Sabiha Yusuf Essack

Complexity and Diversity of Klebsiella pneumoniae Strains with Extended-Spectrum β-Lactamases Isolated in 1994 and 1996 at a Teaching Hospital in Durban, South Africa

ABSTRACT β-Lactamase production was investigated in cultures of 25Klebsiella pneumoniae isolates isolated at a hospital in Durban, South Africa, in 1994 and 1996. Twenty of these isolates gave ceftazidime MIC/ceftazidime plus clavulanate MIC ratios of ≥8, implying production of extended-spectrum β-lactamases (ESBLs), and DNA sequencing identified an ESBL gene (blaTEM-53) in a further two isolates. Pulsed-field gel electrophoresis (PFGE) defined 4 distinct strains among the 12 isolates collected in 1994 and 9 distinct strains among the 13 isolates collected in 1996. In three cases, multiple isolates from single patients varied in their PFGE profiles and antibiograms, implying mixed colonization or infection. Isoelectric focusing and DNA hybridization found both TEM and SHV enzymes and their genes in all 25 isolates. Many isolates had multiple identical or different β-lactamase gene variants, with at least 84blaSHV and blaTEM gene copies among the 25 organisms. Sequencing identified the genes for the SHV-1, -2, and -5 enzymes and for four new SHV types (SHV-19, -20, -21, and -22). These new SHV variants had novel mutations remote from sites known to affect catalytic activity. Sequencing also found the genes for TEM-1, TEM-53, and one novel type, TEM-63. All the isolates had multiple and diverse plasmids. These complex and diverse patterns of ESBL production and strain epidemiology are far removed from the concept of an ESBL outbreak and suggest a situation in which ESBL production has become endemic and in which evolution is generating a wide range of enzyme combinations. This complexity and diversity complicates patient management and the design of antibiotic use policies.

Antibiotic Resistance in the Food Chain: A Developing Country-Perspective.

Antibiotics are now “endangered species” facing extinction due to the worldwide emergence of antibiotic resistance (ABR). Food animals are considered as key reservoirs of antibiotic-resistant bacteria with the use of antibiotics in the food production industry having contributed to the actual global challenge of ABR. There are no geographic boundaries to impede the worldwide spread of ABR. If preventive and containment measures are not applied locally, nationally and regionally, the limited interventions in one country, continent and for instance, in the developing world, could compromise the efficacy and endanger ABR containment policies implemented in other parts of the world, the best-managed high-resource countries included. Multifaceted, comprehensive, and integrated measures complying with the One Health approach are imperative to ensure food safety and security, effectively combat infectious diseases, curb the emergence and spread of ABR, and preserve the efficacy of antibiotics for future generations. Countries should follow the World Health Organization, World Organization for Animal Health, and the Food and Agriculture Organization of the United Nations recommendations to implement national action plans encompassing human, (food) animal, and environmental sectors to improve policies, interventions and activities that address the prevention and containment of ABR from farm-to-fork. This review covers (i) the origin of antibiotic resistance, (ii) pathways by which bacteria spread to humans from farm-to-fork, (iii) differences in levels of antibiotic resistance between developed and developing countries, and (iv) prevention and containment measures of antibiotic resistance in the food chain.

Prevalence of antibiotic resistance in Campylobacter isolates from commercial poultry suppliers in KwaZulu-Natal, South Africa.

OBJECTIVES Campylobacter jejuni isolated from broiler and layer chickens from registered abattoirs in KwaZulu-Natal, South Africa, were tested for their susceptibility to eight antibiotics. METHODS Using agar dilution, susceptibility to eight antibiotics was determined for C. jejuni recovered from the caeca. RESULTS A total of 155 isolates were collected of which 77 were identified as C. jejuni (broilers n = 56 and layers n = 21). Resistance was highest to tetracycline (broilers 98.2% and layers 100%) and ceftriaxone (broilers 96.4% and layers 100%). High susceptibility was found to ciprofloxacin (broilers 91% and layers 76%) and gentamicin (broilers 98% and layers 81%). Susceptibilities to each of the antibiotics for the broilers and layers, respectively, were: 50% and 57% for erythromycin, 45% and 24% for clarithromycin, 68% and 43% for ampicillin and 64% and 48% for nalidixic acid. Statistically significant differences were detected for the MIC(50) of gentamicin, ciprofloxacin and tetracycline between broilers and layers (P < 0.001) with the MIC(90) of gentamicin also of significant difference (P = 0.01). Multiresistance was detected in 23% and 43% of the isolates from broiler and layer chickens, respectively. CONCLUSIONS Mass therapy procedures used in animal husbandry have a potential impact on antibiotic resistance development in C. jejuni.

