Analysis of the Trends of Methicillin-Resistant Staphylococcus aureus in Gauteng Public Hospitals from 2009 to 2018

Most investigations into the distribution of methicillin resistant Staphylococcus aureus (MRSA) have focused exclusively on bloodborne infections within individual health care institutions for shorter time periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. Therefore, in this study we determined the demographic and geographical patterns of MRSA infections and their fluctuation in 10 years within all public hospitals in Gauteng, South Africa. A retrospective analysis of S. aureus samples was done by deduplicating samples in two groups. The sample groups were placed into subsets with respect to demographic and geographical fields and compared across the studied period. Logistic regression was utilized to determine odds ratios for resistant infections in univariate and multivariable configurations. A total of 66,071 unique infectious events were identified from the 148,065 samples received over a 10-year period, out of which 14,356 were identified as bacteremia. MRSA bacteremia rates in Gauteng peaked in 2015 and have since decreased. Within Gauteng, metropolitan areas have the greatest burden of MRSA with children under 5 years of age and males being most affected. Medical wards have the highest S. aureus bacteremia rates, while intensive care units have the highest MRSA bacteremia rates. Patient age, admitting ward, and geographical district are the most important associated factors of resistance. MRSA acquisition rates have shown tremendous growth since 2009 but have since spiked and subsequently decreased. This may be due to the initiation of the National Guidelines on Antimicrobial Stewardship and Infectious Disease Surveillance. Further studies to determine the trajectory of infections are required to support these claims. IMPORTANCE S. aureus is the leading cause of a variety of devastating clinical conditions, including infective endocarditis, bacteremia, and pleuropulmonary infections. It is an important pathogen responsible for substantial morbidity and mortality. MRSA is a variant of interest originally responsible for difficult to treat hospital-acquired infections that has since achieved community spread throughout the world. Most investigations into the distribution of MRSA have focused exclusively on bloodborne infections within individual health care institutions for shorter periods. This has limited the analysis of a community-spread pathogen to snapshots within the hospital domain. This study sought to determine the demographic and geographical patterns of MRSA infections as well as how these have fluctuated over time within all public hospitals. This will also help in understanding the epidemiology and resistance trends of S. aureus, which will help clinicians to understand the clinical prospective and policy makers to design guidelines and strategies for treating such infections.

A position statement and practical guide to the use of particulate filtering facepiece respirators (N95, FFP2, or equivalent) for South African health workers exposed to respiratory pathogens including Mycobacterium tuberculosis and SARS-CoV-2

SUMMARY

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is transmitted mainly by aerosol in particles <10 µm that can remain suspended for hours before being inhaled. Because particulate filtering facepiece respirators ('respirators'; e.g. N95 masks) are more effective than surgical masks against bio-aerosols, many international organisations now recommend that health workers (HWs) wear a respirator when caring for individuals who may have COVID-19. In South Africa (SA), however, surgical masks are still recommended for the routine care of individuals with possible or confirmed COVID-19, with respirators reserved for so-called aerosol-generating procedures. In contrast, SA guidelines do recommend respirators for routine care of individuals with possible or confirmed tuberculosis (TB), which is also transmitted via aerosol. In health facilities in SA, distinguishing between TB and COVID-19 is challenging without examination and investigation, both of which may expose HWs to potentially infectious individuals. Symptom-based triage has limited utility in defining risk. Indeed, significant proportions of individuals with COVID-19 and/or pulmonary TB may not have symptoms and/or test negative. The prevalence of undiagnosed respiratory disease is therefore likely significant in many general clinical areas (e.g. waiting areas). Moreover, a proportion of HWs are HIV-positive and are at increased risk of severe COVID-19 and death.

