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.

Molecular characterization of clinical methicillin-resistant Staphylococcus aureus isolates in South Africa.

Eighty-two percent of 320 clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates from various infection sites collected throughout South Africa were separated into five major globally prevalent clusters by SmaI pulsed-field gel electrophoresis, spa, and SCCmec typing. Only one Panton-Valentine leukocidin-positive isolate was detected. This is the first detailed MRSA epidemiology study for the whole country.

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.

Efflux pump activity in fluoroquinolone and tetracycline resistant Salmonella and E. coli implicated in reduced susceptibility to household antimicrobial cleaning agents.

It has been shown that the inappropriate use of antimicrobial household agents selects for organisms with resistance mechanisms (e.g. efflux pumps), which could lead to the development of antibiotic resistance. The reverse hypothesis, that antibiotic-resistant organisms become tolerant to other antibacterial agents (e.g. disinfectants) due to the action of efflux pumps, has however not been extensively examined. The objective of this study was to establish whether there is a link between antibiotic resistance in potential gastrointestinal pathogens and reduced sensitivity of these organisms to commonly used household antimicrobial agents. In this study, tetracycline and ofloxacin sensitive and resistant Escherichia coli (9 strains) and Salmonella spp. (8 strains) were isolated from poultry and clinical samples. In order to assess whether these bacteria had active efflux pumps, ethidium bromide accumulation assays were performed. Extrusion of the active components of three commercial household agents (triclosan, sodium salicylate, and ortho-phenylphenol) by efflux pumps was tested using spectrophotometric accumulation assays. In order to simulate the kitchen environment, in-use disinfectant testing using the commercial household agents was performed to determine changes in their efficacy due to antibiotic resistance. Active efflux pump activity and extrusion of all three active ingredients was observed only in the antibiotic resistant organisms. The antibiotic sensitive bacteria were also more susceptible than the resistant isolates to the household antimicrobial agents at concentrations below that recommended by the manufacturer. These resistant bacteria could potentially be selected for and result in hard to treat infections.

Contamination of chicken carcasses in Gauteng, South Africa, by Salmonella, Listeria monocytogenes and Campylobacter.

The presence of the foodborne pathogens, Salmonella spp., Listeria monocytogenes and Campylobacter spp., on 99 fresh and frozen chicken carcasses sourced from various retailers in Gauteng, South Africa, was investigated. Using culture methods, 60.6% of the carcasses were found to be contaminated with one or more pathogens, with 19.2%, 19.2% and 32.3% of the carcasses being found to harbour Salmonella, L. monocytogenes and Campylobacter, respectively. The extent of contamination with one or more pathogens was not significantly different (p>0.1) between fresh or frozen samples or between samples from butcheries, supermarkets or street vendors. Significantly more (p<0.1) fresh carcasses from butcheries than from other outlets were contaminated with Salmonella, while more fresh carcasses from supermarkets were contaminated with Campylobacter. The proportion of carcasses with L. monocytogenes from all sources were similar. Polymerase chain reaction (PCR) results indicate an even higher extent of pathogen contamination, but the PCR techniques need to be further refined before they can be used routinely.

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.

Candida parapsilosis detected in TPN using the BacT/Alert system and characterized by randomly amplified polymorphic DNA.

Candida parapsilosis was detected in environmental swabs and batches of total parenteral nutrition (TPN) products after routine monitoring. The isolates were analysed using randomly amplified polymorphic DNA (RAPD) to determine clonality and establish the most likely source of contamination. Of 20 isolates analysed, 18 were indistinguishable clonally and were found to be associated with particular work stations. The application of regular testing using a system such as the BacT/Alert, and molecular studies for epidemiological analysis, is of benefit to producers of medical products such as TPN to ensure patient safety.

Prevalence survey of healthcare-associated infections in Argentina; comparison with England, Wales, Northern Ireland and South Africa.

BACKGROUND: Prevalence surveillance methodology is the systematic observation of the occurrence and distribution of healthcare-associated infections (HCAIs) so that appropriate actions can be taken. AIM: The objectives of a prevalence survey with an international validated methodology were to determine the prevalence of HCAIs for the first time in Argentina, and to provide data which could be used for international benchmarking. METHODS: In 2008, an HCAI prevalence survey was carried out in 39 hospitals in seven of 23 provinces in Argentina, with methodology identical to that employed by the Hospital Infection Society in the third prevalence survey of HCAIs in acute hospitals in the British Isles. Data collected were processed and analysed at the Northern Ireland Healthcare-Associated Infection Surveillance Centre at Belfast. FINDINGS: A total of 4249 patients were surveyed; 480 of these had at least one HCAI, resulting in a prevalence of 11.3% of patients. Male prevalence was 13.6% and female 9.0%. The most common HCAIs were pneumonia (3.3%), urinary tract infection (3.1%), surgical site infection (2.9%), primary bloodstream infection (1.5%), and soft tissue infections (1.2%). Among the 1027 patients who underwent surgery, the prevalence of surgical site infection was 10.2%. The prevalence of meticillin-resistant Staphylococcus aureus was 1.1%, accounting for 10.0% of all HCAI isolates. The results for Argentina show higher HCAI rates compared with corresponding findings for England, Wales, Northern Ireland and South Africa. CONCLUSION: This survey will contribute to the prioritization of resources and help to inform Departments of Health and hospitals in the continuing effort to reduce HCAIs.

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.

Antimicrobial susceptibility of methicillin-resistant Staphylococcus aureus isolates from South Africa.

OBJECTIVE: Trends in the antibiotic susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) are regularly investigated in many countries, but minimal countrywide data are available for South Africa. The aim of this study was to describe the antibiotic susceptibility patterns of MRSA isolates collected in South Africa. DESIGN: Susceptibility testing of 248 MRSA isolates collected from 15 National Health Laboratory Services (NHLS) and 8 private laboratories against 17 antibiotics was performed using the disc diffusion method. Demographic data were collected and correlated with antibiotic resistance patterns. RESULTS: Antibiotic resistance of MRSA to erythromycin, tetracycline, trimethoprim/sulfamethoxazole, gentamicin and ciprofloxacin ranged between 55% and 78%, while all isolates were susceptible to teicoplanin, linezolid, vancomycin and quinopristin/dalfopristin. A significant difference in the resistance pattern of the isolates towards certain antimicrobial agents was identified among adults and children, as well as between isolates collected from the private and NHLS laboratories. CONCLUSION: This is the first extensive report on the antimicrobial susceptibilities of South African MRSA isolates. These data can assist treatment decisions and form a baseline for further surveillance.

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.

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.

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.