Molecular methods for the detection of TEM- and SHV-related beta lactamase genes in members of the Enterobacteriaceae

Bacterial resistance to antibiotics is a common and important clinical problem. Beta lactam resistance in Gram negative bacilli is mediated predominantly by beta lactamases, enzymes able to hydrolyse the beta lactam ring. The commonest plasmid mediated beta lactamases in the Enterobacteriaceae are those related to either TEM-1 or SHY-1. Although TEM-1, TEM-2 and SHY-1 do not have activity against extended spectrum beta lactams, their derivatives (TEM-3 and SHY-2 onwards) are able to confer resistance to one or more of these antibiotics. A problem encountered in clinical microbiology laboratories is the lack of a reliable method for the detection of ESBLs, along with the lack of a quick, reliable method of differentiating TEM-related genes from SHY -related genes. The primary aim of this study was to evaluate two molecular techniques for the detection of SHY and TEM-related genes in clinical isolates. The study sample consisted of 209 clinical isolates of enteric Gram negative bacilli, isolated at Groote Schuur Hospital microbiology laboratory. The isolates had all been selected on the basis of resistance to one or more of the extended spectrum beta lactams. These isolates were all identified, and the susceptibility of each to a variety of beta lactam antibiotics determined. Using this information, 45 isolates, belonging to different genera and with differing antimicrobial sensitivity patterns, were selected for this pilot study. These 45 isolates consisted of 24 Klebsiella spp., 14 Enterobacter spp., 3 Citrobacter spp., 2 Salmonella spp., 1 Pantoea agglomerans and 1 Serratia marcescens

Molecular characterization of multidrug-resistant Klebsiella pneumoniaeand Escherichia coliharbouring extended spectrum beta-lactamases andcarbapenemases genes at a tertiary hospital, Kenya

Background: Multidrug-resistant (MDR) Gram negative rods are increasingly being reported in sub-Saharan Africa. Molecular investigations play an important role, alongside other measures, in controlling nosocomial infections attributed to these organisms. This study aimed to determine the common extended spectrum beta-lactamases (ESBL) and carbapenemases genes, and clonal relationship in MDR Klebsiella pneumoniae and Escherichia coli. Methods: Fifty-four MDR isolates collected at the Aga Khan University hospital, Nairobi in the month of August 2012 formed the study. These were picked after an increase in the number of resistant strains during the said period was experienced. Results: blaCTXM was present in 41 (74%) of the isolates, while blaSHV was detected in 18 (33%) and blaTEM in 13 (24%) of the isolates. Nine (16.7%) of the isolates harboured all three ESBL genes and 8 (14.8%) harboured two. Eight of the isolates (all E. coli) had none of the ESBL genes tested. Two isolates harboured carbapenemases genotypes: one had blaNDM-1 and the other blaSPM. Sequencing matched CTXM-15 and TEM-1 genes in all the isolates harbouring blaCTXM and blaTEM respectively. However, there was diversity in blaSHV with SHV-11 and SHV-12 genes predominant. The isolates were non-clonal. Conclusions: The isolates mostly harboured blaCTX-M-15 while only a few had carbapenemases genes. Lack of clonality suggests these were the stable circulating strains at the time of the study

Epidemiology of Staphylococcus aureus bacteraemia at a tertiary children's hospital in Cape Town, South Africa

BACKGROUND: Staphylococcus aureus is an important pathogen in paediatric patients with bloodstream infections. The epidemiology of S. aureus bacteraemia, however, has not been well documented in children in South Africa. METHODS: A retrospective study was conducted at a children's hospital in Cape Town, South Africa, to investigate the epidemiology of S. aureus bacteraemia from 2007-2011. The incidence, clinical presentation, risk factors, management and outcomes of methicillin sensitive S. aureus (MSSA) and methicillin resistant S. aureus (MRSA) bacteraemia were compared. RESULTS: Over the five year study period, 365 episodes of S. aureus bacteraemia were identified. The annual incidence was 3.28 cases per 1000 hospital admissions. MRSA was responsible for 26% of S. aureus bacteraemia and 72% of nosocomial infections. Only six possible cases of community-acquired MRSA infections were described. MSSA bacteraemia was more likely to present as pulmonary and bone or joint infections, while bacteraemia without a source was the most common presentation with MRSA.  Infants, children with malnutrition, and residents of long-term care facilities were at highest risk for MRSA bacteraemia. The overall case fatality rate for S. aureus bacteraemia was 8.8% over five years, with MRSA being the only significant risk factor for mortality. CONCLUSION: The incidence of S. aureus bacteraemia and MRSA bacteraemia in children has remained stable over the past five years. MRSA is a predominantly nosocomial pathogen in children with S. aureus bacteraemia in Cape Town, South Africa