RECOMMENDATIONS

Sustained improvements in infection prevention and control (IPC) require reorganisation of systems to prioritise HW and patient safety. While this will take time, it is unacceptable to leave HWs exposed until such changes are made. We propose that the SA health system adopts a target of 'zero harm', aiming to eliminate transmission of respiratory pathogens to all individuals in every healthcare setting. Accordingly, we recommend: the use of respirators by all staff (clinical and non-clinical) during activities that involve contact or sharing air in indoor spaces with individuals who: (i) have not yet been clinically evaluated; or (ii) are thought or known to have TB and/or COVID-19 or other potentially harmful respiratory infections;the use of respirators that meet national and international manufacturing standards;evaluation of all respirators, at the least, by qualitative fit testing; andthe use of respirators as part of a 'package of care' in line with international IPC recommendations. We recognise that this will be challenging, not least due to global and national shortages of personal protective equipment (PPE). SA national policy around respiratory protective equipment enables a robust framework for manufacture and quality control and has been supported by local manufacturers and the Department of Trade, Industry and Competition. Respirator manufacturers should explore adaptations to improve comfort and reduce barriers to communication. Structural changes are needed urgently to improve the safety of health facilities: persistent advocacy and research around potential systems change remain essential.

Outbreak of Listeriosis in South Africa Associated with Processed Meat

BACKGROUND

An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown.

METHODS

We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018.

RESULTS

A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections.

CONCLUSIONS

This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.

Epidemiology of carbapenem-resistant Enterobacteriaceae (CRE) and comparison of the phenotypic versus genotypic screening tests for the detection of carbapenemases at a tertiary level, academic hospital in Johannesburg, South Africa

Background: Carbapenem-resistant Enterobacteriaceae (CRE) cause significant infections and pose a threat to the viability of available antibiotics. Understanding the epidemiology of these infections will assist in guiding appropriate treatment and infection prevention and control (IPC) practices in an institution. In addition, the phenotypic carbapenemase-producing Enterobacteriaceae (CPE) screening tests are widely used in South Africa. However, there is no published literature on their performance against PCR in that setting. Therefore, CRE epidemiology and performance of the Modified Hodge with Imipenem and Imipenem + EDTA combined disk tests (CDT) was evaluated at a tertiary academic hospital in Johannesburg.Method: A retrospective collection of data was performed. Data from January 2015 to December 2016 of all clinical isolates that were CRE OR carbapenem-susceptible Enterobacteriaceae with at least one positive CPE screening test were collected. Information collected included the ward areas from which samples were sent, specimen type that cultured CRE, CRE identification and carbapenem MIC results, phenotypic and genotypic CPE results.Results: Certain ward areas recurred as predominant areas with CRE infection in the two-year period. The prominent sample types that cultured CRE, the predominant Enterobacteriaceae species and carbapenemases identified corresponded with national surveillance data. The predominant carbapenemase type and level of carbapenem resistance conferred changed within one year. The Hodge test performed poorly for carbapenemase detection. The CDT detected metallo-β-lactamases adequately.Conclusion: In this study, the use of the MHT to screen for CPEs performed poorly. Continued surveillance will (i) lead to an understanding of the patient population (including infection type) affected, (ii) detect changes in the carbapenemase profiles, and (iii) inform infection prevention and control and appropriate clinical management.

Synergistic antifungal effect of cyclized chalcone derivatives and fluconazole against Candida albicans

The occurrence of invasive fungal diseases, particularly in immunocompromised patients, is life-threatening and increases the economic burden. The rising problem of multi-drug resistance is becoming a major concern for clinicians. In addition, a repertoire of antifungal agents is far less in number than antibacterial drugs. To combat these problems, combination therapy has gained a lot of interest. We previously reported the synergistic interaction of some mono- and bis-dihydropyrimidinone and thione derivatives with fluconazole and amphotericin B for combination antifungal therapy. In this study we used the same approach and synthesized different azole and non-azole derivatives of mono-(M) and bis-(B) chalcones and evaluated their antifungal activity profile alone and in combination with the most commonly used antifungal drug - fluconazole (FLC) - against seven FLC susceptible and three FLC resistant clinically isolated Candida albicans strains. Based on the minimum inhibitory concentration results, the bis-derivatives showed lower MIC values compared to their mono-analogues. Both fractional inhibitory concentration index and isobologram results revealed mostly synergistic, additive or indifferent interactions between the tested compounds and FLC against different Candida isolates. None of the tested compounds showed any effect on energy dependent R6G efflux, revealing that they do not reverse the mechanism of drug efflux. However, surprisingly, these compounds profoundly decreased ergosterol biosynthesis and showed down regulation of ERG11 gene expression, which is the possible mechanism of reversal of azole drug resistance by these compounds. These results provide a platform for further research to develop pyrimidinone/thione ring containing compounds as promising new antifungal agents, which could be used in antifungal combination therapy.

