Colleen Bamford

A dimorphic fungus causing disseminated infection in South Africa.

BACKGROUND The genus emmonsia contains three species that are associated with human disease. Emmonsia crescens and Emmonsia parva are the agents that cause adiaspiromycosis, and one human case of Emmonsia pasteuriana infection has been described. We report a fungal pathogen within the genus emmonsia that is most closely related to E. pasteuriana in human immunodeficiency virus (HIV)-infected adults in South Africa. METHODS Between July 2008 and July 2011, we conducted enhanced surveillance to identify the cause of systemic, dimorphic fungal infections in patients presenting to Groote Schuur Hospital and other hospitals affiliated with the University of Cape Town, Cape Town, South Africa. DNA sequencing was used to identify pathogenic fungi. RESULTS A total of 24 cases of dimorphic fungal infection were diagnosed, 13 of which were caused by an emmonsia species. All 13 patients were HIV-infected, with a median CD4+ T-cell count of 16 cells per cubic millimeter (interquartile range, 10 to 44), and all had evidence of disseminated fungal disease. Three patients died soon after presentation, but the others had a good response to a variety of antifungal agents and antiretroviral therapy. Phylogenetic analysis of five genes (LSU, ITS1-2, and the genes encoding actin, β-tubulin, and intein PRP8) revealed that this fungus belongs in the genus emmonsia and is most closely related to E. pasteuriana. CONCLUSIONS The findings suggest that these isolates of an emmonsia species represent a new species of dimorphic fungus that is pathogenic to humans. The species appears to be an important cause of infections in Cape Town.

Safety and effectiveness of colistin compared with tobramycin for multi-drug resistant Acinetobacter baumannii infections

BackgroundNosocomial infections due to multi-drug resistant Acinetobacter baumannii are often treated with colistin, but there are few data comparing its safety and efficacy with other antimicrobials.MethodsA retrospective cohort study of patients treated with colistin or tobramycin for A. baumannii infections in intensive care units (ICUs) at Groote Schuur hospital. Colistin was used for A. baumannii isolates which were resistant to all other available antimicrobials. In the tobramycin group, 53% of the isolates were only susceptible to tobramycin and colistin. We assessed ICU mortality, nephrotoxicity and time to the first negative culture.Results32 patients, with similar admission APACHE scores and serum creatinine, were treated with each antimicrobial. There were no significant differences between the colistin and tobramycin groups in ICU mortality (p = 0.54), nephrotoxicity (p = 0.67), change in creatinine from baseline to highest subsequent value (p = 0.11) and time to microbiological clearance (p = 0.75). The hazard ratio for total in-hospital survival in patients treated with colistin compared to tobramycin was 0.43 (95% CI 0.19 to 0.99).ConclusionOur study suggests that colistin and tobramycin have similar risks of nephrotoxicity and are equally efficacious. Colistin is an acceptable antibiotic for the treatment of A. baumanii infections when the organism is resistant to other available antimicrobials.

VIM-2 metallo-β-lactamase-producing Pseudomonas aeruginosa causing an outbreak in South Africa

