1

Surveillance, prevention and control of infectious disease and trauma in South

Australia

A thesis submitted for the degree of Master of Philosophy (Applied Epidemiology) of The Australian National University

Bernadette Kenny

February 2019

Communicable Disease Control Branch / Prevention and Population Health Branch, Department for Health and Wellbeing, SA Health, Government of South Australia

Field Supervisors: NCEPH Academic Supervisor: Dr Megge Miller Dr Tambri Housen Ms Helen Thomas

© Copyright by Bernadette Kenny, 2019 All Rights Reserved

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Originality statement

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“Epidemiology is in large part a collection of methods for finding things

out on the basis of scant evidence, and this by its nature is difficult.”

Alex Broadbent, University of Johannesburg philosopher commenting on epidemiology in ‘The Epi Monitor’

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Acknowledgements

Firstly, I would like to thank each of my field supervisors at SA Health, Dr Megge

Miller and Ms Helen Thomas, for sharing their experience, expertise and advice. Their

guidance and, just as important, their support has been invaluable in making the last two

years a rewarding experience.

Thank you to my Australian National University (ANU) academic supervisor, Dr

Tambri Housen. I especially appreciated Tambri’s support during the writing of this

bound volume and her role in securing my Global Outbreak Alert and Response

Network (GOARN) deployment to Bangladesh.

Thanks especially to Prevention and Population Health Branch Director, Dr Katina

D’Onise, Communicable Disease Control Branch (CDCB) Director, Dr Louise Flood,

and CDCB Disease Surveillance and Investigation Section (DSIS) Manager, Ms Emma

Denehy, and my field supervisors, for allowing me the opportunity to complete the

Master of Philosophy (Applied Epidemiology) (MAE) at SA Health and for kindly

allowing me to be deployed with GOARN during the placement.

Special thanks to my colleagues at SA Health; their friendship and encouragement were

invaluable in making the last two years enjoyable. I would particularly like to thank

Principal Statistician, Kamalesh Venugopal, Public Health Nurse, Emma Collins and

colleagues in CDCB’s Disease Surveillance and Investigation Section whose work

contributed greatly to my field projects. I would also like to thank DSIS Manager,

Emma Denehy, for her ongoing support.

Thanks to my cohort of MAE scholars who provided friendship, practical support and

fun from the first day of the course, especially my ANU course-block housemates, Jana

Sisnowski and Cushla Coffey, and, my colleague in Bangladesh, Julia Maguire.

Thank you to all the ANU team working on the Master of Philosophy (Applied

Epidemiology) (MAE) Program.

Lastly, thank you to my partner, Dr Uwe Kopke, for his unfailing support always and, to

my adult sons, Thomas and William, for their enthusiastic encouragement.

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Table of Contents Originality statement ......................................................................................................... 2 Acknowledgements ........................................................................................................... 4 Chapter 1: Overview of field placement at SA Health and summary of completion of Master of Philosophy (Applied Epidemiology) course requirements .......................... 6

Introduction .................................................................................................................. 7 Summary of completion of Master of Philosophy (Applied Epidemiology) course requirements ...................................................................................................... 8

Field Placement Projects: ........................................................................................ 8 Additional MAE Requirements: .............................................................................. 9

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Chapter 1: Overview of field placement at SA Health and summary of completion of Master of

Philosophy (Applied Epidemiology) course requirements

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Introduction My Master of Philosophy (Applied Epidemiology) (MAE) field placement was within

both the Communicable Disease Control Branch (CDCB) and the Prevention and

Population Health Branch (PPH) of the Department for Health and Wellbeing,

SA Health, Government of South Australia (SA).

CDCB is responsible for implementing the South Australian Public Health Act 2011

with the aim of reducing the communicable disease burden within SA. CDCB develops

and implements policies, best practice guidelines and information and, performs public

health interventions including notifiable infectious disease surveillance, response to

disease outbreaks and, implementation of national and SA immunisation programs. The

branch consists of the following six units which report to the Branch Director:

• Specialist Services (Medical Specialists and SA Rheumatic Heart Disease Program)

• Disease Surveillance and Investigation Section (DSIS)

• Immunisation Section

• Sexually Transmissible Infection & Blood Borne Virus Section

• Infection Control Service

• Data and Corporate Services

Prior to commencing the MAE program, I was working as a Public Health Nurse within

CDCB DSIS and, during my field placement, I continued to work casually as a Public

Health Nurse covering on-call shifts on evenings and weekends; the on-call work

involved interview and follow-up of cases of notifiable infectious diseases such as

invasive meningococcal disease, for which urgent public health action aimed at

preventing further cases is required. As a MAE scholar within CDCB, I participated in

the routine work of DSIS including performing the weekly epidemiological review of

the notification data and presenting a PowerPoint summary of the review to DSIS and

CDCB Medical staff at the weekly epidemiological review meeting.

The Prevention and Population Health Branch monitors, analyses, reports and makes

recommendations on disease, illness, abnormality, injury and related risk-factor

information in SA. The core functions of the Prevention and Population Health Branch

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are mandated under the SA Health Care Act, 2008 and the South Australian Public

Health Act, 2011.

At the commencement of my MAE placement, the Prevention and Population Health

Branch consisted of the following four functional units, all of which report to the

Branch Director:

• SA Cancer Registry (SACR)

• Pregnancy Outcomes (Statistics) Unit (POU)

• Strategic Evaluation and Reporting Unit (SERU)

• Health Statistics Unit (HSU)

Epidemiologists and scholars within the Epidemiology Branch are encouraged to attend

the Epidemiology Branch monthly Journal Club and to take turns in presenting journal

articles and leading the discussion. Consequently, I had the opportunity to lead the

discussion of an article which assessed the effectiveness of a community treatment

program on the prevalence and infection intensity of lymphatic filariasis and soil

transmitted helminth infections.

In March 2018 I was deployed with the World Health Organization Global Outbreak

Alert and Response Network (GOARN) via the Australian Response MAE Network

(ARM). My role was to assist health services serving the refugee Rohingya population

in Cox’s Bazar, Bangladesh with infection prevention and control. This was a rewarding

experience on many levels including witnessing ‘Field Epidemiology Training

Program’ graduates from around the world working collaboratively together.

Summary of completion of Master of Philosophy (Applied Epidemiology) course requirements Field Placement Projects: Analyse a public health data set

To generate the first state-wide descriptive South Australian Trauma Registry (SATR)

Annual Report, I analysed data for trauma events managed, and recorded in the SATR

by the three South Australian Major Trauma Service hospitals between 1 July 2011 and

30 June 2016 (Chapter 4). Analysis of a public health dataset was also a component of

my three other completed field projects (Chapter 2 and Chapter 3).

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Investigate an acute public health problem or threat

I was the Lead Investigator for a protracted outbreak of Salmonella Hessarek infection

in South Australia from March 2017 to July 2018 (Chapter 2). I was also the Lead

Investigator for the investigation into a cluster of seven cases of Salmonella

Typhimurium phage-type 9 associated with a hotel in South Australia in January 2018

and, I participated in other CDCB DSIS outbreak investigations, for example,

I interviewed persons designated as ‘controls’ in a case-control study for an outbreak of

Salmonella Havana in SA in April 2018. In April 2017, I was the Lead Investigator for

an investigation into a cluster of three cases of invasive meningococcal disease,

serotype W, in residents of a remote Aboriginal community in the far North of SA. The

three cases were part of a multistate outbreak of meningococcal serotype W infection in

central Australia with most cases occurring in Northern Territory residents. Whilst no

further cases occurred in South Australia, my role as Lead Investigator facilitated

experience in communication with colleagues in other Australian jurisdictions and

multiple organisations participating in a targeted vaccination campaign.

