SAHR_17.10.22_Chapter 8 HEALTH EMERGENCIES, AMR AND COVID-19 RESPONSE

Chapter 8 HEALTH EMERGENCIES, AMR AND COVID-19 RESPONSE

Kerrigan McCarthy, Kamy Chetty, Marc Mendelson, Patrick Moonasar, Tsakani Furumele, Olga Perovic, Raveen Naidoo Introduction Health emergencies, defined as ‘any situation whose scale, timing or unpredictability threatens to overwhelm routine capabilities’1, cause disruption and derail the usual functioning of health systems, and thus set back gains made towards universal health care2. In this chapter, we evaluate why disaster risk reduction and preparedness foster health system resilience. We reflect on the global context emerging from the 2012–2014 Ebola outbreak in West Africa which set the international agenda for emergency preparedness and response in South Africa, 2015–2020. We then review South African preparedness efforts, drawing extensively from South Africa’s participation in, and findings and outcomes of the joint external evaluation of adherence to the International Health Regulations (IHR) 2005. We identify health emergencies that took place from 2015–2020 and discuss in some depth two South African health emergencies that unfolded over this time. We reflect on health system responses to the unfolding COVID-19 pandemic over 2020, illustrating how these drew on experience gained by stakeholders in earlier South African emergencies. Finally, we offer pointers to support strengthening South Africa’s emergency preparedness and response over the next five years.

THE SOUTH AFRICA HEALTH REFORMS 2015-2020

Resilient health systems need to incorporate disaster risk reduction, emergency preparedness and response systems Not only do health emergencies disrupt services, but they may also precipitate crises in other areas of the health system, and/or lead to a broad range of poor health outcomes in unrelated areas, sometimes for extended periods after the emergency2. Typically, health emergencies disproportionately affect disadvantaged groups who may have limited resources or access to supportive services3. It is the responsibility of public health systems to reduce risks and the impact of emergencies in the short and longer term2. ‘Preparedness’ is defined as ‘the capacity of the public health and health care systems, communities and individuals to prevent, protect against, quickly respond to and recover from health emergencies, particularly those whose scale, timing or unpredictability threatens to overwhelm routine activities’1. With adequate preparation, disruptions can be minimised and their impact mitigated through actively managed and effective preventive programmes (such as immunisation), policy and legislative frameworks and through coordinated response efforts. Effective disaster risk management through investment in preparedness contributes to sustainable development4.

Global context in the preparedness and response to health emergencies circa 2012–2015 In the wake of the 2003 SARS crisis, the World Health Assembly revised the IHR (2005)7 and obtained commitment by member states to create and sustain systems for health emergency preparedness and response by 20128. This included development and adherence to ‘core capacities’9 (Table 8.1) grouped around prevention, detection response, other IHR-related hazards and points of entry. However, the process was severely criticised8. By 2014, only 78 out of 196 member states had submitted their IHR core capacity self-assessments to the WHO10. The self-assessment process did not require external verification, allowing countries to report their capacities without accountability8. Countries unable to implement core capacities because of weaker infrastructure and human resource constraints were not provided with financial or other support8. International leadership to prioritise capacity development of member states was weak8. In the wake of these criticisms, the WHO in consultation with member states developed the joint external evaluation (JEE) process to support assessment of member state adherence to IHR, identify areas that require strengthening and develop structured plans to achieve adherence11. Key components of the JEE were self-evaluation, a ‘whole-of-government approach’, peer review and voluntary external evaluation. By 2017, the process had gained considerable momentum and widespread acceptance, with participating countries identifying new ways of collaborating, and ownership over the process12.

Following the lessons learnt from the emergency response to the earthquake in Haiti, in January 2010, the WHO implemented the Emergency Medical Team (EMT) Initiative13. The purpose of the EMT initiative is twofold: firstly, to improve the timeliness and quality of health services provided by national and international EMTs; and secondly, to enhance the capacity of the affected nations health systems in

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leading the activation and coordination of this response in the immediate aftermath of a disaster, outbreak and/or other emergency. Teams may include public health expertise and logistics support either within the team or as specific public health or logistics rapid response teams. Presently, this initiative is at various stages of accreditation by the WHO globally. South Africa has subscribed to the general principles of the EMT Initiative, however, the establishment and accreditation by WHO has been delayed by the current COVID-19 pandemic.

Included in the IHR (2005) ‘core capacities’ is the requirement to create and utilise emergency operating centres (EOC). The concept of a public health EOC was developed by the WHO following the 2003 SARS crisis, and refined over subsequent years with the creation of a framework and handbook for EOC14,15. EOCs use the incident management system (IMS) which is a scalable, flexible and adaptable, command-and-control system for coordinating resources and responses during public health emergencies. Following the successful functioning of the EOC in Nigeria during the West African Ebola crisis, member states were encouraged to create these centres and implement the IMS during EOC activations16.

