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

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

Clonal expansion of colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa

CITATION: Snyman, Y., et al. 2020. Clonal expansion of colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa. International Journal of Infectious Diseases, 91:94-100, doi:10.1016/j.ijid.2019.11.021.The original publication is available at https://www.journals.elsevier.com/international-journal-of-infectious-diseasesPublication of this article was funded by the Stellenbosch University Open Access FundObjectives: To describe colistin-resistant Acinetobacter baumannii isolates in Cape Town, South Africa. Methods: A. baumannii isolates identified on Vitek 2 Advanced Expert System were collected from Tygerberg Hospital referral laboratory between 2016 and 2017. Colistin resistance was confirmed using broth microdilution and SensiTest. mcr-1–5 were detected using PCR and strain typing was performed by rep-PCR. Whole genome sequencing (WGS) was performed on a subset of isolates to identify chromosomal colistin resistance mechanisms and strain diversity using multilocus sequence typing (MLST) and pairwise single nucleotide polymorphism analyses. Results: Twenty-six colistin-resistant and six colistin-susceptible A. baumannii were collected separately based on Vitek susceptibility; 20/26 (77%) were confirmed colistin-resistant by broth microdilution. Four colistin-resistant isolates were isolated in 2016 and 16 in 2017, from five healthcare facilities. Thirteen colistin-resistant isolates and eight colistin-susceptible isolates were identical by rep-PCR and MLST (ST1), all from patients admitted to a tertiary hospital during 2017. The remaining colistin-resistant isolates were unrelated. Conclusions: An increase in colistin-resistant A. baumannii isolates from a tertiary hospital in 2017 appears to be clonal expansion of an emerging colistin-resistant strain. This strain was not detected in 2016 or from other hospitals. Identical colistin-susceptible isolates were also isolated, suggesting relatively recent acquisition of colistin resistance.https://www.clinicalkey.com/#!/content/playContent/1-s2.0-S1201971219304606?returnurl=https:%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1201971219304606%3Fshowall%3Dtrue&referrer=https:%2F%2Fpubmed.ncbi.nlm.nih.gov%2FPublisher's versio

Shale gas reserve evaluation by laboratory pyrolysis and gas holding capacity consistent with field data

Exploration for shale gas occurs in onshore basins, with two approaches used to predict the maximum gas in place (GIP) in the absence of production data. The first estimates adsorbed plus free gas held within pore space, and the second measures gas yields from laboratory pyrolysis experiments on core samples. Here we show the use of sequential high-pressure water pyrolysis (HPWP) to replicate petroleum generation and expulsion in uplifted onshore basins. Compared to anhydrous pyrolysis where oil expulsion is limited, gas yields are much lower, and the gas at high maturity is dry, consistent with actual shales. Gas yields from HPWP of UK Bowland Shales are comparable with those from degassed cores, with the ca. 1% porosity sufficient to accommodate the gas generated. Extrapolating our findings to the whole Bowland Shale, the maximum GIP equate to potentially economically recoverable reserves of less than 10 years of current UK gas consumption

Vision function in children 10 years after grade 3 or 4 intraventricular haemorrhage with ventricular dilation: A masked prospective study

Aim We examined children 10 to 11 years after grade 3 or 4 intraventricular haemorrhage and ventricular dilation (IVHVD) and investigated whether the grade of IVHVD affected their visual outcome. We explored associations between visual outcomes with cognitive outcomes and extra support at school. Method The visual examinations were part of a 10-year follow-up study for children in a randomized trial. Testers followed a protocol and were masked to whether the child had experienced grade 3 or grade 4 IVHVD and all other data. Results Thirty-two children were tested: 24 were male and mean (standard deviation) age was 10 years 5 months (1 year 2 months); range 8 years 9 months to 12 years 9 months. All had at least one visual impairment. The median (interquartile range) number of impairments per child was six (six to nine) for children who experienced a grade 4 IVHVD compared with three (two to four) for children who experienced a grade 3 IVHVD (p = 0.003). Each extra vision impairment per child was associated with increased educational support at school, after adjustment for developmental age equivalence (odds ratio = 1.7 [95% confidence interval 1.1–2.6], p = 0.015). Interpretation Children who experience grade 3 or 4 IVHVD have a high level of visual morbidity at age 10 to 11 years. These children may have unmet visual needs and their outcomes might improve if these needs could be addressed. What this paper adds Parent-reported questionnaire responses underestimated directly assessed visual morbidity. Grade 4 intraventricular haemorrhage and ventricular dilatation (IVHVD) was followed by more vision impairments than grade 3 IVHVD. Simple tests of visual perceptual skills correlated with the neuropsychology tests. Children with supranuclear eye movement disorders were more likely to be receiving extra help at school. Each additional visual impairment increased the likelihood of extra educational support

