains that can facilitate adaptation to local environments. The isolates exhibited several permutations and combinations of ARGs, virulence genes and MGEs, pointing to a complex milieu of mobilized antibiotic resistance and pathogenic characteristics in clonal and multiclonal strains. The study necessitates surveillance of CoNS as emerging pathogens.
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.
Molecular characterization of multi-drug resistant (MDR) gram-negative bacterial pathogens from environments, patients and staff in a teaching hospital in Ghana.
(2023) Yeboah, Esther Eyram Asare.; Essack, Sabiha Yusuf.; Owusu-Ofori, Alexander.; Agyepong, Nicholas.; Abia, Akebe Luther King.; Amoako, Daniel Gyamfi.; Mbanga, Joshua.
Multidrug resistant Gram-negative bacteria (MDR GNB) are implicated in serious infections both of community and nosocomial origin and may be disseminated in the hospital in the absence of efficient infection prevention and control (IPC) practices. The prevalence and risk factors for rectal colonization of MDR GNB among patients, the carriage of MDR GNB on healthcare workers’ (HCWs’) hands and the contamination patients’ environments with MDR GNB were investigated in a teaching hospital in Ghana. In this prospective study, conducted between April 2021 to July 2021, the phenotypic profiles of the MDR GNB isolates were determined using the VITEK 2 system. Risk factors for colonization with MDR GNB were assessed using univariate and multivariate analysis of associated data. The resistome, virulome, mobilome and genetic relatedness of MDR extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and ESBL-producing or carbapenem resistant Klebsiella pneumoniae isolates from patients and their environment were also determined using whole genome sequencing performed on the Nextseq 550 (2 x 150 bp) and bioinformatics analysis. A total of 585 samples were collected from patients, HCWs’ hands and the hospital environment within the study period. The prevalence of MDR GNB rectal colonization among patients was 50.62% on admission and 44.44% after 48 hours. MDR GNB, frequently E. coli and K. pneumoniae were isolated from 6 (5.26%) and 24 (11.54%) of HCW’s hand swabs and environmental swabs, respectively. Previous hospitalization (p-value = 0.021, OR,95% CI= 7.170 (1.345-38.214) was significantly associated with colonization by MDR GNB after 48 hours of admission while age (21-30 years) (p-value =0.022, OR, 95% CI =0.103(0.015-0.716) was significantly identified as a protective factor associated with a reduced risk of rectal MDR GNB colonization. Rectal carriage and acquisition of ESBL-producing E. coli among patients was 13.65% and 11.32% respectively. blaTEM-1B and blaCTX-M-15 were commonly associated with IncFIB plasmid replicons and co-occurred with aminoglycoside, macrolide, and sulfamethoxazole/trimethoprim resistance. Multiple virulence genes, predominantly, terC were detected in the ESBL E. coli isolates. Sequence types (STs) were diverse and included one novel ST (ST13846) present in two isolates. Phylogenetic analysis grouped the ESBL E. coli isolates into four main clusters. High genetic relatedness was observed between two carriage isolates of ST940 and between a carriage isolate and an environmental isolate of ST648. Isolates with different STs, collected at different times and locations, also showed genetic similarities. Of the ten selected MDR K. pneumoniae isolates, the β-lactamase gene, blaCTX-M-15 was observed in six isolates. Mutations were found in both ompK36 and ompK37 in all isolates (both carriage isolates and isolates from hospital environments). Genes encoding resistance to fluoroquinolone (qnrB), aminoglycosides (aadA1, aadA2, aac(3)-IIa, aac(6')-Ib-cr,aph(3'')-Ib , aph(6)-Id) sulphamethoxazole/trimethoprim (sul1, sul2, dfrA14, dfrA15) were also detected. The K. pneumoniae isolates belonged to seventeen different STs with ST39 most commonly observed and common to both carriage isolates and isolates from hospital environments. A myriad of virulence genes, including irp1, irp2, iutA, gndA, ompA, fes, fep, mrkD and fimH were detected in both carriage and isolates from the hospital environment. IncFIB was the most abundant plasmid replicon occurring in nine (four carriage isolates and five isolates from hospital environments). ESBL-producing K. pneumoniae isolates appeared to be introduced into the hospital from the community. The high colonization of MDR GNB in patients, the carriage of MDR GNB on HCW’s hands, the contamination of hospital environments and the circulation of ESBL-producing E. coli and K. pneumoniae isolates with diverse genomic characteristics, highlights the need for patient screening, and stringent infection prevention and control practices to prevent the spread of MDR GNB in hospitals. The observed clonal relatedness among isolates from patients and the hospital environment, as well as between different patients, suggests a possible transmission within and between sources, hence infection prevention and control practices need to be enhanced to prevent the dissemination and transmission of these resistant strains in the hospital. This study further highlights the usefulness of whole genome sequencing as an effective tool in AMR surveillance.