Sir, Pseudomonas aeruginosa is an opportunistic pathogen that has been implicated in nosocomial outbreaks in immunocompromised patients worldwide. We present an outbreak caused by a multidrug-resistant P. aeruginosa (MRPA) clone in a haematology unit of a tertiary academic hospital in Cape Town, South Africa. Fifteen MRPA isolates were recovered from separate patients between January 2010 and April 2011, including 10 from blood, 2 from stool, 1 from bile, 1 from urine and 1 from a catheter tip. The majority of the patients were severely neutropenic following stem cell transplants and eight of them died. The genetic relatedness of the isolates was investigated using PFGE according to a previously published protocol with minor amendments. Whole genomic DNA was digested in situ with SpeI (New England Biolabs, Inc., UK) and the resulting restriction fragments were separated on a 1% agarose gel using a CHEF-DRII GeneNavigator apparatus (GE Healthcare, Piscataway, NJ, USA). Restriction profiles were analysed using GelCompar II version 5.1 (Applied Maths, St-Martens-Latem, Belgium). A dendrogram indicating the levels of similarity between the isolates was created using the Dice similarity coefficient. The band tolerance and optimizations were set at 1%, and a similarity threshold of 80% was used to define clusters. The profiles of 10 of the 15 isolates were indistinguishable and were assigned to cluster A. One isolate, with 77% similarity to cluster A, was assigned subtype A1. The remaining four isolates were all unique. To further characterize the genetic background of this MRPA clone, multilocus sequence typing (MLST) of three representative isolates from cluster A, spanning the defined outbreak period, were selected. MLST indicated that these three isolates belong to sequence type (ST) 233. Identification and susceptibility testing was performed on Vitek 2 (bioMerieux, Marcy l’Etoile, France). Imipenem and meropenem MICs were determined by Etests, according to the manufacturer’s specification (bioMerieux). Fourteen of the isolates expressed high levels of resistance to imipenem (MIC ≥128 mg/L) and meropenem (MIC ≥128 mg/L). The 15th strain was susceptible to both imipenem (MIC ≤1 mg/L) and meropenem (MIC ≤2 mg/L). As metallo-b-lactamases (MBLs) are considered a major mechanism of carbapenem resistance in P. aeruginosa, PCR assays were carried out using primers for the detection of the MBL-encoding genes blaIMP (IMPF 5′-ATTGACACTCCATTTAC-3′/ IMPR 5′-AACAACCAGTTTTGC-3′) and blaVIM (VIMF 5′-GTGAGTATCC GACAGTC-3′/VIMR 5′-GAGCAAGTCTAGACCG-3′). Although a PCR product of the expected size was obtained from a control P. aeruginosa strain carrying blaIMP-1 (gift from Y. Hirakata, Tohuku University Graduate School of Medicine, Japan), no products were obtained from the 15 Cape Town P. aeruginosa isolates. However, amplicons of the expected size for the blaVIM gene were obtained for the 10 strains in PFGE cluster A and the closely related strain, A1, as well as the blaVIM-2 positive control (gift from P. Nordmann, Hopital de Bicetre, France). No PCR products were obtained from the four unrelated P. aeruginosa isolates. PCR products from the 11 strains were purified (QIAquick PCR purification kit, QIAGEN, Germany) and sequencing analysis revealed the blaVIM-2 gene in all 11 strains. Additional PCR screening for the NDM, SPM, KPC and GES b-lactamase genes for all 15 isolates revealed that the single isolate, sensitive to both imipenem and meropenem and cultured from a catheter tip, carried a blaGES-2 gene, which has previously been implicated in a South African outbreak. MLST typing indicated that this carbapenem-susceptible strain belonged to ST625, a new genotype not previously described. Relatively little is known regarding the prevalence of carbapenem-hydrolysing enzymes in African countries. This outbreak of MBL blaVIM-2-carrying P. aeruginosa highlights the urgent need for the development of more active surveillance systems in South Africa and the importance of molecular epidemiology in a hospital outbreak situation.

Antibiotic stewardship ward rounds and a dedicated prescription chart reduce antibiotic consumption and pharmacy costs without affecting inpatient mortality or re-admission rates

Background Antibiotic consumption is a major driver of bacterial resistance. To address the increasing burden of multi-drug resistant bacterial infections, antibiotic stewardship programmes are promoted worldwide to rationalize antibiotic prescribing and conserve remaining antibiotics. Few studies have been reported from developing countries and none from Africa that report on an intervention based approach with outcomes that include morbidity and mortality. Methods An antibiotic prescription chart and weekly antibiotic stewardship ward round was introduced into two medical wards of an academic teaching hospital in South Africa between January-December 2012. Electronic pharmacy records were used to collect the volume and cost of antibiotics used, the patient database was analysed to determine inpatient mortality and 30-day re-admission rates, and laboratory records to determine use of infection-related tests. Outcomes were compared to a control period, January-December 2011. Results During the intervention period, 475.8 defined daily doses were prescribed per 1000 inpatient days compared to 592.0 defined daily doses/1000 inpatient days during the control period. This represents a 19.6% decrease in volume with a cost reduction of 35% of the pharmacy’s antibiotic budget. There was a concomitant increase in laboratory tests driven by requests for procalcitonin. There was no difference in inpatient mortality or 30-day readmission rate during the control and intervention periods. Conclusions Introduction of antibiotic stewardship ward rounds and a dedicated prescription chart in a developing country setting can achieve reduction in antibiotic consumption without harm to patients. Increased laboratory costs should be anticipated when introducing an antibiotic stewardship program.