By October 2021, 47 out of 52 AFRO region countries had submitted JEE reports17. Critical evaluation of the JEE process seems to show high levels of concordance between JEE scores, assessments and outbreak response18,19.

Table 8.1 Core capacities required to implement IHR, and South African scores during the JEE process, 201720. (Scores: 1=No capacity; 2=Limited capacity; 3=Developed capacity; 4=Demonstrated capacity; 5=Sustainable capacity)

Core Capacity

Indicators

Score

Recommendations and areas for strengthening

1

Legislation, laws, regulations, administrative requirements, policies, or other government instruments in place are sufficient for implementation of IHR (2005)

2

Assess legal framework and policies to ensure all are aligned with IHR (2005); Enact IHR and NAPHISA Bills; Map national health risks and resources with other departments/sectors.

National legislation, policy and financing

The state can demonstrate 2 that it has adjusted and aligned its domestic legislation, policies, and administrative arrangements to enable compliance with IHR (2005) 2

IHR coordination, communication and advocacy

Functional mechanism is established for the coordination and integration of relevant sectors in the implementation of IHR

139

4

Evaluate and strengthen the INR national focal point to support IHR coordination, communication and advocacy within and across sectors; Conduct simulation exercises or evaluate past events.

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3

4

Antimicrobial resistance

Zoonotic diseases

Antimicrobial resistance (AMR) detection

3

Surveillance of infections caused by antimicrobial-resistant pathogens

3

Health care-associated infection (HCAI) prevention and control programmes

1

Antimicrobial stewardship activities

2

Surveillance systems in place for priority zoonotic diseases/pathogens

4

Veterinary or animal health workforce

4

Mechanisms for responding to infectious and potential zoonotic diseases are established and functional

4

5

Food safety

Mechanisms for multisectoral collaboration are established to ensure rapid response to food safety emergencies and outbreaks of foodborne diseases

6

Biosafety and biosecurity

Whole-of-government 3 biosafety and biosecurity system is in place for human, animal and agriculture facilities

7

Immunisation

3

Biosafety and biosecurity training and practices

3

Vaccine coverage (measles) as part of national programme

3

National vaccine access and delivery

5

140

Develop and implement a ‘One Health’ national AMR strategy; Develop and implement a national multisectoral plan for HCAI and AMR prevention.

1

Develop and approve a national policy for ‘One Health’; Conduct training and joint simulation exercises on recognition and response to zoonotic emergencies; ensure ongoing improvement through evaluation of simulation exercises and past responses; Strengthen laboratory coordination between animal and human health; ensure training of veterinarians in FETP courses.

Conduct monitoring and evaluation of places/institutions with high risk for foodborne outbreaks; Link surveillance and response staff and focal points for food safety and animal health; Conduct multisectoral risk assessment and management of foodborne outbreaks; ensure ongoing improvement through evaluation of simulation exercises and past responses with documentation of lessons learnt; strengthen timeliness of reporting and responses.

Establish a national biosafety and biosecurity committee; Review and harmonise legislation and policies; Develop a ‘dual use’ policy; Strengthen and resource governmental oversight activities; Consolidate national lists of pathogens and laboratories; standardise and deliver training in biosafety and biosecurity.

Fully implement ‘reach every district’ strategy in provinces through resourcing national EPI oversight, developing health facility micro plans including tracking of defaulters, involving the private sector; Strengthen EPI disease surveillance; Strengthen data quality through validation of coverage data with an EPI coverage survey, including public sector data.

Health emergencies, AMR and Covid-19 response

8

9

10

11

12

13

National laboratory system

Real-time surveillance

Reporting

Laboratory testing for detection of priority diseases

5

Specimen referral and transport system

4

Effective modern point-ofcare and laboratory-based diagnostics

3

Laboratory quality system

3

Indicator- and event-based surveillance systems

3

Interoperable, interconnected, electronic real-time reporting system

2

Integration and analysis of surveillance data

4

Syndromic surveillance systems

4

System for efficient reporting to FAO, OIE and WHO

3

Reporting network and protocols in country

3

Workforce development Human resources available to implement IHR core capacity requirements

Preparedness

Immunisation

3

FETP1 or other applied epidemiology training programme in place

4

Workforce strategy

2

National multi-hazard public health emergency preparedness and response plan is developed and implemented

2

Priority public health risks and resources are mapped and utilised

3

Capacity to activate emergency operations

2

EOC operating procedures and plans

2

Emergency operations programme

4

Case management procedures implemented for IHR relevant hazards

4

141

Strengthen ICT systems to link laboratory information systems with public health surveillance systems; increase availability of basic testing and improve turnaround times; link NHLS, strengthen NHLS procurement and supply chain mechanisms; veterinary and private sector laboratories; establish a national laboratory quality framework; support pathology residents and intern scientists/ technicians to complete training.