Design and conduct an epidemiological study

I conducted a descriptive epidemiological study of SA notifications of Shiga toxin-

producing Escherichia coli infection between 1 February 2017 and 30 June 2018

(Chapter 3).

Evaluate or establish a surveillance or other health information system

I evaluated the SA surveillance system for Shiga toxin-producing Escherichia coli

infection, from June 2016 to December 2018 (Chapter 3).

Additional MAE Requirements: Critical review of the scientific literature

A literature review was completed for each of the field projects listed above (Chapter 2,

Chapter 3 and Chapter 4).

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An abstract and oral presentation at a national or international scientific conference

I presented a summary of the SA Salmonella Hessarek investigation at the 9th Southeast

Asia & Western Pacific Bi-regional Training Programs in Epidemiology and Public

Health Interventions Network (TEPHINET) Scientific Conference, 5-9 November 2018.

Kenny B, Miller MJ, Housen T. A protracted outbreak of Salmonella Hessarek

infection associated with one brand of eggs, South Australia, March 2017- July

2018 presented at the 9th Southeast Asia & Western Pacific Bi-regional Training

Programs in Epidemiology and Public Health Interventions Network

(TEPHINET) Scientific Conference, Vientiane, Laos; 5-9 November 2018.

(Chapter 2)

Preparation of an advanced draft of a paper for publication in a national or international peer reviewed journal

I have published an article summarising the SA S. Hessarek investigation in the peer-

reviewed scientific journal, ‘Communicable Diseases Intelligence’ (CDI).

Kenny B, Miller MJ, McEvoy V, Centofanti A, Stevens CP, Housen T. A

protracted outbreak of Salmonella Hessarek infection associated with one brand of

eggs, South Australia, March 2017 - July 2018. Commun Dis Intell (CDI)

[Internet]. 2019 May [cited 15 May 2019];43:1-9.

Available at https://doi.org/10.33321/cdi.2019.43.22 (Chapter 2)

In partnership with other MAE scholars and graduates, I published an article reflecting

our experience during deployment to Bangladesh with GOARN in Global Biosecurity.

Alam N, Kenny B, Maguire JE, McEwen S, Sheel M, Tolosa MX. Field

epidemiology in action: an Australian perspective of epidemic response to the

Rohingya health emergencies in Cox’s Bazar, Bangladesh. Global Biosecurity

[Internet]. 2019 Feb [cited 14 February 2019];1(1):119–122.

DOI: http://doi.org/10.31646/gbio.14

A report for a non-scientific audience

Whilst deployed to the World Health Organization in Cox’s Bazar, Bangladesh,

I prepared and presented a PowerPoint presentation about infection prevention and

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control measures for Cholera for non-clinical staff at two health services servicing the

Rohingya refugee population.

Kenny B. Infection Prevention and Control (IPC) at Oral Rehydration Points

(ORPs) presented to clinical and non-clinical staff from two proposed Oral

Rehydration Points for acute watery diarrhoea, Cox’s Bazar, Bangladesh; 6 May

2018. (Chapter 5)

Teaching including Lessons from the Field (LFF)

I conducted a ‘lessons from the field’ education session on performing risk assessment

during outbreak investigations for my MAE peers, taught in two course-block education

sessions for first-year MAE scholars, prepared and taught infection prevention and

control education sessions for clinical and non-clinical Health Service staff in Cox’s

Bazar, Bangladesh and participated in a panel presentation and discussion session for

the Master of Public Health course, ‘Global Public Health’, at the University of

Adelaide.

Kenny B. Lessons from the field 6: Rapid risk assessment in outbreak

investigation; conducted via teleconference, 20 March 2018 (Chapter 5).

Kenny B, Willis G. Public health surveillance workshop; presented at MAE

course-block, 1 March 2018 (Chapter 5).

Willis G, Kenny B, Strobel N, Jones R. Writing tips; presented at MAE course-

block, 9 March 2018 (Chapter 5).

Kenny B. Infection Prevention and Control (IPC) at Oral Rehydration Points

(ORPs); presented to clinical and non-clinical staff from two proposed Oral

Rehydration Points for acute watery diarrhoea, Cox’s Bazar, Bangladesh, 6 May

2018 (Chapter 5).

Kenny B, Hornsey E. Infection Prevention and Control for Healthcare Workers;

presented to clinical staff from five Health Services, Cox’s Bazar, Bangladesh,

7 May 2018 (Chapter 5).

Panel presentation and discussion for the Master of Public Health course, ‘Global

Public Health’, at the University of Adelaide, 9 July 2018.

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MAE Course blocks

I completed the following five required course-blocks at ANU in 2017 and 2018:

• POPH8917 Public Health Surveillance

• POPH8915 Outbreak Investigation

• POPH8913 Analysis of Public Health Data

• POPH8916 Research Design and Methods

• POPH8914 Issues in Applied Epidemiology

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Chapter 2: An investigation into a protracted outbreak of Salmonella Hessarek

infection, South Australia, March 2017 to July 2018

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Table of Contents Chapter 2: An investigation into a protracted outbreak of Salmonella Hessarek infection, South Australia, March 2017 to July 2018 ..................................................... 13

List of Figures ............................................................................................................ 14

List of Tables .............................................................................................................. 14

Prologue ...................................................................................................................... 15

My role................................................................................................................... 15

Lessons learned ...................................................................................................... 16

Impact of the work ................................................................................................. 18

Acknowledgements................................................................................................ 19

Master of Philosophy (Applied Epidemiology) core activity requirements .......... 20

Scope of this chapter .............................................................................................. 20

CDI article: A protracted outbreak of Salmonella Hessarek infection associated with one brand of eggs - South Australia, March 2017- July 2018 ............................ 21

Abstract .................................................................................................................. 21

Introduction............................................................................................................ 22

Methods ................................................................................................................. 23

Results ................................................................................................................... 24

Discussion .............................................................................................................. 27

Appendix 2.1: OzFoodNet Salmonella Hypothesis Generating Questionnaire ......... 31

Appendix 2.2: South Australian CDCB ‘Outbreak Meeting - Risk Assessment’ template ...................................................................................................................... 40

Appendix 2.3: PowerPoint presentation for the 9th Southeast Asia & Western Pacific Bi-regional Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET) Scientific Conference, Vientiane, Laos, 7 Nov 2018. ................................................................................................................... 45

References .................................................................................................................. 49

Chapter 3 ......................................................................................................................... 52

List of Figures Figure 1: Notifications of Salmonella Hessarek infection by month of illness onset, 1 Jan 2012 to 3 July 2018 ................................................................................................ 25

List of Tables Table 1: Food items consumed by cases of S. Hessarek infection, South Australia, 1 March 2017 to 3 July 2018 .......................................................................................... 26

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Prologue My role For a protracted outbreak of Salmonella Hessarek infection in South Australia,

I reviewed all original laboratory and medical notifications, identified the increase in

S Hessarek notifications occurring in March 2017, initiated the investigation into the

increase in notifications and, was the Lead Investigator for the epidemiological

investigation.

During the investigation, I conducted a literature search, reviewed the South Australian

(SA) Communicable Disease Control Branch’s (CDCB’s) records of previous

S. Hessarek cluster investigations, conducted hypothesis generating telephone

interviews of cases using the OzFoodNet Salmonella Hypothesis Generating

Questionnaire (Appendix 2.1), recorded the information obtained via the questionnaires

in a food-frequency Microsoft Excel spreadsheet and performed the epidemiological

analysis for the investigation. My role as Lead Investigator included documentation of

the outbreak and the investigation; specifically, I initiated and maintained the CDCB

Notifiable Infectious Diseases Surveillance (NIDS) database system investigation

record and a time-line summary of the investigation and saved all related

correspondence to CDCB’s secure, on-line episode folder for this investigation.