The potential to transmit Mycobacterium tuberculosis at a South African tertiary teaching hospital.

OBJECTIVES To assess the risk of nosocomial transmission by confirmed pulmonary tuberculosis (PTB) patients in a high TB/HIV incidence environment. METHODS Between November 2006 and April 2007, we carried out a cross-sectional survey of PTB patients with positive smears or cultures at an academic tertiary hospital in the Western Cape, South Africa. RESULTS Of 394 confirmed PTB patients, only 199 (50.5%) had a known HIV status, of whom 107 (53.8%) were HIV-co-infected. Sensitivity testing for Mycobacterium tuberculosis (TB) was done in 49.3% of patients with available cultures (140/284). Of these patients, 9.3% (13/140) had multidrug-resistant (MDR) TB strains. The turnaround times (TAT) for culture and susceptibility testing were delayed: mean TAT for cultures was 27 days (range 63 days) and for susceptibility testing was 42 days (range 63 days). One fifth of PTB patients (82/394) were diagnosed from wards that do not deal with TB on a daily basis. PTB inpatients were hospitalized for an average of 13 days and were on average transferred twice. Only 14.2% of all PTB patients were notified to the South Africa Provincial Department of Health. Throughout their hospitalization, PTB patients were potentially infectious. CONCLUSIONS The potential for nosocomial TB transmission in a setting of high TB and HIV co-infection with a high MDR prevalence, inconsistent infection prevention and control measures, and delayed diagnosis cannot be ignored. Barriers to TB infection control must urgently be addressed.

Extended −10 Promoter in ISAba-1 Upstream of blaOXA-23 from Acinetobacter baumannii

Molecular studies showed that carbapenem-resistant Acinetobacter baumannii strains isolated from patients in hospitals in Cape Town contain bla OXA-23 ([7][1]). Concordant with the findings of others ([4][2], [11][3]), PCR assays showed that of the 43 strains investigated, bla OXA-23 was

Outbreak of Multi-Drug Resistant Pseudomonas aeruginosa Bloodstream Infection in the Haematology Unit of a South African Academic Hospital

Objective To describe an outbreak of multi-resistant Pseudomonas aeruginosa bloodstream infections (MRPA-BSI) that occurred in the haematology ward of a tertiary academic hospital in Cape Town, South Africa, and determine risk factors for acquisition of MRPA-BSI. Methods The outbreak investigation included a search for additional cases, review of patient records, environmental and staff screening, molecular typing using pulsed-field gel electrophoresis (PFGE) and Multi-locus sequencing (MLST) and a retrospective case-control study. Results Ten MRPA-BSI cases occurred in the haematology ward between January 2010 and January 2011. The case fatality rate was 80%. Staff screening specimens were negative for MRPA and an environmental source was not identified. PFGE showed that 9/10 isolates were related. MLST showed that 3 of these 9 isolates belonged to Sequence type (ST) 233 while the unrelated isolate belonged to ST260. Conclusion We have described an outbreak of MRPA-BSI occurring over an extended period of time among neutropenic haematology patients. Molecular typing confirms that the outbreak was predominantly due to a single strain. The source of the outbreak was not identified, but the outbreak appears to have been controlled following intensive infection control measures.