Resources for NMC at provincial level should be increased; Submission of surveillance data should be electronic; Event-based and indicator-based surveillance needs to be interoperable and linked; data collation at each level should be strengthened; community-based surveillance should be strengthened.

Simulation exercises should be done; Electronic sharing of surveillance and other data between animal and human health sectors needs to be made available.

Assess public health workforce requirements, map existing resources and include mechanisms for increasing workforce in HRH strategy; Fast-track institutionalisation of epidemiology as a specialisation; Strengthen epidemiology training through provision of courses and finances.

Develop one overarching multisectoral national public health emergency preparedness and response plan; conduct a national risk assessment; prioritise development of the public health emergency committee; advocate for full-time operation of NATHOC. Establish a legal framework with clear roles and responsibilities of EOC and its relationship with the National Disaster Management Centre; Increase human resources of PHOC and conduct training and simulation using the IMS; update EOC SOPs, cascade EOC/IMS to lower levels.

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14

Linking public health and security authorities

Public health and security 4 authorities (e.g. law enforcement, border control, customs) are linked during a suspected or confirmed biological event

Conduct national emergency scenarios and simulation exercises with all stakeholders; ensure procedures address interdepartmental cooperation in response to biological incidents, establish communication channels during non-crisis events; review policy on management of chemical, biological, radiation and nuclear incidents.

15

Medical countermeasures and personnel deployment

System in place for sending and receiving medical countermeasures during a public health emergency

2

System in place for sending and receiving health personnel during a public health emergency

2

Finalise a comprehensive plan to send and receive medical countermeasures and personnel; review experiences and conduct simulation exercises of the above; examine the regulatory framework for sub-regional exchange of medical countermeasures and personnel.

Risk communication systems (plans, mechanisms, etc.)

3

Internal and partner communication and coordination

3

Public communication

4

Communication engagement with affected communities

3

Dynamic listening and rumour management

4

Routine capacities established at PoE

4

16

17

Risk communication

Points of entry (PoE)

4 Effective public health response at PoE 18

19

Chemical events

Radiation emergencies

Mechanisms established and functioning for detecting and responding to chemical events or emergencies

3

Enabling environment in place for management of chemical events

3

Mechanisms established and functioning for detecting and responding to radiological and nuclear emergencies

2

Enabling environment in place for management of radiation emergencies

2

1

Develop national-level risk communication preparedness and response plans including surge support and sustainability; perform risk communication simulation exercises.

Review HR capacity for PoE; finalise memoranda of understanding for safe referral and transport of ill travellers; review, evaluate and disseminate public health contingency plans for all sectors at PoE and establish mechanisms to improve compliance.

Develop mechanism for timely and systematic information exchange between appropriate chemical units, surveillance units and other relevant sectors about urgent chemical events and potential chemical risks and their response; Conduct simulation exercises; formalise agreements between government and private institutions to collaborate and share information.

Finalise comprehensive national plan for detection, assessment and response to radiation emergencies; Link radiological and nuclear regulatory bodies with DoH/IHR NFP; Establish improved health surveillance and case management for radio-nuclear emergencies.

See section on antimicrobial resistance below. IHR=International Health Regulations (2005); FAO=Food and Agriculture Organisation of United Nations, OIE=World Organisation for Animal Health; ICT=information and communication technology; FETP=Field epidemiology training programme; NMC=notifiable medical conditions; IMS=Incident Management System

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South African preparedness and response to health emergencies 2015–2020 South Africa entered 2015 with the West African Ebola crisis abating, and finding itself equipped with legal, policy, laboratory and public health structures well able to support health emergencies.

The right to health and the broader legal framework for public health were ensured by the Constitution21, the National Health Act 61 of 200322, including the notifiable medical conditions regulations23, the National Health Laboratory Services Act24 and the Disaster Management Act25. The International Health Regulations (IHR) Bill26 had been proposed in 2013 and was awaiting enactment.