I also coordinated and chaired the outbreak investigation meetings between personnel

from CDCB, the SA Health Food and Controlled Drugs Branch (FCDB), the

Department of Primary Industries and Regions SA Biosecurity SA division (PIRSA)

and, on one occasion, the SA Health Chief Public Health Officer. For these meetings,

I prepared ‘Outbreak Meeting - Risk Assessment’ documents (Please see Appendix 2.2

and Chapter 5 Appendix 5.1 ‘Lessons from the field: Rapid Risk Assessment’) which

summarised the epidemiological data, outbreak status (monitor, escalate or stand-

down), overall risk assessment (consequences of the outbreak and likelihood of the

consequences occurring) and completed and planned investigation action items for each

outbreak meeting and, prepared and distributed formal Situation Reports which

communicated the status of the outbreak and the investigation to the SA Health Chief

Public Health Officer and CDCB, FCDB and PIRSA personnel.

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My role also included liaison with the CDCB OzFoodNet Senior Epidemiologist to

periodically obtain Australian national data for S. Hessarek notifications, discuss

whether OzFoodNet epidemiologists in other Australian states and territories were

willing to interview cases of S. Hessarek in their jurisdictions and, discuss the

possibility of conducting whole genome sequencing (WGS) of human and egg

S. Hessarek isolates in SA for the period during and prior to the investigation.

Additionally, I attended meetings of CDCB, OzFoodNet, SA Pathology (including the

Australian Salmonella Reference Centre (ASRC)) and South Australian Health and

Medical Research Institute (SAHMRI) personnel to discuss options and current

limitations for WGS testing of SA S. Hessarek isolates.

In addition to preparing ‘Outbreak Meeting - Risk Assessment’ documents and

Situation Reports, I reported the epidemiology of the outbreak and progress of the

investigation to CDCB personnel both verbally at CDCB daily morning meetings and

periodically via PowerPoint presentations at CDCB’s weekly epidemiological review

meetings. I submitted an abstract to the 9th Southeast Asia & Western Pacific

Bi-regional Training Programs in Epidemiology and Public Health Interventions

Network (TEPHINET) Scientific Conference; the abstract was accepted for an oral

presentation, and I presented a summary of the investigation (Appendix 2.3) at the

conference on 7 November 2018. Finally, I was the primary author of an article

summarising the outbreak and investigation which was published in ‘Communicable

Diseases Intelligence’ (CDI) in May 2019.1

Lessons learned • Investigation of outbreaks of disease which include only small numbers of cases are

worthwhile as they can be productive in determining risks to public health and

opportunities for public health action.

• In addition to conducting a literature search, review of the information from

previously conducted, unpublished local investigations, which may or may not have

identified sources of previous outbreaks, can cumulatively assist exposure

assessment in subsequent outbreak investigations.

• The availability of well-researched and well-tested ready-to-use questionnaires such

as the OzFoodNet Salmonella Hypothesis Generating Questionnaire, prior to the

commencement of an investigation, can facilitate timely collection of high-quality

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data when conducting investigations into diseases where the epidemiology is

established.

• Ideally, when investigating outbreaks of foodborne disease, an analytical study

such as a case-control study is conducted to obtain information on exposure to

suspected source food items for both affected persons and a comparison group of

persons who were not unwell; the results of such a study may or may not

statistically support the investigation hypothesis about the source of the

outbreak. However, it is not always feasible to conduct a timely and informative

analytical study for outbreaks which include only small numbers of cases and

thus, the level of evidence might rely on descriptive epidemiological evidence

and laboratory evidence only.

• In addition to the immediate outbreak investigation team which, for this

investigation, included CDCB, FCDB and PIRSA, many other organisations,

such as OzFoodNet, other Australian state and territory communicable disease

units and SAHMRI, can contribute to an investigation by providing information

and/or practical assistance.

• Individual members of outbreak investigation teams may reach differing

conclusions regarding the public health risks and the nature and urgency of

outbreak control actions which are deemed necessary at various stages of the

investigation; differing perspectives result from numerous factors including the

differing roles of the outbreak team members and, the relevant legislation and

priorities for their particular units and organisations.

• Formal communication tools, such as the CDCB ‘Outbreak Meeting - Risk

Assessment’ template (Please see Appendix 2.2 and Chapter 5 Appendix 5.1

‘Lessons from the field: Rapid Risk Assessment’) and the associated ‘Incident

Response Protocol’ can assist outbreak investigation teams by providing a

formal process for managing the investigation ensuring shared:

o comprehensive documentation of known and missing hazard, exposure and

context outbreak assessment information, required for assessing the overall

level of risk (consequences and likelihood of the consequences occurring)

associated with the outbreak;

o risk-assessment and assessment of the current outbreak status (monitor,

escalate or stand-down) by all involved in the investigation;

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o documentation of completed and planned investigation actions;

o documentation of the formal communications, such as Situation Reports, to

occur following each outbreak investigation meeting and, the date or

circumstances that will trigger the next outbreak meeting.

• It is important for the outbreak investigation team collectively to have a good

understanding of the circumstances in which the outbreak is occurring and the

circumstances in which outbreak control activities will occur; these circumstances

include, for example, the industry production and supply processes pertaining to

contaminated food items and any legislation or standards which may influence

outbreak control activity, such as, the Primary Production and Processing Standard

for Eggs and Egg Products (Standard 4.2.5) of the Australian Food Standards

Code.

• There is not always a quick and easy way to eliminate sources of outbreaks in the

short-term; human health risks may need to be considered in, for example, the

context of long-term, industry-wide management of the factors posing risk of

disease.

Impact of the work This investigation:

• Identified a protracted source of salmonellosis in humans; the implicated egg brand

was found to be the cause of illnesses occurring in SA during a period of

17 months, 1 March 2017 to 3 July 2018, and there is suggestive evidence that the

particular egg brand may be the source of SA cases of Salmonella Hessarek

occurring over a four year period, since 2014.

• Raises questions about whether the risk of contamination of eggs with Salmonella

in Australia has changed since the risk assessment conducted and considered during

development of the Primary Production and Processing (PPP) Standard for Eggs

and Egg Products (Standard 4.2.5) of the Australian Food Standards Code

(gazetted in 2011). Isolation of Salmonella Hessarek in the contents of the

implicated egg brand but not in the whole egg rinse samples, both during this

investigation and during a SA retail food survey in 2014, challenge the premise

that, in Australia, Salmonella contamination in eggs occurs via dirty or cracked

eggs, a premise which was a component of the risk assessment for Standard 4.2.5.

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• Triggered a research study “Understanding the behaviour of Salmonella

Typhimurium and Salmonella Hessarek; their ability to penetrate egg shells and

their growth in eggs stored at different temperatures” which is being conducted by

the University of Adelaide in conjunction with SA Health.

• Triggered a proposed WGS study of Salmonella Hessarek isolates from 2010 to

2018; the SAHMRI is proposing to undertake this study in partnership with CDCB

and SA Pathology.

• Contributed to the Global Literature on Salmonella Hessarek which, prior to this

investigation, included only one published report of a S. Hessarek outbreak in

humans.4

Acknowledgements I wish to acknowledge and thank:

• OzFoodNet Senior Epidemiologist, Dr Megge Miller and, the Manager and staff of

CDCB’s Disease Surveillance and Investigation Section (DSIS).