PANC Study (Pancreatitis: A National Cohort Study): national cohort study examining the first 30 days from presentation of acute pancreatitis in the UK

Abstract Background Acute pancreatitis is a common, yet complex, emergency surgical presentation. Multiple guidelines exist and management can vary significantly. The aim of this first UK, multicentre, prospective cohort study was to assess the variation in management of acute pancreatitis to guide resource planning and optimize treatment. Methods All patients aged greater than or equal to 18 years presenting with acute pancreatitis, as per the Atlanta criteria, from March to April 2021 were eligible for inclusion and followed up for 30 days. Anonymized data were uploaded to a secure electronic database in line with local governance approvals. Results A total of 113 hospitals contributed data on 2580 patients, with an equal sex distribution and a mean age of 57 years. The aetiology was gallstones in 50.6 per cent, with idiopathic the next most common (22.4 per cent). In addition to the 7.6 per cent with a diagnosis of chronic pancreatitis, 20.1 per cent of patients had a previous episode of acute pancreatitis. One in 20 patients were classed as having severe pancreatitis, as per the Atlanta criteria. The overall mortality rate was 2.3 per cent at 30 days, but rose to one in three in the severe group. Predictors of death included male sex, increased age, and frailty; previous acute pancreatitis and gallstones as aetiologies were protective. Smoking status and body mass index did not affect death. Conclusion Most patients presenting with acute pancreatitis have a mild, self-limiting disease. Rates of patients with idiopathic pancreatitis are high. Recurrent attacks of pancreatitis are common, but are likely to have reduced risk of death on subsequent admissions. </jats:sec

Plasmid-mediated mcr-1 colistin resistance in Escherichia coli and Klebsiella spp. clinical isolates from the Western Cape region of South Africa

CITATION: Newton-Foot, M., Snyman, Y., Maloba, M. R. B. & Whitelaw, A. C. 2017. Plasmid-mediated mcr-1 colistin resistance in Escherichia coli and Klebsiella spp. clinical isolates from the Western Cape region of South Africa. Antimicrobial Resistance & Infection Control, 6:78, doi:10.1186/s13756-017-0234-8.The original publication is available at https://aricjournal.biomedcentral.comBackground: Colistin is a last resort antibiotic for the treatment of carbapenem-resistant Gram negative infections. Until recently, mechanisms of colistin resistance were limited to chromosomal mutations which confer a high fitness cost and cannot be transferred between organisms. However, a novel plasmid-mediated colistin resistance mechanism, encoded by the mcr-1 gene, has been identified, and has since been detected worldwide. The mcr-1 colistin resistance mechanism is a major threat due to its lack of fitness cost and ability to be transferred between strains and species. Surveillance of colistin resistance mechanisms is critical to monitor the development and spread of resistance.This study aimed to determine the prevalence of the plasmid-mediated colistin resistance gene, mcr-1, in colistin-resistant E. coli and Klebsiella spp. isolates in the Western Cape of South Africa; and whether colistin resistance is spread through clonal expansion or by acquisition of resistance by diverse strains. Methods: Colistin resistant E. coli and Klebsiella spp. isolates were collected from the NHLS microbiology laboratory at Tygerberg Hospital. Species identification and antibiotic susceptibility testing was done using the API® 20 E system and the Vitek® 2 Advanced Expert System™. PCR was used to detect the plasmid-mediated mcr-1 colistin resistance gene and REP-PCR was used for strain typing of the isolates. Results: Nineteen colistin resistant isolates, including 12 E. coli, six K. pneumoniae and one K. oxytoca isolate, were detected over 7 months from eight different hospitals in the Western Cape region. The mcr-1 gene was detected in 83% of isolates which were shown to be predominantly unrelated strains. Conclusions: The plasmid-mediated mcr-1 colistin resistance gene is responsible for the majority of colistin resistance in clinical isolates of E. coli and Klebsiella spp. from the Western Cape of South Africa. Colistin resistance is not clonally disseminated; the mcr-1 gene has been acquired by several unrelated strains of E. coli and K. pneumoniae. Acquisition of mcr-1 by cephalosporin- and carbapenem-resistant Gram negative bacteria may result in untreatable infections and increased mortality. Measures need to be implemented to control the use of colistin in health care facilities and in agriculture to retain its antimicrobial efficacy.https://aricjournal.biomedcentral.com/articles/10.1186/s13756-017-0234-8Publisher's versio