Systematic review of the evidence for rational dosing of colistin

BACKGROUND There is an alarming global increase in the incidence of nosocomial infections with multidrug-resistant Gram-negative bacteria, which are often only susceptible to colistin. Colistin was developed prior to current methods of establishing dosing using pharmacokinetic-pharmacodynamic relationships. Dosing regimens differ in package inserts from different manufacturers and in different guidelines. It is imperative to avoid under-dosing with colistin in order to limit the development of resistance, as it is the last line of defence. METHODS We conducted a systematic review of the literature to develop guidelines for rational dosing of intravenous colistin, with a particular focus on critically ill patients. RESULTS Colistin is administered as the inactive pro-drug colistimethate sodium. Colistin demonstrates concentration-dependent bacterial killing, suggesting that higher doses should be administered less frequently to achieve higher peak concentrations. Dose-related nephrotoxicity occurs, making it impossible to safely achieve concentrations that prevent the selection of resistant mutants or the effective eradication of bacteria with higher minimum inhibitory concentrations. Theoretically, combination therapy should be used to reduce the risk of selection of resistant bacteria. In critically ill patients, a loading dose should be given to rapidly achieve therapeutic concentrations, followed by maintenance doses of 4.5 MU 12-hourly. Maintenance dose adjustment is necessary with renal impairment. CONCLUSION Easier access to colistin is needed in South Africa, where it is not a registered medicine. Further research is needed to better characterise colistins pharmacokinetic-pharmacodynamic relationships in humans and to establish whether combinations of colistin with other antimicrobials result in improved clinical outcomes or a reduction in selection of resistant bacteria.

Antimicrobial susceptibility patterns of selected bacteraemic isolates from South African public sector hospitals, 2010

We report on antimicrobial susceptibility surveillance data for six key bloodstream pathogens (Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Pseudomonas aeruginosa, Acinetobacter baumannii and Staphylococcus aureus) identified in public sector hospitals in South Africa during 2010. Major findings include the accelerated emergence of carbapenem resistance among K. pneumoniae and Enterobacter species, with overall susceptibility rates of 98% and 96% for ertapenem, and above 99% for meropenem and imipenem. Levels of resistance among P. aeruginosa and A. baumannii remain high in all centres, with few changes since 2009. Large decreases in piperacillin-tazobactam susceptibility rates were noted at three institutions, probably related to methodological issues. S. aureus remains a major pathogen countrywide, with between 30-60% of isolates resistant to cloxacillin [methicillin-resistant S. aureus (MRSA)]. Ongoing surveillance for antimicrobial resistance is vital, and the use of a centralised data ...

Prevalence and trends of Staphylococcus aureus bacteraemia in hospitalized patients in South Africa, 2010 to 2012 : laboratory-based surveillance mapping of antimicrobial resistance and molecular epidemiology

Introduction We aimed to obtain an in-depth understanding on recent antimicrobial resistance trends and molecular epidemiology trends of S. aureus bacteraemia (SAB). Methods Thirteen academic centres in South Africa were included from June 2010 until July 2012. S. aureus susceptibility testing was performed on the MicroScan Walkaway. Real-time PCR using the LightCycler 480 II was done for mecA and nuc. SCCmec and spa-typing were finalized with conventional PCR. We selected one isolate per common spa type per province for multilocus sequence typing (MLST). Results S. aureus from 2709 patients were included, and 1231 (46%) were resistant to methicillin, with a significant decline over the three-year period (p-value = 0.003). Geographical distribution of MRSA was significantly higher in Gauteng compared to the other provinces (P<0.001). Children <5 years were significantly associated with MRSA with higher rates compared to all other age groups (P = 0.01). The most prevalent SCCmec type was SCCmec type III (531 [41%]) followed by type IV (402 [31%]). Spa-typing discovered 47 different spa-types. The five (87%) most common spa-types were t037, t1257, t045, t064 and t012. Based on MLST, the commonest was ST612 clonal complex (CC8) (n = 7) followed by ST5 (CC5) (n = 4), ST36 (CC30) (n = 4) and ST239 (CC8) (n = 3). Conclusions MRSA rate is high in South Africa. Majority of the isolates were classified as SCCmec type III (41%) and type IV (31%), which are typically associated with hospital and community- acquired infections, respectively. Overall, this study reveals the presence of a variety of hospital-acquired MRSA clones in South Africa dominance of few clones, spa 037 and 1257. Monitoring trends in resistance and molecular typing is recommended to detect changing epidemiological trends in AMR patterns of SAB.