Report into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at Netcare St. Augustine’s Hospital

This report presents the findings and recommendations of an investigation into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at St. Augustine’s Hospital in Durban, South Africa. The investigation began on 4 April after the identification of a number of confirmed COVID-19 cases and three deaths at the hospital. Investigation methods included medical record reviews, ward visits, and interviews with health care workers and management. A detailed timeline of patient cases was constructed to generate hypotheses as to the spread of infection through the hospital. In addition, DNA sequencing of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) nucleic acid extracted from nasopharyngeal and oropharyngeal swab samples was performed and phylogenetic analysis was conducted.

Report into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at Netcare St. Augustine’s Hospital

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Between 9 March and 30 April 2020, 119 confirmed cases were identified at St. Augustine’s Hospital (39 patients and 80 staff). The 80 staff represent approximately 5% of all staff tested for SARS-CoV-2. The most plausible hypothesis is that there was a single introduction of SARS-CoV-2 to the hospital on 9 March, most likely as a result of transmission from a patient attending the Emergency Department for investigation of COVID-19 to another patient present in the ED at the same time who was then admitted to the cardiac intensive care unit with a suspected stroke. The infection then spread rapidly through the hospital, involving patients on at least five wards. The spread through the hospital was facilitated by the frequent movement of patients between and within wards. The evidence suggests that indirect contact and fomite transmission were likely to be the predominant modes of patient to patient transmission. We hypothesize that the main outbreak also seeded smaller outbreaks at a local nursing home (four additional cases) and at the National Renal Care outpatient dialysis unit on the hospital campus (nine additional patient cases and eight additional staff cases). Overall, we estimate that up to 135 infections may have been nosocomially acquired as a result of the single introduction of the virus to the hospital, accounting for about 14% of all cases in KwaZulu-Natal reported by 30 April. Phylogenetic analysis supports the main hypothesis of a unique introduction followed by widespread transmission in the hospital. All of the 18 SARS-CoV-2 genomes produced (nine from patients and nine from health care workers) clustered together with limited genetic diversity. All of the sequences belong to the A2a clade associated with infections from Europe.

Fifteen of the 39 patients infected with SARS-CoV-2 in the main outbreak died (case fatality rate 38.5%). Most of the deaths were in elderly patients with multimorbidity. In most cases, a medical decision was taken not to intubate and ventilate because of the comorbidities and poor prognosis. There was no evidence that, once these patients had been infected with SARS--CoV-2, any specific intervention would have prevented their death. With the benefit of hindsight, there were a number of opportunities where earlier problem recognition and earlier intervention might have limited the extent of the outbreak. The first opportunity was with the unexplained fever of a 81-year-old female on 13 March following a transient ischaemic attack; the second was when a 46 year-old female was readmitted with an acute respiratory illness on 21 March; the third was when the 81 year-old female was readmitted with severe pneumonia on 22 March; and the fourth was with the first confirmed case in a health care worker (a nurse from cardiac ICU), reported on 23 March. Earlier recognition of possible COVID-19 infection in the patients, leading to earlier isolation, tracing of potential sources of infection, and appropriate management of exposed contacts could potentially have averted infections and limited onward transmission. Earlier investigation of the first health care worker case to identify potential sources of infection within the hospital could also have uncovered the problem at an earlier stage.

This outbreak highlights how easily and rapidly SARS-CoV-2 can spread through a hospital, exposing weaknesses in respiratory virus infection prevention and control (IPC). It underlines that personal protective equipment (PPE) is only one component of a comprehensive approach to IPC and does not replace the need for good IPC systems and practices. The extent of the outbreak underlines the potential for nosocomial transmission to be a major amplifier of transmission in South Africa. There is no reason to believe that a similar outbreak cannot and will not happen in other hospitals and institutions in South Africa, in both the private and public sector.

To reduce the risk of similar outbreaks, we need to strengthen infection prevention and control systems and practices throughout our hospitals. Management must promote a culture that IPC is everyone’s responsibility and that everyone has a role to play. Hospitals need to establish separate zones (and separate entry points) for people who might have COVID-19 and people who are unlikely to have COVID-19. There needs to be vigilance throughout the hospital for acute respiratory illness, especially in green zones where patients considered low risk for COVID-19 have been admitted. Training on COVID-19, especially on infection prevention & control, should be mandatory for all staff and implementation of IPC practices should be monitored closely. The importance of hand hygiene needs to be continually emphasised and hand hygiene practices need to be monitored. Environmental cleaning practices need to be aligned with the national COVID-19 IPC guidelines and the national IPC framework manual. Cleaning should be monitored closely using visual inspection and fluorescent markers. The importance of regular cleaning of surfaces and of medical equipment between patient contacts to reduce fomite transmission should be highlighted to all staff. Physical distancing within the hospital should be promoted through the use of floor markings and prominent signage. Consideration should be given to weekly PCR testing of all frontline staff and the early use of DNA sequencing and phylogenetic analysis to investigate potential nosocomial transmission. The COVID-19 epidemic is an unprecedented challenge for the health system and the community in South Africa. We hope that lessons learnt from this nosocomial outbreak can be used to highlight areas that can be strengthened across the private and public health system, so as to prevent nosocomial outbreaks becoming a major amplifier of COVID-19 transmission.

Short Video of the SARS-CoV-2 Genotyping Process at KRISP:

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KRISP and UKZN Foundation campaign to support South African Scientists on the front line

News date: 2020-05-22


KRISP has been created by the coordinated effort of the University of KwaZulu-Natal (UKZN), the Technology Innovation Agency (TIA) and the South African Medical Research Countil (SAMRC).

Location: K-RITH Tower Building
Nelson R Mandela School of Medicine, UKZN
719 Umbilo Road, Durban, South Africa.
Director: Prof. Tulio de Oliveira