Review of established and innovative detection methods for carbapenemase-producing Gram-negative bacteria

The minimal antibiotic options for carbapenemase‐producing Gram‐negative bacteria necessitate their rapid detection. A literature review of a variety of phenotypic and genotypic methods is presented. Advances in culture methods and screening media are still subject to long incubation hours. Biochemical methods have shorter turnaround times and higher sensitivities and specificities, but cannot differentiate between various types and variants. Spectrophotometric methods are cheap and efficient, but are uncommon in many clinical settings, while the MALDI‐TOF MS is promising for species identification, typing and resistance gene determination. Although next generation sequencing (NGS) technologies provide a better platform to detect, type and characterize carbapenem‐resistant bacteria, the different NGS platforms, the large computer memories and space needed to process and store genomic data and the nonuniformity in data analysis platforms are still a challenge. The sensitivities, specificities and turnaround times recorded in the various studies reviewed favours the use of the biochemical tests (Carba NP or Rapid Carb screen tests) for the detection of putative carbapenemase‐producing isolates. MALDI‐TOF MS and/or molecular methods like microarray, loop‐mediated isothermal amplification and real‐time multiplex PCR assays could be used for further characterization in a reference laboratory. NGS may be used for advanced epidemiological and molecular studies.

Colistin and tigecycline resistance in carbapenemase-producing Gram-negative bacteria: emerging resistance mechanisms and detection methods.

A literature review was undertaken to ascertain the molecular basis for tigecycline and colistin resistance mechanisms and the experimental basis for the detection and delineation of this resistance particularly in carbapenemase‐producing Gram‐negative bacteria. Pubmed, Google Scholar and Science Direct were searched with the keywords colistin, tigecycline, resistance mechanisms and detection methods. Trans‐complementation and comparative MIC studies, mass spectrometry, chromatography, spectrofluorometry, PCR, qRT‐PCR and whole genome sequencing (WGS) were commonly used to determine tigecycline and colistin resistance mechanisms, specifically modifications in the structural and regulatory efflux (acrAB, OqxAB, kpgABC adeABC‐FGH‐IJK, mexAB‐XY‐oprJM and soxS, rarA robA, ramRAB marRABC, adeLRS, mexRZ and nfxb) and lipid A (pmrHFIJFKLM, lpxA, lpxC lpxD and mgrB, pmrAB, phoPQ,) genes respectively. Mutations in the ribosomal 16S rRNA operon rrnBC, also yielded resistance to tigecycline through target site modifications. The mcr‐1 gene conferring resistance to colistin was identified via WGS, trans‐complementation and a murine thigh infection model studies. Common detection methods are mainly antibiotic sensitivity testing with broth microdilution while molecular identification tools are mostly PCR and WGS. Spectrofluorometry, MALDI‐TOF MS, micro‐array and real‐time multiplex PCR hold much promise for the future as new detection tools.

Prescriber and Patient Responsibilities in Treatment of Acute Respiratory Tract Infections — Essential for Conservation of Antibiotics.

Inappropriate antibiotic use in normally self-limiting acute respiratory tract infections (RTIs), such as sore throat and the common cold, is a global problem and an important factor for increasing levels of antibiotic resistance. A new group of international experts—the Global Respiratory Infection Partnership (GRIP)—is committed to addressing this issue, with the interface between primary care practitioners and their patients as their core focus. To combat the overuse of antibiotics in the community, and facilitate a change from prescribing empiric antibiotic treatment towards cautious deferment combined with symptomatic relief, there is a need to introduce and enhance evidence-based dialogue between primary care practitioners and their patients. Communication with patients should focus on the de-medicalisation of self-limiting viral infections, which can be achieved via a coherent globally endorsed framework outlining the rationale for appropriate antibiotic use in acute RTIs in the context of antibiotic stewardship and conservancy. The planned framework is intended to be adaptable at a country level to reflect local behaviours, cultures and healthcare systems, and has the potential to serve as a model for change in other therapeutic areas.