• The staff of FCDB and the staff of PIRSA.

• Dr Lex Leong (SAHMRI) .

• Helen Hocking (ASRC) and, Dr Rod Ratcliff (former, SA Pathology).

• The staff of the Food and Environmental Laboratory (SA Pathology).

• The Australian OzFoodNet epidemiologists in Victoria and New South Wales.

• SA Health Chief Public Health Officer, Dr Paddy Phillips, and CDCB Director, Dr

Louise Flood.

• Dr Tambri Housen, Australian National University.

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Master of Philosophy (Applied Epidemiology) core activity requirements This chapter is written in fulfilment of the field placement core activity requirements:

• Investigation of an acute public health problem.

• An abstract and oral presentation of a project presented at a national or international

scientific conference (Appendix 2.3).

• Preparation of an advanced draft of a paper for publication in a national or

international peer reviewed journal.

Scope of this chapter This chapter describes a South Australian outbreak of Salmonella Hessarek and the

subsequent epidemiological investigation into the cause of the outbreak by reproducing

an article published by the peer-reviewed scientific journal, ‘Communicable Diseases

Intelligence’.1

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CDI article: A protracted outbreak of Salmonella Hessarek infection associated with one brand of eggs - South Australia, March 2017- July 2018 Authors

B Kenny,1 MJ Miller, 1, 2 V McEvoy,3 A Centofanti, 3 CP Stevens, 3 T Housen.4

1. Communicable Disease Control Branch, Department for Health and Wellbeing,

SA Health, Government of South Australia.

2. OzFoodNet

3. Food and Controlled Drugs Branch, Department for Health and Wellbeing,

SA Health, Government of South Australia.

4. National Centre for Epidemiology and Population Health, Research School of

Population Health, Australian National University.

Abstract Salmonella Hessarek is an uncommon serovar in Australia. We report on the

investigation of a protracted outbreak of 25 cases of S. Hessarek gastroenteritis in which

cases were defined as any laboratory confirmed case of Salmonella Hessarek notified to

the South Australian Communicable Disease Control Branch from 1st March 2017 to 3

July 2018. We conducted a descriptive case series investigation interviewing all cases

and 17 (68%) reported consuming brand X free-range eggs. Four samples of one-dozen

brand X eggs were cultured for the presence of Salmonella spp. One out of the four

samples returned positive for S. Hessarek in the contents of the eggs; Salmonella was

not present in any of the whole egg rinses of the four samples. The high proportion of

cases reporting the consumption of brand X free-range eggs and the isolation of S.

Hessarek from sampling four dozen brand X eggs is an unusually strong signal

implicating brand X eggs as the source of this outbreak. From a public health

perspective, it is important to understand the behaviour of S. Hessarek including its

ability to be present in the content of eggs and further research is recommended. The

findings in this investigation into a rare Salmonella serovar highlight the need for

continuous monitoring of the epidemiology of Salmonella in Australia including the

epidemiology of egg-associated Salmonella outbreaks of human disease.

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Key words Salmonella, Hessarek, gastroenteritis, foodborne disease, eggs

Introduction Salmonella Hessarek is an uncommon serovar in Australia. From 1 January 2012 to

31 December 2016, there were 96 notifications of S. Hessarek nationally, (the National

Notifiable Diseases Surveillance System Salmonella public dataset does not include

Salmonella notified in the Australian Capital Territory), representing 0.1% of Australian

Salmonella notifications for the five-year period.2 Of the 96 notifications, 52 (54%)

were for residents of South Australia, a state in which 7% of the Australian population

resides. For the five-year period, the rate of S. Hessarek notifications in South

Australians was more than seven times higher than the rate for Australians overall; 3.1

compared to 0.4 notifications per 100,000 persons.3 Globally, there is one published

report of a S. Hessarek outbreak in humans; in 2005, five cases notified within the

Australian Capital Territory were sourced to free range eggs served at a restaurant.4

S. Hessarek was originally isolated from a Common Raven (Corvus corax) in Iran in

19535 and has subsequently been detected in outbreaks of septicaemic salmonellosis in

wild birds (Song Thrushes and European Starlings)6,7,8 and, in European mammals

(lynx9, red foxes10 and free-range pigs11), possibly transmitted through ingestion of

infected birds.6

The South Australian (SA) Communicable Disease Control Branch (CDCB) observed

an increase in S. Hessarek notifications beginning around mid-2014. Between

November 2016 and February 2017, two to six S. Hessarek cases per month (Figure 1)

amongst a total of 136 Salmonella notifications per month were being monitored. On 21

March 2017, the CDCB became aware of five cases of S. Hessarek notified in the three

weeks since 1 March 2017. This was more than the expected 0.8 S. Hessarek

notifications in March, based on data for the years 2012 to 2016. An investigation

commenced to identify any common cause of illness for which appropriate public health

action could be implemented to prevent further cases.

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Methods Epidemiological investigation

A retrospective review of previous S. Hessarek cluster investigations in SA was

undertaken. We extracted outbreak records from 1 January 2001 to 21 March 2017 from

the SA OzFoodNet Outbreak Register and the SA Notifiable Infectious Disease

Surveillance System, identified investigations of S. Hessarek and, reviewed the

investigation summaries to look for potential sources of the pathogen.

A case-series investigation was conducted to generate hypotheses about the source of

S. Hessarek infection in cases notified in SA since 1 March 2017. We interviewed all

persons notified with S. Hessarek infection between 1 March 2017 and 3 July 2018

using the national OzFoodNet Salmonella Hypothesis Generating Questionnaire. The

data collected via the questionnaire include demographic details, clinical information

including date of illness onset and symptoms experienced, information regarding any

contact with persons with gastroenteritis in the seven days prior to onset of illness,

travel history, environmental exposures such as animal contact and consumption of

untreated water, food items eaten outside of the home, a seven day open-ended food

history and specific questions regarding poultry and egg consumption.

Questionnaire responses relating to egg consumption, including brands of eggs

consumed, were compared with data from 20 other SA community Salmonella clusters

which were investigated using the same Salmonella Hypothesis Generating

Questionnaire between 1 March 2017 and 3 July 2018. This comparison was intended to

identify whether the pattern of consumption of particular egg brands reported during the

S. Hessarek investigation was similar to the pattern of consumption of particular egg

brands reported in SA in general. A case-control study was not conducted as we initially

anticipated that there would be insufficient cases to generate a meaningful result and,

later in the investigation, there was deemed to be sufficient epidemiological and

laboratory evidence to identify the source of the outbreak without case-control study

evidence.

An outbreak case was defined as any laboratory confirmed case of Salmonella Hessarek

notified to the South Australian Communicable Disease Control Branch from 1st March

2017 to 3 July 2018. All S. Hessarek notifications were confirmed by the Australian

Salmonella Reference Centre.

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Data were analysed using Microsoft Excel 2010 (Microsoft USA).

The investigation was conducted under the auspices of the SA Public Health Act, 2011

and covered under the Australian National University Human Research Ethics

Committee approval (2017/909). The SA Department for Health and Ageing Human

Research Ethics Committee granted approval for publication of the findings

(HREC/17/SAH/113).

Environmental investigation

Based on the responses of seven cases interviewed between 22 March and 7 April 2017,

on 10 April 2017 the SA Health Food and Controlled Drugs Branch (FCDB) conducted

retail sampling of brand X free-range eggs; four samples of one-dozen eggs with best

before dates between 21 April and 12 May 2017 were collected from two retail stores

and cultured for the presence of Salmonella spp. by the SA Pathology Food and

Environmental Laboratory.