Molecular characterisation of clinical and environmental isolates of Mycobacterium kansasii isolates from South African gold mines

Mycobacterium kansasii (M. kansasii) is a major cause of non-tuberculous mycobacterial pulmonary disease in the South African gold-mining workforce, but the source of infection and molecular epidemiology are unknown. This study investigated the presence of M. kansasii in gold and coal mine and associated hostel water supplies and compared the genetic diversity of clinical and environmental isolates of M. kansasii. Five M. kansasii and ten other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. Polymerase chain reaction-restriction analysis of the hsp65 gene on 196 clinical and environmental M. kansasii isolates revealed 160 subtype I, eight subtype II and six subtype IV strains. Twenty-two isolates did not show the typical M. kansasii restriction patterns, suggesting that these isolates may represent new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 clinical and three environmental subtype I isolates demonstrated genetic diversity amongst the isolates. This study demonstrated that showerheads are possible sources of M. kansasii and other pathogenic non-tuberculous mycobacterial infection in a gold-mining region, that subtype I is the major clinical isolate of M. kansasii strain and that this subtype exhibits genetic diversity.

Clinically significant anaerobic bacteria isolated from patients in a South African academic hospital: antimicrobial susceptibility testing

BACKGROUND. Increasing resistance to some antimicrobial agents among anaerobic bacteria has made susceptibility patterns less predictable. METHOD. This was a prospective study of the susceptibility data of anaerobic organisms isolated from clinical specimens from patients with suspected anaerobic infections from June 2005 until February 2007. Specimens were submitted to the microbiology laboratory at Charlotte Maxeke Johannesburg Academic Hospital, where microscopy, culture and susceptibility testing were performed the using E test® strip minimum inhibitory concentration method. Results were interpreted with reference to Clinical and Laboratory Standards Institute guidelines for amoxicillin-clavulanate, clindamycin, metronidazole, penicillin, ertapenem, cefoxitin, ceftriaxone, chloramphenicol and piperacillin-tazobactam. RESULTS. One hundred and eighty anaerobic isolates were submitted from 165 patients. The most active antimicrobial agents were chloramphenicol (100% susceptible), ertapenem (97.2%), piperacillin-tazobactam (99.4%) and amoxicillin-clavulanic acid (96.7%). Less active were metronidazole (89.4%), cefoxitin (85%), clindamycin (81.7%), ceftriaxone (68.3%) and penicillin (33.3%). CONCLUSION. Susceptibility testing should be performed periodically to identify emerging trends in resistance and to modify empirical treatment of anaerobic infections.

Pseudomonas aeruginosa bacteraemia in an academic hospital in South Africa

OBJECTIVES

The aim of the study was to determine the clinical manifestations, outcome of and prognostic factors associated with Pseudomonas aeruginosa bacteraemia at Chris Hani Baragwanath Hospital, Johannesburg, during the period 1998 - 1999, to describe and quantify resistance to antipseudomonal drugs, to characterise bacteraemic isolates, and to investigate the clustering and genotype distribution of drug-susceptible and multiply-resistant strains in the hospital.

METHODS

Clinical and laboratory investigations, culture and antimicrobial susceptibility testing were performed. Bacteraemic isolates were typed by endonuclease macrorestriction. Those with > or = 97% band pattern similarity were assigned genotype status.