NOTA: a potent metallo-β-lactamase inhibitor

Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Biomedical Resource Unit, Westville Campus, University of KwaZulu-Natal, Durban, South Africa; Department of Virology, National Health Laboratory Service/University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, Durban, South Africa; Science for Life Laboratory, Drug Discovery and Development Platform, and Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden

A framework for the non-antibiotic management of upper respiratory tract infections: towards a global change in antibiotic resistance.

Antibiotic resistance has become a critical health issue on a global scale, with much of the problem resulting from inappropriate use of antibiotics in primary care. To change this practice, the global respiratory infection partnership has formulated a pentagonal (five P) framework for the non‐antibiotic management of upper respiratory tract infections (URTIs) – one of the most common conditions in primary care for which antibiotics are prescribed. The framework presents the rationale for focusing on URTIs to promote antibiotic stewardship in primary care and elaborates on five key areas to focus on to bring about change: policy, prevention, prescribers, pharmacy and patients. The ultimate aim is to adopt a patient‐centred symptomatic management strategy using a flexible framework that can be adapted across countries to create a consistent global approach to change behaviour.

The Molecular Epidemiology and Genetic Environment of Carbapenemases Detected in Africa.

Research articles describing carbapenemases and their genetic environments in Gram-negative bacteria were reviewed to determine the molecular epidemiology of carbapenemases in Africa. The emergence of resistance to the carbapenems, the last resort antibiotic for difficult to treat bacterial infections, affords clinicians few therapeutic options, with a resulting increase in morbidities, mortalities, and healthcare costs. However, the molecular epidemiology of carbapenemases throughout Africa is less described. Research articles and conference proceedings describing the genetic environment and molecular epidemiology of carbapenemases in Africa were retrieved from Google Scholar, Scifinder, Pubmed, Web of Science, and Science Direct databases. Predominant carbapenemase genes so far described in Africa include the blaOXA-48 type, blaIMP, blaVIM, and blaNDM in Acinetobacter baumannii, Klebsiella pneumoniae, Enterobacter cloacae, Citrobacter spp., and Escherichia coli carried on various plasmid types and sizes, transposons, and integrons. Class D and class B carbapenemases, mainly prevalent in A. baumannii, K. pneumoniae, E. cloacae, Citrobacter spp., and E. coli were the commonest carbapenemases. Carbapenemases are mainly reported in North and South Africa as under-resourced laboratories, lack of awareness and funding preclude the detection and reporting of carbapenemase-mediated resistance. Consequently, the true molecular epidemiology of carbapenemases and their genetic environment in Africa is still unknown.

Observational study of the prevalence and antibiotic resistance of Campylobacter spp. from different poultry production systems in KwaZulu-Natal, South Africa.

Campylobacter bacteria are important foodborne pathogens that cause acute diarrheal illness, and infection is often associated with contaminated poultry. In a blind observational study, the prevalence and resistance profiles of thermophilic Campylobacter strains collected from different poultry production systems were tested against the clinically used antibiotics ciprofloxacin, tetracycline, erythromycin, gentamicin, and streptomycin. Campylobacter strains were isolated from chickens in rural production systems, a free-range commercial facility, and industrially raised broiler and egg-laying chickens all situated in KwaZulu-Natal, South Africa. Isolates were collected from the chicken cecae and were identified with conventional methods and tested for antibiotic resistance with the Clinical and Laboratory Standards Institute agar dilution method. The prevalence of Campylobacter spp. isolates in chickens was 68% (56 samples) in rural production, 47% (140 samples) in commercial free-range broilers, 47% (133 samples) in industrial broilers, and 94% (34 samples) in industrial layer hens. Isolates from the rurally raised chickens showed significantly (P < 0.01) less resistance against ciprofloxacin (7.9%), erythromycin (0%), and tetracycline (21.6%) than those from commercially produced chickens. Isolates from the commercially raised chickens (free range and industrial) were highly resistant to tetracycline (98.9 to 100%). The incidence of gentamicin and streptomycin resistance was 1.6 and 11.5%, respectively, in commercial free-range broilers, 1.7 and 16.4%, respectively, in industrially raised broilers, and 12.9 and 40%, respectively, in industrially raised layers. It is possible that variations among the poultry production systems, including antimicrobial usage, result in differences in antibiotic resistance profiles in Campylobacter.