Results Epidemiological investigation

CDCB had investigated previous clusters of S. Hessarek infection in SA; in 2006 a

cluster of nine cases of S. Hessarek was associated with raw or semi-cooked eggs, in

2014, an investigation of eight cases found that seven cases consumed chicken and six

consumed eggs with three cases consuming brand X free-range eggs and, in January

2016, an investigation of six cases found that four consumed eggs, with one case

reporting consumption of brand X eggs and another case reporting purchase of eggs of

an unknown brand in the isolated SA region where brand X eggs are produced.

Between 1 March 2017 and 3 July 2018, 25 cases met the case definition (Figure 1).

The median age of cases was 49 years (age range 1-91 years) with nine cases (36%)

aged 71 years or older. Fifteen cases were male and ten were female. Twenty-one cases

lived in metropolitan Adelaide and four were non-metropolitan residents. Ten cases

(40%) were hospitalised and two other cases occurred in pregnant women.

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Figure 1: Notifications of Salmonella Hessarek infection by month of illness onset, 1 Jan 2012 to 3 July 2018

Twenty-four of the 25 cases (96%) reported eating eggs; 23 cases (92%) consumed eggs

at home including five cases (20%) who consumed eggs both at home and away from

home and, one case (4%) consumed eggs away from home only. Seventeen cases (68%)

are known to have consumed brand X free-range eggs, another brand of eggs was

named by three cases (12%). Twenty-four cases responded to questions about food

items other than eggs and one case declined these questions. Ten cases (42% of 24

respondents) consumed poultry cooked at home and eight cases (33% of 24

respondents) consumed chicken which was purchased cooked however, there were no

chicken items with common brands or from common retail outlets. Eleven other food

items were reported by more than 25% of cases but, with the exception of bottled water,

no common brands or common retail outlets were identified. Three brands of bottled

water were each named by two to four cases (8-17%). Contact with dogs, cats and/or

dried pet food was reported by seven to ten cases (29-42%) but further detail did not

indicate any of these exposures as a possible common source (Table 1).

The eggs consumed were cooked in a variety of ways including; fried, boiled,

scrambled, poached, as omelette and in Béchamel sauce. Seven cases consumed raw

egg; in smoothies (three cases), in raw cake batter (three cases) and one case sucked raw

eggs (Table 1).

26

Table 1: Food items consumed by cases of S. Hessarek infection, South Australia, 1 March 2017 to 3 July 2018

* The number of cases interviewed varies as one case declined interview for all food items except eggs.

27

Environmental investigation

One out of four samples returned positive for S. Hessarek in the contents of the eggs.

Salmonella was not present in any of the whole egg rinses of the four egg samples.

Additionally, FCDB identified that S. Hessarek had been isolated from the content of

brand X brand eggs but not the whole egg rinse during a retail food survey in 2014.12

Discussion The high proportion of cases reporting the consumption of brand X free-range eggs and

the isolation of S. Hessarek from sampling four dozen brand X eggs is an unusually

strong signal implicating brand X eggs as the source of this protracted S. Hessarek

outbreak in South Australia. There is also absence of another possible source based on

the hypothesis generating interviews.

Brand X eggs are produced in SA and are predominantly sold in SA. A limitation of the

epidemiological investigation is that we did not have information on the proportion of

the SA population who usually consume brand X eggs. For reasons stated previously, a

case-control study was not conducted and, SA lacks a food frequency consumption

database to compare cluster investigation results with the foods that are consumed by

healthy people in the community. Egg consumption data, obtained from case interviews

in 20 other SA Salmonella clusters during the same time period, 1 March 2017 to 3 July

2018, found that only 5/189 (3%) of interviewed persons and 5/125 (4%) of respondents

reporting egg consumption, consumed brand X eggs. This suggests that the proportion

of cases reporting consumption of brand X eggs in the S. Hessarek investigation is not

simply a reflection of market share for brand X eggs within SA, however, it is possible

that egg consumption patterns for persons who have not experienced Salmonella

infection may differ from those who have and who were interviewed.

The ongoing nature of this outbreak reflects the difficulty in controlling Salmonella

infection in free range laying flocks. Brand X eggs are produced on a free-range farm

and birds raised in free range production systems are potentially exposed to different

environmental stressors than caged birds, including social stress and aggression,

predation, or thermal challenges with stress known to be a determinant of shedding of

Salmonella.13 Additionally, the control of rodents and other potentially infected animals

and environments is challenging on free-range farms. Salmonella contamination of eggs

is a complex issue affected by variables at each stage of the food production process.

28

Currently, the literature regarding the benefits of free range, barn and caged production

processes with respect to Salmonella contamination is conflicting. However, the current

literature does indicate that it is not yet achievable to produce eggs guaranteed to be

Salmonella free.14

Because Salmonella can be highly persistent in both infected birds and diverse

environmental reservoirs, global egg safety programs include interventions at multiple

stages of egg production and supply to the public.15 However, the specific interventions,

such as requirements for vaccination of laying flocks against specific Salmonella

serovars, requirements for monitoring for Salmonella on egg farms, requirements for

egg pasteurisation or other actions when Salmonella is detected in a laying flock,

requirements for washing of eggs, and requirements for mandatory refrigeration of eggs

vary vastly between countries and vary with respect to which specific Salmonella

serovars the interventions apply to (often, interventions are applicable to Salmonella

serovars S. Enteritidis and S. Typhimurium only).15 To illustrate, egg washing with

sanitizers is one of the most common methods of reducing eggshell contamination in

Australia, Japan, and the USA but the technique is banned in the European Union16; the

major advantage of egg washing is the removal of faecal debris thereby reducing the

overall bacterial load on the eggshell surface however, the process requires strict

control, especially of rinse water temperature and quality, to avoid adverse results

including cracking of the shell, damage to the egg cuticle layer and egg penetration by

Salmonella bacteria.17

The variation in egg safety programs internationally results from variation in the

perceived risk of contaminated eggs between countries; each country’s risk management

/ tolerance / perception being influenced by local industry, environmental, cultural and

epidemiological factors, for example, the types of Salmonella contaminating eggs.

Stringent egg safety programs in the USA and Europe have resulted from the prevalence

of Salmonella Enteritidis in those countries. S. Enteritidis has a special ability to

colonize the ovary/oviduct of laying hens for long periods and therefore to internally

contaminate eggs, and has been the most frequent serovar associated with egg-related

foodborne outbreaks in Europe since the mid-1980s.18 S. Enteritidis is, however, not

endemic to Australian commercial layer flocks, a factor which was taken into account

during the Food Standards Australia New Zealand (FSANZ) risk assessment of egg

production and processing in Australia, a component of the development of the Primary

29

Production and Processing (PPP) Standard for Eggs and Egg Products (Standard 4.2.5),

gazetted in May 2011.19

In Australia, egg producers must comply with Standard 4.2.5 and under clause 11(1) an

egg producer must not sell or supply eggs or egg pulp for human consumption if it

knows, ought to reasonably know or to reasonably suspect, that the eggs are

‘unacceptable’. ‘Unacceptable egg’ is defined as; a cracked egg or a dirty egg or, ‘egg

product’ (defined as the contents of an egg in any form) which has not been pasteurised

or subjected to heating or other processes that provide a lethal effect on any pathogenic

micro-organisms in the egg product or, egg product which contains a pathogenic micro-

organism whether or not the egg product has been processed as previously described.20

The definition of ‘unacceptable egg’ and clauses restricting the sale of such product do

not automatically restrict the sale of whole eggs which are not known to be

contaminated but are from a producer or farm where Salmonella has been isolated

within whole eggs or when a farm or producer has been associated with an outbreak of

human disease.