South African structures for health emergencies in 2015 included the National Joint Operational and Intelligence Structure (NATJOINTS) and the associated National Joint Operations Centre (NATJOC), the Multisectoral National Outbreak Response Team (MNORT), the National Disaster Management Centre (NDMC) and the National Institute of Communicable Diseases’ (NICD) Public Health Emergency Operation Center (PHEOC). NATJOINTS is a structure convened by the South African Police Service with the task of securing lives and livelihoods from internal and external threats, including political and social unrest, environmental hazards and health emergencies. NATJOINTS has representation from all tiers of government including health. This structure is replicated in each of the nine provinces by the Provincial Joint Operational and Intelligence Structures and Provincial Joint Operations Centres. In addition, local government authorities provide for coordination of disasters including health emergencies at municipal level as provided for under the Disaster Management Act 57 of 2002. The MNORT was convened in the late 1990s and constituted with the aim of supporting multisectoral collaboration and response to communicable disease outbreaks. Monthly MNORT meetings were attended by national and provincial health authorities (including those responsible for communicable diseases, tuberculosis (TB), HIV, maternal and child health, environmental health and port health), laboratory services, animal health, civil aviation, international relations and cooperation, private sector hospitals and emergency medicine. A significant development was the signing of a memorandum of agreement between the NDoH and the NHLS/NICD to delegate responsibility for creation of an EOC in January 2015. In 2015, the NICD employed an EOC manager, developed operating procedures including criteria for activation and introduced the IMS. The NICD was tasked with development of an electronic notifiable medical conditions surveillance system (the NMC-SS) through a memorandum of agreement between the NDoH and the NHLS in October 2015.

At a provincial level, responsibility for communicable disease control and response was assigned to the Communicable Disease Control Coordinator aided by a data capturer, who worked with the Expanded Programme of Immunisation team, and the vertical TB and HIV programmes where necessary. The NICD Outbreak Response Unit27 provided technical support to the provinces in event of outbreaks, often providing staff including field epidemiologists with training in a crisis.

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Over the course of the 2013–2016 West African Ebola outbreak, these structures, and a new structure, the National Health Operations Centre (NATHOC) were integrally involved in supporting South African health responses, which included direct assistance through provision of laboratory diagnostics28, restriction of non-essential travel to the affected region, screening of returning travellers29, training of health care workers in recognition of Ebola Virus Disease (EVD) cases, health system readiness through designation of hospitals for management of EVD cases and health promotion.

A collaborative process commenced in 2016 when the Director General Health initiated a JEE of IHR preparedness in accordance with IHR (2005). The process required an internal self-evaluation, which was to be reviewed collaboratively with external partners in November 201711. Scores and recommendations of the JEE team are tabulated in Table 8.1. The JEE process identified a key weakness in actualising IHR requirements at a legislative and resource level in that the IHR Bill was yet to be enacted, and that IHR functions at the NDoH were under-resourced (Table 8.1, Capacity 2). A second key weakness was identified as the absence of integration of different response sectors, institutions and structures (including the NDMC, NATHOC and EOC) in an overarching legislative and policy framework (Table 8.1, Capacity 1) and that there was no integrated and overarching emergency response plan (Table 8.1, Capacity 12 and 13).

In 2017, regulations relating to the surveillance and control of notifiable medical conditions regulations30 were updated to include an expanded list of notifiable conditions (including listeriosis and antimicrobial resistant organisms), and introduced compulsory reporting by diagnostic laboratories, medical schemes and clinicians.

Notable health emergencies 2015–2020 Table 8.2 lists communicable disease events and health emergencies that occurred in 2015–2020. NATHOC continued to operate in 2015 until restrictions on travel to West Africa during the Ebola outbreak eased. The NICD’s EOC was activated on two occasions: in 2017 to support relocation of mental health care users following the Life Esidimeni crisis in Gauteng province, and in 2018 with the support of the WHO to respond to a national listeriosis outbreak following contamination of a ready-to-eat (RTE) meat production facility in Polokwane, Limpopo Province31.

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Table 8.2 Significant communicable disease events and health emergencies, 2015–2020 Date