RESULTS

Of 91 P. aeruginosa blood isolates, 52 (57.1%) were nosocomially acquired. Underlying conditions associated with episodes were burns in 24 (28%) and HIV infection in 21 (24%). Multidrug resistance was present in 14 (15.4%) of isolates from 91 episodes. In 79 episodes where the outcome was known, 37 (46.8%) of the patients died. Case fatality rates were 75% in adults and 25% in children. Being a child, receiving appropriate antimicrobial treatment and admission to a specialised care unit were significantly associated with improved prognosis.

CONCLUSION

P. aeruginosa bacteraemia was associated with outbreaks caused by two multiply-resistant genotypes. Eighteen antimicrobial-susceptible isolates from bacteraemic episodes in paediatric wards, 9 in HIV-seropositive children, could be linked to small outbreaks in both hospitalised and community-based children.

Genotypic diversity of extensively drug-resistant tuberculosis (XDR-TB) in South Africa

SETTING

The epidemiology of extensively drug-resistant tuberculosis (XDR-TB), an emerging threat to TB control, is not well understood.

OBJECTIVE

To gain insight into the genotypic population structure of XDR Mycobacterium tuberculosis strains in South Africa using a molecular approach and thereby determine whether XDR-TB is mainly acquired or transmitted.

DESIGN

Sputum isolates from patients with multidrug-resistant tuberculosis (MDR-TB) were submitted to the National Referral Laboratory for second-line drug susceptibility testing. The XDR-TB isolates were spoligotyped and these data were compared to the geographic origin of the isolate.

RESULTS

Of the 699 MDR-TB isolates submitted for testing between June 2005 and December 2006, 101 (17%) patients had a culture that was resistant to either ofloxacin or kanamycin, and 41 (6%) were resistant to both drugs (XDR-TB). Spoligotyping of the XDR-TB isolates identified 17 genotypes. As a result of the high genotypic diversity and geographical distribution, we estimate that between 63% and 75% of cases developed XDR-TB through acquisition.

CONCLUSION

Acquisition of extensive drug resistance appears to be the primary mechanism driving the XDR-TB epidemic in South Africa. This urgent TB control issue has to be addressed to prevent the spread of this potentially incurable disease.

Antimicrobial resistance in developing countries. Part II: strategies for containment

The growing threat from resistant organisms calls for concerted action to prevent the emergence of new resistant strains and the spread of existing ones. Developing countries have experienced unfavourable trends in resistance-as detailed in part I, published last month--and implementation of many of the containment strategies recommended by WHO is complicated by universal, as well as developing country-specific, factors. The control of selective pressure for resistance could potentially be addressed through educational and other interventions for orthodox and unorthodox prescribers, distributors, and consumers of antimicrobials. At national levels, the implementation of drug use strategies--eg, combination therapy or cycling--may prove useful to lengthen the lifespan of existing and future agents. Programmes such as the Integrated Management of Childhood Illnesses (IMCI) and directly observed short-course therapy (DOTS) for tuberculosis are prescriber-focused and patient-focused, respectively, and have both been shown to positively influence factors that contribute to the selective pressure that affects resistance. The institution of interventions to prevent the transmission of infectious diseases could also lead to beneficial effects on the prevalence of resistance, as has vaccination against Haemophilus influenzae type B and Streptococcus pneumoniae. There has been an upsurge in the number of organisations and programmes that directly address issues of resistance, and collaboration could be one way to stem the dire trend. Additional factors such as unregulated drug availability, inadequate antimicrobial drug quality assurance, inadequate surveillance, and cultures of antimicrobial abuse must be addressed to permit a holistic strategy for resistance control.