An important consideration in the risk assessment on which the Primary Production and

Processing (PPP) Standard for Eggs and Egg Products (Standard 4.2.5) of the Australian

Food Standards Code is based is the premise that, in Australia, Salmonella

contamination in eggs occurs via dirty or cracked eggs. Our finding of S. Hessarek in

the content of eggs but not in the egg-shell rinse on two occasions and, our association

of S. Hessarek contaminated eggs with cases of human salmonellosis raise questions

regarding whether the risk of contamination of eggs with Salmonella in Australia has

changed since Standard 4.2.5 was introduced in 2011.

There are two pathways for eggs to become internally contaminated with Salmonella;

direct contamination occurs during the formation of an egg in the reproductive track of

hens (including ovary and oviduct) whereas, indirect contamination occurs after an egg

has been laid and Salmonella contaminating the outside of the egg penetrates through

the shell membrane.21 From a public health perspective, it is important to understand the

behaviour of S. Hessarek including its ability to be present in the content of eggs and

further research is recommended. It is noted that a high proportion of cases in this

investigation were elderly or pregnant and/or consumed raw egg which suggests that S.

Hessarek might be an opportunistic rather than highly virulent cause of Salmonella

infection in humans.

30

To determine whether cases of S. Hessarek notified prior to March 2017 were associated

with the source identified in this investigation, we explored the possibility of conducting

whole genome sequencing (WGS) of human and egg S. Hessarek isolates in SA since

2014. However, as S. Hessarek is a rare Salmonella, no S. Hessarek reference genome,

required for the WGS analysis, is available globally. Further research incorporating

WGS of S. Hessarek would require generation of a complete reference genome for S.

Hessarek based on consideration of the public health benefit of WGS in understanding

the epidemiology of this rare Salmonella serovar.

The findings in this investigation highlight the need for continuous monitoring of the

epidemiology of Salmonella in Australia including the epidemiology of egg-associated

Salmonella outbreaks of human disease. Any substantial changes in the epidemiology of

egg-associated Salmonella need to be considered in future risk assessments related to

Salmonella in eggs and future reviews of the Primary Production and Processing

Standard for Eggs and Egg Products (Standard 4.2.5) of the Australian Food Standards

Code. Joint efforts from Australian national and state/territory Communicable Disease

Control, Food Safety and Primary Industry organisations are essential to the control of

Salmonella in the Australian egg supply chain.

31

Appendix 2.1: OzFoodNet Salmonella Hypothesis Generating Questionnaire

32

33

34

35

36

37

38

39

40

Appendix 2.2: South Australian CDCB ‘Outbreak Meeting - Risk Assessment’ template

Outbreak Team Meetings- Agenda and Minutes Template

Outbreak name Pathogen (if known) Cluster or Location

Reference No. NIDS Outbreak # / PHMS Event #

Date and time

of meeting

Attendees

Trigger

1. Apologies 2. Actions previous meeting 3. Rapid Risk Assessment

Hazard assessment

What is the pathogen?

If there is no pathogen, what are the symptoms of the illness that has been reported?

How many people are affected?

What are the age groups and sex of cases?

What is the severity of the disease?

Number and % hospitalised:

Number of fatalities:

41

Exposure assessment

What is the most likely mode of transmission? Why?

[please consider the evidence to suggest if foodborne, person-to-person, animal-to-person etc]

What exposures have been associated with this hazard in the past?

[literature review, historical outbreaks etc]

If outbreak is a point source, how many people are known or likely to be exposed?

[is there a booking list or estimate of number of meals served?]

What are the most frequently consumed food items?

[food frequency analysis- is this normal?]

What is the probable source of the outbreak (if known)?

[consider epidemiological information, trace back results, food/environmental sampling results?]

Is there likely to be on-going exposure?

[are cases still being reported? Is product likely to still be in the marketplace? Is the restaurant still serving high risk food?]

Are cases confined to South Australia?

[Is this a possible multi-jurisdictional outbreak?]

42

Context assessment

Are there any factors about the event that might be associated with the environment, behaviours, social or cultural practices?

[is there any particular cuisine being consumed or cultural group affected?]

Are vulnerable populations affected?

[are cases occurring in an aged care facility, child care centre, hospital etc?]

What is the likelihood that all suspected cases will be identified?

[is the event likely to get bigger? Do we need to consider active case finding?]

Are there sufficient resources to respond?

[are their sufficient human resources and laboratory capacity available to respond?]

Are there any political sensitivities?

[media etc.]

43

Overall assessment

[Mark the appropriate box below] Mark Level of overall risk Actions

Low Managed according to standard response protocols between the two primary investigators (in consultation with team managers)

Moderate Consider outbreak meetings and preparation of situation reports. Ensure Directors are informed.

High

Convene outbreak meetings, prepare situation reports and inform Directors. Outbreak meetings will be held as required by the team, but with a minimum of weekly.

Very high Daily outbreak meetings, daily situation reports with distribution to CPHO, legal, media and communications

4. Actions a. From rapid risk assessment

(e.g. assigning actions to fill any gaps in evidence such as literature review about the pathogen etc.)

b. Further investigations

i. Epidemiological Options include: obtain medical notifications for cases with pending typing, continue hypothesis generating interviews, move to analytical epidemiological study.

ii. Microbiological Options include: request samples, request further typing at reference laboratory

iii. Environment and food chain Options include: traceback, sampling plan (include numbers of samples, types of samples), correspondence with Local Govt/regulators, correspondence with Food Business.

c. Control measures

44

5. Communications

People/organisations Yes/No/NA Person responsible/method

Situation Report

Branch Directors

CPHO/CMO

Minister

Media /communications unit

Legal

Public

Healthcare providers

Local Government EHOs National bodies (OFN/NFIRP/ CDNA/AHPPC/BFSN)

Others (specify)

6. Assess outbreak status

i. Monitor/ Escalate/ Stand Down

7. Next Meeting (Date, time, location)

45

Appendix 2.3: PowerPoint presentation for the 9th Southeast Asia & Western Pacific Bi-regional Training Programs in Epidemiology and Public Health Interventions Network (TEPHINET) Scientific Conference, Vientiane, Laos, 7 Nov 2018.

.

46

47

48

49

References 1. Kenny B, Miller MJ, McEvoy V, Centofanti A, Stevens CP, Housen T. A

protracted outbreak of Salmonella Hessarek infection associated with one brand

of eggs, South Australia, March 2017 - July 2018. Commun Dis Intell [Internet].

2019 May [cited 15 May 2019];43:1-9. Available at

https://doi.org/10.33321/cdi.2019.43.22

2. Australian Government Department of Health. National Notifiable Disease

Surveillance System; Salmonella Public Dataset [Internet]. Canberra. 2018

[Revised 4 July 2018, Cited 4 July 2018]. Available at:

http://www9.health.gov.au/cda/source/pub_salmo.cfm

3. Australian Bureau of Statistics. 3101.0 - Australian Demographic Statistics, Dec

2013 [Internet] Canberra. 2014 [Revised 24 September 2014, Cited 8 August

2018]. Available at:

http://www.abs.gov.au/AUSSTATS/abs@.nsf/allprimarymainfeatures/FA627C

A7C5708380CA257D5D0015EB95?opendocument

4. OzFoodNet Working Group. OzFoodNet: Enhancing foodborne disease

surveillance across Australia: quarterly report, January to March 2005. Commun

Dis Intell [Internet] 2005 [cited 2 Jun 2018];29(2):196-9. Available at

https://search-informit-com-

au.virtual.anu.edu.au/documentSummary;dn=507997363216461;res=IELAPA

5. Neel R, Le Minor L, Kawah M. Une nouvelle espe`ce de salmonella isole´e chez

un corbeau (Corvus corax): Salmonella Hessarek. Annales de l’Institut Pasteur.