Location

April 2015

Event

Nature of event

Affected persons

Scope of response

Northern Cape Diarrhoeal disease

CD

>600

NCP DoH, NICD

July 2015

KwaZulu-Natal Diphtheria outbreak

CD

15

KZN DoH, NICD, NDoH

August 2015

Western Cape

Leptospirosis

CD

2

WCP DOH, NDoH, NICD

October 2015

Gauteng

Enteroviral meningitis

CD

>30

Gauteng DoH

November 2015

Lesotho

Dysentery outbreak

CD

>500

Technical advice to Kingdom of Lesotho

May 2016

Eastern Cape

XDR-TB

CD

>100

ECP DoH, NICD

July 2016

Eastern Cape

Influenza

CD

>200

ECP DoH, NICD

July 2016

KwaZulu-Natal Diphtheria outbreak

CD

2

KZN DoH, NICD, NDoH

August 2016

Eastern Cape

Clostridium difficile

CD

8

Local hospital level

December 2016

KwaZulu-Natal Norovirus outbreak

CD

>600

KZN DoH, NICD

January 2017

Gauteng

Sindbis

CD

56

NICD

January 2017

Western Cape

Measles

CD

22

WCP DoH, NICD

February 2017

Gauteng

Life Esidimeni

Health Services

>1 500

GDoH, NDoH, NICD

June 2017

Western Cape

Knysna wildfire

Fire

>10 000

Fire Services, WC EMS

June 2017

Gauteng

Measles

>200

Gauteng DoH, NICD

June 2017

Limpopo, Gauteng

H5N8 avian influenza outbreak

CD

>50

Multisectoral, led by DAFF

August 2017

Western Cape

Diphtheria outbreak

CD

4

WCP DoH, NICD

August 2017

South Africa

Listeriosis

CD

>1 500

NDoH, NICD, WHO

September 2017

KwaZulu-Natal Measles

CD

>30

KZN DoH

October 2017

Gauteng

Foodborne illness

CD

>90

Gauteng DoH, NICD

October 2017

Gauteng

Group A streptococcus CD with necrotising fasciitis

>20

Gauteng DoH

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Date

Location

Event

Nature of event

Affected persons

Scope of response

November 2017

Limpopo

Typhoid

CD

>100

Limpopo DoH, NICD

November 2017

Western Cape, Eastern Cape

Enteroviral meningitis

CD

>3 400

WCP and ECP DoH, NICD

November 2017

Gauteng

Staphylococcus aureas

CD

>350

NICD and institution

December 2017

Western Cape

Pseudomonas contamination of water

CD

>2 000

WCP

January 2018

Western Cape

Vaccine-derived poliovirus

CD

1

WCP, NDoH, WHO, NICD

February 2018

KwaZulu-Natal Cholera case

CD

1

Single case, led by NDoH, KZN DoH and NICD

April 2018

Gauteng

Multidrug resistant Klebsiella

CD

>50

Gauteng DoH, NICD

July 2018

Mpumalanga

Wasterborne illness outbreak

CD

>1 500

MPU DoH, NICD

October 2018

Gauteng

Vaccine-derived poliovirus

CD

1

Gauteng DoH, NDoH, WHO, NICD

October 2018

Eastern Cape

Pertussis

CD

>250

ECP DoH, NICD

October 2018

Gauteng

Foodborne illness outbreak

CD

>200

Gauteng DoH

November 2018

Limpopo, Gauteng

CD

Imported from Zimbabwe, led by <10 cases Limpopo and Gauteng DoH

Cholera cases

Government response to request for health and humanitarian aid to affected neighbouring countries

Gauteng, Mozambique, Malawi, Madagascar and Zimbabwe

Cyclone Idai

May 2019

Gauteng

Presidential Inauguration

Mass gath>35 000 ering

All government departments

May 2019

North West Province

Mumps

CD

>150

NW DoH, NICD

Tropical Storm Eloise

Flooding, CD

>175 000

NDMC, NDoH, affected provinces Health and Local Government structures

March 2019

January 2021

Limpopo, Gauteng, Mpumalanga, Free State, Northern Cape, North West

Flooding, CD

<2.2 million

Gauteng DoH, NDoH, NICD

*DAFF=Department of Agriculture, Forestry and Fisheries

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Listeriosis outbreak case study Following alerts from public hospitals of increases in listeriosis cases in July and August 2017, an outbreak investigation was initiated by the NICD. Molecular typing identified an outbreak clone ‘ST6’. A total of 937 cases were reported during the outbreak period from June 11, 2017 until April 7, 2018, with case numbers peaking at 41 per week in mid-November 2017 (epidemiologic week 46)31, making the outbreak the largest global listeriosis outbreak ever reported32. In March 2018, the outbreak strain was found to be contaminating an RTE meat production facility in Polokwane, Limpopo province.

Cases decreased dramatically after recall of the implicated products on March 4, 2018.

In April 2018, the NDoH activated the NICD EOC. On 28 March 2018, the WHO increased their internal risk assessment of the listeria outbreak from grade 1 to grade 2, making provision for deployment of a WHO Country Office incident management team (IMT), repurposing of the WHO staff and deployment of additional resources and surge teams (including food safety, risk communications and EOC experts and epidemiologists). The joint RSA-WHO IMT, described in Figure 8.1a, coordinated drafting and implementation of an emergency response plan (Figure 8.1b).