Role of infection control in combating antibiotic resistance

CITATION: Whitelaw, A. C. 2015. Role of infection control in combating antibiotic resistance. South African Medical Journal, 105(5):421, doi:10.7196/SAMJ.9650.The original publication is available at http://www.samj.org.zaInfection control has been identified as one of the key interventions in controlling the threat of antibiotic resistance. Reducing the transmission of multidrug-resistant organisms (MDROs) reduces the need for broad-spectrum antibiotics in particular, while interventions that decrease the risk of infection have an impact on the use of any antibiotic. Hand hygiene remains the cornerstone of decreasing the transmission of MDROs. Alcohol-based hand rubs are a cheap, effective and convenient means of performing hand hygiene. Patients colonised or infected with MDROs should be placed on contact precautions, although implementation remains challenging in resourcelimited environments. Screening for certain MDROs may play a role in curbing transmission of these organisms. If implemented, screening must be part of a comprehensive infection control strategy. In resource-limited settings, the costs and potential benefits of screening programmes need to be carefully weighed up. Care bundles have been shown to reduce the incidence of common healthcare-associated infections, including catheter-associated urinary tract infection, ventilator-associated pneumonia, central line-associated bloodstream infection and surgical site infection. These bundles are relatively inexpensive, and can play an important role in reducing antibiotic use and improving clinical outcomes.http://www.samj.org.za/index.php/samj/article/view/10011Publisher's versio

The emergence of resistance to the benzimidazole anthlemintics in parasitic nematodes of livestock is characterised by multiple independent hard and soft selective sweeps

Anthelmintic resistance is a major problem for the control of parasitic nematodes of livestock and of growing concern for human parasite control. However, there is little understanding of how resistance arises and spreads or of the “genetic signature” of selection for this group of important pathogens. We have investigated these questions in the system for which anthelmintic resistance is most advanced; benzimidazole resistance in the sheep parasites Haemonchus contortus and Teladorsagia circumcincta. Population genetic analysis with neutral microsatellite markers reveals that T. circumcincta has higher genetic diversity but lower genetic differentiation between farms than H. contortus in the UK. We propose that this is due to epidemiological differences between the two parasites resulting in greater seasonal bottlenecking of H. contortus. There is a remarkably high level of resistance haplotype diversity in both parasites compared with drug resistance studies in other eukaryotic systems. Our analysis suggests a minimum of four independent origins of resistance mutations on just seven farms for H. contortus, and even more for T. circumincta. Both hard and soft selective sweeps have occurred with striking differences between individual farms. The sweeps are generally softer for T. circumcincta than H. contortus, consistent with its higher level of genetic diversity and consequent greater availability of new mutations. We propose a model in which multiple independent resistance mutations recurrently arise and spread by migration to explain the widespread occurrence of resistance in these parasites. Finally, in spite of the complex haplotypic diversity, we show that selection can be detected at the target locus using simple measures of genetic diversity and departures from neutrality. This work has important implications for the application of genome-wide approaches to identify new anthelmintic resistance loci and the likelihood of anthelmintic resistance emerging as selection pressure is increased in human soil-transmitted nematodes by community wide treatment programs

Guideline for the optimal use of blood cultures

The incidence of sepsis is increasing globally, with high morbidity and mortality. Prompt, accurate detection of bacteraemia and fungaemia is imperative for improving patient care, yet health care professionals lack training in correct blood culture techniques. These guidelines discuss the clinical importance of blood cultures, the indications for their use and the correct technique for optimal yield of pathogenic micro-organisms that cause sepsis

Genetic basis of rifampicin resistance in methicillin-resistant Staphylococcus aureus suggests clonal expansion in hospitals in Cape Town, South Africa

<p>Abstract</p> <p>Background</p> <p>Since 2001, several studies have reported high rifampicin resistance rates (45 - 100%) among methicillin-resistant <it>Staphylococcus aureus </it>(MRSA) isolates from South Africa. The authors previously characterised 100 MRSA isolates from hospitals in Cape Town, South Africa; forty-five percent of these isolates were rifampicin-resistant. The majority (44/45) corresponded to ST612-MRSA-IV, which is prevalent in South Africa, but has not been reported frequently elsewhere. The remaining rifampicin-resistant isolate corresponded to ST5-MRSA-I. The aim of this study was to investigate further the prevalence and genetic basis of rifampicin-resistance in MRSA isolates from hospitals in Cape Town.</p> <p>Results</p> <p>Between July 2007 and June 2011, the prevalence of rifampicin-resistant MRSA in hospitals in Cape Town ranged from 39.7% to 46.4%. Based on the results of the aforementioned study, nine ST612-MRSA-IV isolates, the rifampicin-resistant ST5-MRSA-I isolate, and two rifampicin-susceptible MRSA isolates were investigated. Four previously described ST612-MRSA-IV isolates, including two each from South Africa and Australia, were also included.</p> <p>The ST5-MRSA-I isolate carried a single mutational change, H₄₈₁Y, commonly associated with high-level rifampicin resistance. All ST612-MRSA-IV isolates carried an uncommon double amino acid substitution in RpoB, H₄₈₁N, I₅₂₇M, whilst one of the Australian ST612-MRSA-IV isolates carried an additional mutation within <it>rpoB</it>, representing a novel <it>rpoB </it>genotype: H₄₈₁N, I₅₂₇M, K₅₇₉R. All ST612-MRSA-IV isolates also shared a unique silent single nucleotide polymorphism (SNP) within <it>rpoB</it>.</p> <p>Conclusions</p> <p>That local ST612-MRSA-IV isolates described here share an uncommon <it>rpoB </it>genotype and a unique silent SNP suggests this clone may have undergone clonal expansion in hospitals in Cape Town. Further, the data suggest that these isolates may be related to rifampicin-resistant ST612-MRSA-IV previously described in South Africa and Australia.</p