1953;85:271-4.

6. Velarde R, Porrero MC, Serrano E, Marco I, García M, Téllez S et al.

Septicemic salmonellosis caused by Salmonella Hessarek in wintering and

migrating Song Thrushes (Turdus philomelos) in Spain. Journal of Wildlife

Diseases [Internet] 2012 [cited 2 Jun 2018];48(1):113-21. Available at

http://www.bioone.org.virtual.anu.edu.au/doi/pdf/10.7589/0090-3558-48.1.113

7. Singer NY, Weissman Y, Yom-Tov Y, Marder U. Isolation of Salmonella

Hessarek from starlings (Sturnus vulgaris). Avian Diseases. 1977;21:117-9.

https://doi.org/10.33321/cdi.2019.43.22

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8. Magistrali CM, Latini E, Manuali C, Neri C, Panzieri V, Bazzucchi A et al.

Cases of salmonellosis from S. Hessarek in European Starling (Sturnus vulgaris)

in the center of Italy. Sanita` Pubblica Veterinaria. 2008;49.

http://indice.spvet.it/arretrati/numero-49/005.html. Accessed September 2011.

[In Italian]

9. OIE (World Organization for animal health). Report of the meeting of the OIE

working group on wildlife diseases: 73rd Annual General Session of the

International Committee. [Internet] Paris. 2005. [cited 1 Jul 2018]. Available at

http://www.oie.int/doc/ged/D3888.PDF.

10. `Handeland K, Nesse LL, Lillehaug A, Vikøren T, Djønne B, Bergsjø B. Natural

and experimental Salmonella Typhimurium. infections in foxes (Vulpes vulpes).

Veterinary Microbiology 2008;132:129-34.

11. Gomez-Laguna J, Hernandez M, Creus E, Echeita A, Otal J, Herrera-Leon S et

al. Prevalence and antimicrobial susceptibility of Salmonella infections in free

range pigs. Veterinary Journal. 2011;190:176-8.

12. South Australian Department of Health and Ageing. SA Health Food Act

Report: year ending 30 June 2014. [Internet] Adelaide. Government of South

Australia. 2014 [cited 2 Jun 2018]. Available from

http://www.sahealth.sa.gov.au/wps/wcm/connect/1bd053004659eb248ff1bf7950

15c38d/14155%2BFood%2BAct%2BReport%2B2013-

14_WEB.PDF?MOD=AJPERES&CACHE=NONE&CONTENTCACHE=NON

E

13. Chousalkar KK, McWhorter A. Egg Production Systems and Salmonella in

Australia. In: Ricke SC, Gast RK, editors. Producing safe eggs: microbial

ecology of Salmonella. [Internet] London, United Kingdom, San Diego, CA,

United States, Academic Press. Elsevier Science & Technology. 2016 [cited 2

Jun 2018]:71-85. Available at https://ebookcentral-proquest-

com.virtual.anu.edu.au/lib/anu/detail.action?docID=4690602

14. Whiley H, Ross K. Salmonella and eggs: from production to plate. Int. j. Res.

Public Health. 2015;12:2543-56. Available at

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377917/

15. Gast RK. Microbiology of shell egg production in the United States. In: Ricke

SC, Gast RK, editors. Producing safe eggs: microbial ecology of Salmonella.

[Internet] London, United Kingdom, San Diego, CA, United States, Academic

Press. Elsevier Science & Technology. 2016 [cited 2 Jun 2018]:25-44. Available

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at https://ebookcentral-proquest-

com.virtual.anu.edu.au/lib/anu/detail.action?docID=4690602

16. Messens W. Egg Decontamination by Washing. In: Van Immerseel F, Nys Y,

Bain M, editors. Improving the Safety and Quality of Eggs and Egg Products.

Cambridge. Woodhead Publishing Limited. 2013:163-77.

17. Galiş AM, Marcq C, Marlier D, Portetelle D, Van I, Beckers Y et al. Control of

Salmonella contamination of shell eggs—preharvest and postharvest methods: a

review. Compr. Rev. Food Sci. Food Saf. 2013;12:155-82.

18. Thorns CJ. Bacterial food-borne zoonoses. Rev. Sci. Tech. 2000;19:226-39.

19. Food Standards Australia New Zealand. Primary Production and Processing

Standard for Eggs and Egg Products: Final assessment Report. (Proposal P301).

7 Apr 2011. Available from

http://www.foodstandards.gov.au/code/proposals/documents/P301%20Eggs%20

_%20Egg%20Products%20PPPS%20FAR%20FINAL%20AMENDED%20240

61.pdf

20. Food Standards Australia New Zealand. Primary Production and Processing

(PPP) Standard for Eggs and Egg Products (Standard 4.2.5) of the Australian

Food Standards Code. 20 May 2011. Available at

https://www.legislation.gov.au/Details/F2011L00860

21. Howard ZR, O’Bryan CA, Crandall PG, Ricke SC. Salmonella Enteritidis in

shell eggs: Current issues and prospects for control. Food Res. Int. 2012;45:755-

64. Available at https://www-sciencedirect-

com.virtual.anu.edu.au/science/article/pii/S0963996911002602

https://www-sciencedirect-com.virtual.anu.edu.au/science/article/pii/S0963996911002602https://www-sciencedirect-com.virtual.anu.edu.au/science/article/pii/S0963996911002602

52

Chapter 3

Chapter 3 of this bound volume is for restricted access only and has been submitted as a

separate document. Chapter 3 includes:

• Section 1: Shiga toxin producing Escherichia coli: overview, epidemiology and

public health significance.

• Section 2: Evaluation of the South Australian Shiga toxin-producing

Escherichia coli surveillance system.

• Section 3: The epidemiology of Shiga toxin-producing Escherichia coli in

South Australia, February 2017 to June 2018.

53

Chapter 4:

The South Australian Trauma Registry

Annual Report, 1 July 2015 to 30 June

2016: a descriptive epidemiological

analysis

54

Table of Contents

Chapter 4: The South Australian Trauma Registry Annual Report, 1 July 2015 to

30 June 2016: a descriptive epidemiological analysis .......................................................... 53

Index of Figures .................................................................................................................... 55

Index of Tables ..................................................................................................................... 56

Abbreviations ........................................................................................................................ 56

Glossary ................................................................................................................................. 57

Prologue ................................................................................................................................. 59

My role ............................................................................................................................. 59

Lessons learned ............................................................................................................... 59

Impact of the work .......................................................................................................... 60

Acknowledgements ......................................................................................................... 60

Master of Philosophy in Applied Epidemiology core activity requirement ............ 61

Executive Summary ............................................................................................................. 62

Key Findings .................................................................................................................... 62

Introduction ........................................................................................................................... 64

Trauma Services .............................................................................................................. 64

The South Australian Trauma System ......................................................................... 65

Major Trauma Services .................................................................................................. 65

The South Australian Trauma Registry ........................................................................ 66

Aims and objectives of the project ............................................................................... 68

Method ................................................................................................................................... 70

Results ................................................................................................................................... 74

Discussion ............................................................................................................................. 97

Appendix 1 South Australian Trauma Registry (SATR) Inclusion Criteria ............. 105

Appendix 2: SATR data quality issues, 1 July 2011 to 30 June 2016, variables

for inclusion in the Annual Report only .......................................................................... 107

Appendix 3: Summary of initial SATR data checking ................................................. 109

Appendix 4 SPSS Data cleaning syntax for SATR Annual Report, 1 July 2015

to 30 June 2016 ................................................................................................................... 117