Activities supported by the IMT included real-time surveillance and molecular typing of all Listeria monocytogenes (Lm) isolates and prospective patient food-history interviews to support early detection of clusters, strengthening of food and environmental testing for Lm through development and validation of test methodology, training of almost 900 environmental health practitioners in all South African health districts in inspection procedures, food safety systems, legislative aspects of food control, inspection of all RTE production facilities (n=158), amendment of food legislation to require RTE producers to be Hazard Analysis Critical Control Points (HACCP) certified by externally accredited agencies, and health promotion and risk communication activities. The outbreak and response efforts illustrated the impact and capacity of collaborative, multisector and international efforts to strengthen food safety, to safeguard public health and prevent future listeriosis outbreaks.

Figure 8.1b Phase 1, 2 and 3 of the listeriosis public health emergency response plan to halt the listeriosis outbreak and prevent future outbreaks

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Figure 8.1a Structure and functions of joint WHO-RSA listeriosis incident management team.

Antimicrobial resistance Antimicrobial resistance (AMR) has been identified as a ‘global crisis that threatens a century of progress in health and achievement of the Sustainable Development Goals’33. Although described as an ‘invisible pandemic’ which is evolving over the last 50 years, AMR fulfils the definition of a health emergency because it has capacity to overwhelm our existing armamentarium of lifesaving treatments for common bacterial infections, and may result in 10 million deaths per year by 2050 if unchecked34. Only in May 2015, the 68th World Health Assembly adopted the Global Action Plan (GAP) to combat AMR using the ‘One Health’ approach. By introducing the ‘One Health’ concept into the GAP, WHO succeed in engaging the spectrum of sources of AMR, namely veterinary, agricultural and environmental sources in the fight against AMR. Also in 2015, the WHO Global Antimicrobial Resistance and Use Surveillance System (GLASS) was launched with the aim of monitoring AMR and consumption and use (AMC/U) globally so as to support strategic responses to contain AMR. Presently, an AMR indicator (the proportion of bloodstream infections due to selected types of resistant pathogens) is included in the Sustainable Development Goals (SDGs) linked to target 3.d: ‘Strengthen the capacity of all countries, in particular developing countries, for early warning, risk reduction and management of national and global health risks’35.

Already in 2011, in a situation analysis, South Africa recognised a quadruple burden of resistant infectious disease, including multidrug-resistant tuberculosis, drug-resistant HIV, resistant malaria and antibacterial/antifungal resistance36. In October 2014, the Minister of Health launched the National AMR Strategic Framework, which was updated in 2018 to increase the focus on a One Health

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response37. This current framework spans seven years (2018–2024) and outlines the country’s plan for the management of AMR, the improvement of patient outcomes, and mitigation strategies for AMR in animal and environmental health (Table 8.2).

Notable achievements over 2015–2020 include: convening of a ministerial advisory committee (MAC) on antimicrobial resistance20, developing the framework for antimicrobial governance regulation, and utilisation at national, provincial, institutional and district levels38, scaling up of AMR surveillance programmes39,40, development of national training centres and train-the-trainer programmes to support provinces with limited stewardship human resources, implementation of facility and provincial antimicrobial stewardship programmes41, reporting of AMR and antimicrobial usage data to WHO’s GLASS initiative42 (from 2016 onwards), and a toolkit to enable antimicrobial stewardship in South African hospitals43. The surveillance report issued by the AMR MAC in 2018 represents currently available information relating to AMR in humans and antimicrobial consumption in animals and humans in South Africa44.

The current South African AMR surveillance system in humans was built through collaboration between public and private sector laboratory services and reports on AMR in blood cultures for the WHO-required pathogens (Klebsiella pneumonia, E. coli, S. aureus, P. aeruginosa, A. baumannii, and enterococci). In addition, infection prevention and control (IPC) is a cornerstone for combating healthcare-associated infections and AMR. The South African IPC framework45 and manual are linked to the AMR programme and endorsed by the MAC. Table 8.3 Strategic framework and activities to preserve effectiveness of antimicrobials, improve use of antibiotics and strengthen effective management of antibiotic resistant organisms according to the National AMR Strategy Framework37 1

Strategic objective

Activities

Strengthen interdisciplinary efforts through One Health governance structures

Establish an interdisciplinary national advisory committee Establish governance structures at operational levels of province, district, health establishments and veterinary services

2

Improving diagnostics to guide patient Provide timely microbiological data to allow delivery of safer, more and animal treatment effective and efficient treatment

3

Optimise surveillance and early detection of AMR

Strengthen surveillance of local and national resistance patterns and antimicrobial use Develop early warning systems of sentinel organisms and outbreaks Participate in international databases on AMR and antimicrobial use

4

Enhance infection prevention and control, and biosecurity to prevent spread of resistant microbes amongst patients, between animals, farms and countries