Antimicrobial resistance in developing countries. Part I: recent trends and current status

The global problem of antimicrobial resistance is particularly pressing in developing countries, where the infectious disease burden is high and cost constraints prevent the widespread application of newer, more expensive agents. Gastrointestinal, respiratory, sexually transmitted, and nosocomial infections are leading causes of disease and death in the developing world, and management of all these conditions has been critically compromised by the appearance and rapid spread of resistance. In this first part of the review, we have summarised the present state of resistance in these infections from the available data. Even though surveillance of resistance in many developing countries is suboptimal, the general picture is one of accelerating rates of resistance spurred by antimicrobial misuse and shortfalls in infection control and public health. Reservoirs for resistance may be present in healthy human and animal populations. Considerable economic and health burdens emanate from bacterial resistance, and research is needed to accurately quantify the problem and propose and evaluate practicable solutions. In part II, to be published next month, we will review potential containment strategies that could address this burgeoning problem.

Coping with hygiene in South Africa, a water scarce country

The burden of infectious diseases may be reduced by adopting effective infection control measures. Some of these are dependent on the provision of adequate and safe water supplies for maintenance of basic standards of personal, domestic and healthcare hygiene. Consequences of scarce, and sometimes unsafe, waters supplies in South Africa are highlighted with reference to healthcare-associated infections, community acquired infectious intestinal diseases and domestic practices as infection sources. Availability of water in more than 67% of South African municipal hospitals and primary health care facilities (delivered by water tanker in 12.5% of satellite clinics, 5% from river or dam sources, 12.4% relying on rainwater) does not necessarily guarantee that it's quality is safe for utilisation. In the Northern Province and Mpumalanga, water needs to be purified prior to usage in 14.4 and 33% of satellite clinics respectively. Simple, low maintenance and low-cost interventions to maximise use and safety of limited water resources may be implemented: micro-organism (S. dysenteriae) inactivation by direct UV-exposure in sunlight abundant environments, water purification by filtration mechanisms and making use of iron pots in the community for pasteurisation, decontamination and boiling procedures. Education is paramount in promoting healthy domestic food handling practices, changing cultural perceptions of hygiene, hand-washing technique and mechanisms of domestic environmental decontamination. Water provision cannot be separated from other inter-related factors such as sanitation. Although the present government has taken initiatives to reduce the number of people not having access to water by 50% in 2002, provision of sanitation has been slower (>38% inadequate sanitation in 2002). Adoption of integrated environmental management approaches in conjunction with community participation (WASH Campaign--2002), by the government, aims to address the sanitation problems.

Nosocomial infections in HIV-infected/AIDS patients

Several pathogenetic processes are involved in the progression to AIDS in HIV-infected individuals. These include a gradual, but ultimately profound, depletion in CD4 lymphocytes, defects in B lymphocytes, neutrophil dysfunction and the breakdown of the integument as a consequence of AIDS-related dermatological conditions such as bacterial and fungal dermatoses and Kaposi's sarcoma. Each of these factors has important implications regarding host susceptibility to nosocomial infections. This review deals with some of the difficulties that are encountered in precisely defining the interrelationships between HIV infection/AIDS and nosocomial sepsis, and some of the controversies that surround respiratory, bloodstream (including central venous catheter-related infections) and gastrointestinal infections that may be acquired within healthcare centres. Because of the lack of accurate, detailed information on this subject, parallels will sometimes be drawn from observations made in other immunologically impaired patient groups and from data examining the rates of community-acquired infections in HIV-infected patients compared to controls. Appropriate and rational infection practice to minimize the risk of acquisition of nosocomial infection is highlighted. Finally, some of the common methodological problems commonly encountered in the current literature regarding nosocomial infections in this population group, and future challenges in the study of these infections, are reviewed.

Molecular epidemiology of an outbreak of Enterobacter cloacae in the neonatal intensive care unit of a provincial hospital in Gauteng, South Africa

An outbreak of Enterobacter cloacae in the neonatal intensive care unit of a provincial hospital in Gauteng, South Africa, resulting in nine deaths was investigated. Macrorestriction analysis using pulsed-field gel electrophoresis revealed that three isolates of E. cloacae from blood cultures of patients, six from environmental sources, and one from the hands of a staff member belonged to the same genotypic cluster.