Plasmid-mediated mcr-1 colistin resistance in Escherichia coli and Klebsiella spp. clinical isolates from the Western Cape region of South Africa

Abstract Background Colistin is a last resort antibiotic for the treatment of carbapenem-resistant Gram negative infections. Until recently, mechanisms of colistin resistance were limited to chromosomal mutations which confer a high fitness cost and cannot be transferred between organisms. However, a novel plasmid-mediated colistin resistance mechanism, encoded by the mcr-1 gene, has been identified, and has since been detected worldwide. The mcr-1 colistin resistance mechanism is a major threat due to its lack of fitness cost and ability to be transferred between strains and species. Surveillance of colistin resistance mechanisms is critical to monitor the development and spread of resistance.This study aimed to determine the prevalence of the plasmid-mediated colistin resistance gene, mcr-1, in colistin-resistant E. coli and Klebsiella spp. isolates in the Western Cape of South Africa; and whether colistin resistance is spread through clonal expansion or by acquisition of resistance by diverse strains. Methods Colistin resistant E. coli and Klebsiella spp. isolates were collected from the NHLS microbiology laboratory at Tygerberg Hospital. Species identification and antibiotic susceptibility testing was done using the API® 20 E system and the Vitek® 2 Advanced Expert System™. PCR was used to detect the plasmid-mediated mcr-1 colistin resistance gene and REP-PCR was used for strain typing of the isolates. Results Nineteen colistin resistant isolates, including 12 E. coli, six K. pneumoniae and one K. oxytoca isolate, were detected over 7 months from eight different hospitals in the Western Cape region. The mcr-1 gene was detected in 83% of isolates which were shown to be predominantly unrelated strains. Conclusions The plasmid-mediated mcr-1 colistin resistance gene is responsible for the majority of colistin resistance in clinical isolates of E. coli and Klebsiella spp. from the Western Cape of South Africa. Colistin resistance is not clonally disseminated; the mcr-1 gene has been acquired by several unrelated strains of E. coli and K. pneumoniae. Acquisition of mcr-1 by cephalosporin- and carbapenem-resistant Gram negative bacteria may result in untreatable infections and increased mortality. Measures need to be implemented to control the use of colistin in health care facilities and in agriculture to retain its antimicrobial efficacy

Characterisation of mcr-4.3 in a colistin-resistant Acinetobacter nosocomialis clinical isolate from Cape Town, South Africa

CITATION: Snyman, Y., et al. 2021. Characterisation of mcr-4.3 in a colistin-resistant Acinetobacter nosocomialis clinical isolate from Cape Town, South Africa. Journal of Global Antimicrobial Resistance, 25:102-106, doi:10.1016/j.jgar.2021.03.002.The original publication is available at https://www.sciencedirect.comPublication of this article was funded by the Stellenbosch University Open Access FundObjectives: Colistin resistance in Acinetobacter spp. is increasing, resulting in potentially untreatable noso- comial infections. Plasmid-mediated colistin resistance is of particular concern due to its low fitness cost and potential transferability to other bacterial strains and species. This study investigated the colistin resistance mechanism in a clinical Acinetobacter nosocomialis isolate from Cape Town, South Africa. Methods: A colistin-resistant A. nosocomialis isolate was identified from a blood culture in 2017. PCR and Illumina whole-genome sequencing (WGS) were performed to identify genes and mutations conferring resistance to colistin. Plasmid sequencing was performed on an Oxford Nanopore platform. mcr function- ality was assessed by broth microdilution after cloning the mcr gene into pET-48b( + ) and expressing it in SHuffle®T7 Escherichia coli and after curing the plasmid using 62.5 mg/L acridine orange. Results: The colistin minimum inhibitory concentration (MIC) of the A. nosocomialis isolate was 16 mg/L. The mcr-4.3 gene was detected by PCR and WGS. No other previously described colistin resistance mech- anism was found by WGS. The mcr-4.3 gene was identified on a 24 024-bp RepB plasmid (pCAC13a). Functionality studies showed that recombinant mcr-4.3 did not confer colistin resistance in E. coli. How- ever, plasmid curing of pCAC13a restored colistin susceptibility in A. nosocomialis . Conclusion: We describe the first detection of a plasmid-mediated mcr-4.3 gene encoding colistin re- sistance in A. nosocomialis and the first detection of mcr-4.3 in a clinical isolate in Africa. Recombinant expression of mcr-4.3 did not confer colistin resistance in E. coli , suggesting that its functionality may be RepB plasmid-dependent or species-specific.https://www.sciencedirect.com/science/article/pii/S2213716521000679Publisher's versio