Prevent new infections through vaccination programmes and effective water, sanitation and hygiene (WASH) services Prevent and control the spread of resistant micro-organisms in humans and health institutions Strengthen and monitor biosecurity and hygiene from farm to retailer Ensure environmental health and water quality monitoring

5

Promote appropriate use of antimicrobials in human and animal health

Ensure access to safe, effective and affordable antimicrobials Institutionalise antimicrobial stewardship in human and animal health

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Organisation of responses to COVID-19 Shortly after the identification of SARS-CoV-2 in Wuhan on the 5th of January 202046, preparedness activities commenced in South Africa with activation of the EOC (30 January 2020) and convening of an incident management team (IMT). Following detection of the first South African laboratory-confirmed case of SARS-CoV-2 on March 5, 2020,47 an ‘inter-ministerial committee’ comprising the entire cabinet was formed to coordinate government responses on 15 March 2020 and named the ‘National COVID-19 Command and Control Council’ (NCCC)48. A National State of Disaster was declared on 18 March 202049. On 27 March a nationwide ‘level 5’ lockdown was implemented50, halting non-essential business and confining all persons to their residences until easing of restrictions on 30 April 2020. Within the first eight weeks following importation of SARS-CoV-2, over 270 000 diagnostic tests had been conducted, and over 7 800 cases identified51. A National Plan for COVID-19 Health Response was formally adopted in May 202048, and comprised nine strategic priorities, namely: 1) to provide effective governance and leadership; 2) to strengthen surveillance and strategic information; 3) to augment health systems readiness including emergency medical services; 4) to enhance community engagement; 5) to improve laboratory capacity and testing; 6) to clarify care pathways; 7) to scale-up infection prevention and control measures, 8) to boost capacity at ports of entry; and 9) to expedite research and introduce therapeutics, diagnostics and vaccines.

Pre-existing health structures to support outbreak response were configured around the NCCC (Figure 8.2), and new structures were created, namely the COVID-19 Ministerial Advisory Committee, the project management office (responsible for finance and administration) and the COVID-19 Ministerial Advisory Committee. The MNORT was not convened during the COVID-19 pandemic, as including intersectoral decision-making was assumed by the NCCC. The National IMT was responsible for health sector responses only and was organised into functional areas that aligned to the nine strategic priorities in the National COVID-19 Response Plan.

Each province convened their own IMT to support provincial and district health service delivery. Communication with provinces was formally conducted through the NATJOC and provincial joint operations committee and through the National Health Council as in pre-COVID-19 operations. Other structures, such as NATHOC and the EOC were not formally utilised.

Two key developments supporting COVID-19 responses were the creation of a National COVID-19 Response Plan52,48 and data systems to support epidemiological intelligence and case management53. The national response plan identified and delineated key activities in nine strategic priority areas, as outlined above. Systems were created for immediate transmission of laboratory diagnostic test results from public and private sectors to a central data repository at the NICD, as well as mechanisms for electronic and manual geocoding and data cleaning. A second data management system, DATCOV was also set up by the NICD early in the outbreak to support data collection on hospitalisations, bed occupancy and outcomes54.

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Figure 8.2 National and provincial structures supporting SARS-CoV-2 responses as of October 2021.

The emergency operations centre

Emerging lessons in public health emergency preparedness and response, 2015–2020 The years 2015–2020 have seen a gradual increase in number, intensity and severity of health emergencies, culminating in the SARS-CoV-2 pandemic. The foundations for South Africa’s current response capacity were laid through the preparations for potential imported EVD cases from the West African Ebola outbreak in 2014–2016. These led to improvements in preparedness at ports of entry, diagnostic laboratories, infection prevention and control guidelines and training, and hospital-level service delivery. The listeriosis outbreak allowed key stakeholders to gain experience from the WHO in utilising and working within an incident management structure. Surveillance for antimicrobial resistance and antimicrobial stewardship programmes were strengthened through policy and guideline development.

For South Africa, as with other AFRO regional countries55, the JEE process in 2017 was instrumental in supporting multisectoral collaboration and preparedness planning as well as identifying areas requiring additional support. Globally, the JEE process has been shown to correlate with effectiveness of COVID-19 control when adjusting for country income, population density and human development56. Therefore, the recommendations identified by South Africa’s JEE and other opportunities for strengthening, which have been made apparent by the COVID-19 pandemic, need to be addressed if health services are not to be further disrupted and appreciable achievements in universal health coverage are not lost. We highlight six areas for focused attention as follows:

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Firstly, governance and the role of legislation and policy is key to bring countries in line with IHR requirements57. The absence of a legislative framework supporting IHR implementation across sectors and at all levels of government, and the absence of a multisectoral health response plan were identified by the JEE process in 2018. The creation of new emergency response structures and reconfiguration or dropping of existing structures to support the COVID-19 response illustrated the inadequacy of pre-COVID-19 preparedness and response plans to address an event of pandemic proportions. South Africa will need to reformulate and enact the IHR Bill26 to ensure progress towards IHR (2005) implementation.