Molecular epidemiology of antibiotic resistant Campylobacter spp. from farm-to-fork in an intensive pig production system in Kwazulu-Natal, South Africa.
(2021) Sithole, Viwe.; Amoako, Daniel Gyamfi.; Essack, Sabiha Yusuf.; Abia, Akebe Luther King.; Bester, Linda Antionette.
Background: Campylobacter spp. are among the leading foodborne pathogens, causing Campylobacteriosis, a zoonotic infection that results in bacterial gastroenteritis and diarrhea disease in animals and humans. The emergence and transmission of antibiotic resistance and virulence in Campylobacter spp. is increasingly reported. We investigated the molecular epidemiology of antibiotic resistant Campylobacter spp. isolated across the farm-to-fork-continuum in an intensive pig production system in the uMgungundlovu District, Kwazulu-Natal, South Africa. Methodology: Following ethical approval, samples were collected over a period of sixteen weeks from selected critical points (farm, transport, abattoir and retail) using a farm-to-fork sampling approach according to WHO-AGISAR guidelines. Overall, 520 samples were investigated for the presence of Campylobacter spp. which were putatively identified using selective media with identity and speciation confirmed by polymerase chain reaction (PCR) of specific genes. Resistance profiles were ascertained by the Kirby-Bauer disk diffusion method according to EUCAST and/or CLSI guidelines. Selected antibiotic resistance and virulence genes were identified using PCR and DNA sequencing. Clonal relatedness among the isolates was determined using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR). Results: Altogether, 378/520 (72.7%) samples were positive for Campylobacter spp. with C. coli as the most predominant (73.3%), followed by C. jejuni (17.7%) with 9.0% classified as “other”. Relatively high levels of resistance were observed in C. coli and C. jejuni to erythromycin (89% and 99%), streptomycin (87% and 93%), tetracycline (82% and 96%), ampicillin (69% and 85%), and ciprofloxacin (53% and 67%) respectively. The lowest percentage resistance observed was for gentamicin (12%) for both C. coli and C. jejuni, and nalidixic acid (28% and 27%) for C. coli and C. jejuni respectively. Multi-drug resistance (MDR) was noted among 330/378 (87.3%) isolates. The antibiotic resistance genes observed were the tetO (74.6%), the blaOXA-61 (2.9%) and cmeB (11.1%) accounting for the resistance to tetracycline and ampicillin while the membrane efflux pump could confer resistance to ampicillin, tetracycline, ciprofloxacin, and erythromycin. All C. coli and C. jejuni isolates (21) with the gyrA gene exhibited mutation at the Thr-86-Ile region in the quinolone-resistancedetermining region (QRDR) and all C. coli and C. jejuni isolates (18) exhibiting erythromycin resistance showed common transitional mutations A2075G and A2074C in the 23S rRNA gene. Of the virulence genes tested, ciaB, dnaJ, pldA, cdtA, cdtB, cdtC and cadF were detected in 48.6%, 61.1 %, 17.4%, 67.4%, 19.3%, 51% and 5% of all Campylobacter isolates respectively. The ERIC-PCR banding patterns revealed that isolates along the continuum were highly diverse with isolates from the same sampling points belonging to the same major ERIC-types. Conclusion: We showed relatively high levels of resistance to antibiotics commonly used in intensive pig production in South Africa with some evidence, albeit minimal, of transmission across the farm-tofork continuum. This together with the virulence profiles present in Campylobacter spp. presents a challenge to food safety and a potential risk to human health. This is further exacerbated by the reduction in antibiotic treatment options necessitating routine surveillance and monitoring together with antibiotic stewardship, comprehensive biosecurity, and good animal husbandry in intensive pig production.
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.