Secondly, the disruption of services reported across many health sectors during lockdown illustrated a key deficiency of continuity of care in emergency planning and response. Primary health care service delivery has been severely impaired during COVID-19 as evidenced by a 19% decline in persons tested for TB, a 22% decline in HIV testing and an 18% decline in PHC facility visits over 2020 compared with 201958. Persons with TB have a two to five times greater risk of death following COVID-19 infection59, and these outcomes are likely exacerbated by service delivery impairment60. The use of antimicrobials for the patients in health care facilities is high and likely to exacerbate AMR61. Nyasulu et al. have created a conceptual framework which may support the next phase of preparedness and response planning62.

Thirdly, SARS-CoV-2 has led to appreciable loss of human resources63, whilst also requiring integration and formal career paths for new cadres of staff including community health workers64 and epidemiologists. The burden of disease, the speed of SARS-CoV-2 transmission, high number of institutional and facility outbreaks and overwhelming requirements for contact tracing, have all highlighted the key role of and requirement for skilled epidemiologists with field experience. Already, the JEE process identified the need to fast-track institutionalisation of epidemiology as a specialisation and strengthen epidemiology training through provision of financial support20. Van Ryneveld et al. have identified the key role of governance and capacitation of the NDoH to support alignment of policy, regulatory bodies and human resource requirements65.

Fourthly, the success of NHLS/NICD’s data management pertaining to SARS-CoV-2 tests, cases, admissions and deaths have highlighted the absence of such systems for other communicable and non-communicable disease across human and animal sectors. Investments across all levels of the health sector are required to support ICT requirements of data management. Significant challenges exist in this space, ranging from digital illiteracy, poor infrastructure, the high cost of installing ICT infrastructure, security concerns and irregular electricity supply66. However, the impact of integrating ICT may yield a wide range of benefits across health programmes and sectors.

Fifthly, the emergence and entrenching of anti-vaccine sentiment in South Africa67 may be ascribed to deficient social listening, delayed roll-out of health promotion and communication campaigns48, and inadequate attention to ‘peace time’ efforts to promote trust in science, government and health authorities. Effective communications and leadership are central to the management of pandemics and their rapidly changing societal and economic landscapes68. Government health communications require ongoing engagement in an interactive process of exchange of information with communities, whilst considering the evolving technical knowledge of the pathogen and its epidemiology and relevant social dynamics, socio-cultural diversity, and a rapidly changing media. Key principles of effective communication strategies68 include

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proactive, empathetic, clear, credible messages that recognise uncertainty, account for levels of health literacy and numeracy, consider diverse community needs, appeal to social norms and empower people to act.

Lastly, measures to address the mental health care needs of health practitioners, vulnerable persons and the public, and the inclusion of psychosocial services in response planning was a crucial omission from the National COVID-19 Response Plan69.

Siphelele et al.69 believe that the psychology profession should be integrated into preparedness planning and response measures for individual and community mental health sequelae. Psychologists can contribute to pandemic responses by provision of services and training of mental health professionals in immediate and responsive treatment measures.

What is evident is that each of these six areas for focussed attention over the next five years contribute not only to health emergency response, but also to health systems strengthening and provision of universal health coverage. Many interventions to address SARS-CoV-2, with minimal adaption and if applied consistently, also have potential to strengthen specific disease control programmes70.

Conclusions and way forward The Independent Panel for Pandemic Preparedness and Response, appointed by the WHO Director-General in response to the World Health Assembly resolution 73.1, has provided the WHO and global community with a comprehensive, evidence-based review of global and WHO responses to the COVID-19 pandemic71. Amongst the most urgent of their recommendations for national governments are that these update their national preparedness plans against predetermined WHO targets and benchmarks within six months, that they ensure appropriate and relevant skills, logistics and funding are available to cope with future health crises and that they appoint national pandemic coordinators accountable to the highest levels of government with the man date to drive whole-of-government coordination for both preparedness and response.

South Africa will do well to support and implement these recommendations, as well as the outstanding recommendations from the 2017 JEE recommendations. If addressed, these measures and the six recommendations outlined above will ensure robust, effective containment and response to the next pandemic.

What is certain on review of South Africa’s response to health emergencies over 2015–2020 is that health security requires more than a narrow focus on infectious disease preparedness, detection and response. Universal health coverage and health systems strengthening both support and are supported by health emergency planning and response72.

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