Appendix 5: Summary of consultation with South Australian State Trauma

Committee regarding the content of the Annual Report ............................................... 137

Appendix 6 SPSS Syntax for Data Analysis for SATR Annual Report, 1 July

2015 to 30 June 2016 ......................................................................................................... 138

References ........................................................................................................................... 147

55

Index of Figures

Figure 1: Crude number of trauma events treated at South Australian Major Trauma

Services, injury date 1st July 2011 to 30th June 2016 ........................................................ 76

Figure 2: Number of trauma events treated at South Australian Major Trauma Services by

day of arrival at Major Trauma Service, injury date 1st July 2015 to 30th June 2016 ..... 77

Figure 3: Number of trauma events treated at South Australian Major Trauma Services by

time of arrival at Major Trauma Service, injury date 1st July 2015 to 30th June 2016 .... 77

Figure 4: Number of trauma events treated at South Australian Major Trauma Services by

principal mode of transport to Major Trauma Service, injury date 1st July 2015 to 30th

June 2016 .......................................................................................................................... 78

Figure 5: Proportion of trauma events treated at South Australian Major Trauma Services

by direct or indirect admission to Major Trauma Service and year, injury date 1st July

2011 to 30th June 2016 ..................................................................................................... 79

Figure 6: Proportion of trauma events treated at South Australian Major Trauma Services

by trauma team call-out status and year, injury date 1st July 2011 to 30th June 2016 ....... 80

Figure 7: Number of trauma events treated at South Australian Major Trauma Services by

trauma team call-out status and year, injury date 1st July 2011 to 30th June 2016 ............ 80

Figure 8: Number of trauma events treated at South Australian Major Trauma Services by

number of days admitted, injury date 1st July 2015 to 30th June 2016 ............................ 81

Figure 9: Age-specific annual incidence rate of trauma events treated at South Australian

Major Trauma Services, per 100,000 South Australian population, injury date 1st July

2011 to 30th June 2016 ..................................................................................................... 84

Figure 10: Number of trauma events treated at South Australian Major Trauma Services

by age group and sex, injury date 1st July 2015 to 30th June 2016 ................................... 85

Figure 11: Age and sex-specific annual incidence rate of trauma events treated at South

Australian Major Trauma Services, injury date 1st July 2015 to 30th June 2016 ............ 85

Figure 12: Number of trauma events treated at South Australian Major Trauma Services

by age group, sex and mortality, injury date 1st July 2015 to 30th June 2016 ................. 86

Figure 13: Place of injury for trauma events treated at South Australian Major Trauma

Services, injury date 1st July 2015 to 30th June 2016 ...................................................... 87

Figure 14: Number of trauma events treated at South Australian Major Trauma Services

by region, injury date 1st July 2011 to 30th June 2016 ..................................................... 88

Figure 15: Proportion of trauma events treated at South Australian Major Trauma

Services by NISS and age group, 1st July 2015 to 30th June 2016 ................................... 95

56

Index of Tables

Table 1: Summary statistics for all trauma events treated at South Australian Major

Trauma Services, injury date 1st July 2011 to 30th June 2016 ........................................... 75

Table 2: Trauma events treated at South Australian Major Trauma Services - injury and

death by age group and New Injury Severity Score (NISS), injury date 1st July 2015 to

30th June 2016 .................................................................................................................. 83

Table 3: Trauma events treated at South Australian Major Trauma Services by injury

type, injury date 1st July 2011 to 30th June 2016 ............................................................. 89

Table 4: Trauma events treated at South Australian Major Trauma Services by

mechanism of injury and year, injury date 1st July 2011 to 30th June 2016 .................... 91

Table 5: Road transport related trauma events treated at South Australian Major Trauma

Services by transport mode, 1st July 2011 to 30th June 2016 .......................................... 92

Table 6: Trauma events treated at South Australian Major Trauma Services by

mechanism of injury, sex, region of injury and age group, injury date 1st July 2015 to

30th June 2016 .................................................................................................................. 93

Table 7: Trauma events treated at South Australian Major Trauma Services by NISS and

year, injury date 1st July 2011 to 30th June 2016 ............................................................. 94

Table 8: Trauma events treated at South Australian Major Trauma Services by NISS, sex,

age group, region and mechanism of injury, 1st July 2015 to 30th June 2016 ................. 96

Abbreviations

AIS Abbreviated Injury Scale

ICD-10-AM International Statistical Classification of Diseases and Related Health

Problems, 10th Revision (ICD-10) Version for 2010

ISS Injury Severity Score

NISS New Injury Severity Score

SATS South Australian Trauma System

SATR South Australian Trauma Registry

SASTC South Australian State Trauma Committee

SATRSC South Australian Trauma Registry Sub-Committee

57

Glossary

Abbreviated Injury Scale (AIS)

An anatomically based, consensus derived, global severity scoring system that classifies

an individual injury by body region according to its relative severity on a six-point scale;

AIS 1-Minor, AIS 2-Moderate, AIS 3-Serious, AIS 4-Severe, AIS 5-Critical,

AIS 6-Maximum (currently untreatable).

The AIS scale is a measurement tool for single injuries and is the basis for calculating the

internationally recognised ‘Injury Severity Score’ (ISS) and ‘New Injury Severity Score’

(NISS) for patients with multiple injuries.1

Case fatality rate

The proportion of cases of a specified condition that are fatal within a specified time,

usually expressed as a percentage.2

Clinical Indicators

Quantitative measures that assess health structures, processes and outcomes. For

example, ’Time from arrival in Emergency Department to spinal clearance or diagnosis

should not exceed 4 hours’.

Injury Severity Score (ISS) / New Injury Severity Score (NISS)

The ISS and the NISS assess the combined effects of multiple injuries in a patient and are

based on an anatomical injury severity classification system, the Abbreviated Injury

Scale. The ISS and the NISS are internationally recognised injury severity scoring

systems which correlate with mortality, morbidity and other measures of severity. The

ISS is calculated as the sum of the squares of the highest AIS code in each of the three

most severely injured ISS Body Regions, maximum score = 75.3,4 The NISS is calculated

as the sum of the squares of the three highest AIS codes regardless of body region,

maximum score = 75.5 Trauma events with an ISS score of greater than 12 are considered

‘Major Trauma Events’.

58

Injury Types

• Blunt (non-penetrating) injuries: resulting from an impact with a dull, firm surface

or object, generally occur from mechanisms such as motor vehicle collisions,

pedestrian impacts, falls and sports injuries.6

• Penetrating injuries: require skin penetration by an external force as the principal

component of injury. Examples include stab and gunshot wounds, glass-related

injuries and impalements.7

• Burn injuries: are caused by exposure to electrical, thermal or corrosive agents such

as flames, hot substances, chemicals or radiation. Examples include situations where

electricity has primarily damaged soft tissues (electrical burns).7

• Immersion / Suffocation: placing a body under water or other liquid / the state or

process of being deprived of air or unable to breathe.

Major Trauma

Multiple injuries requiring complex multidisciplinary management or single system

injuries of a potentially life-threatening nature. These usually require complex

management at specifically designated and equipped health facilities.8

Minor Trauma

Less serious injuries that usually involve a single part of the body, and that can be well

managed with less specialised resources in a variety of clinical settings.8

Mechanism of injury

The primary circumstance or cause (external factor) of a trauma event (for example; fall

from a height or high-speed motor vehicle accident).

MedSTAR

Operated by the South Australian Ambulance Service, MedSTAR is a twenty-four-hour

emergency medical retrieval service that utilises specially trained teams to provide South

Australians with the highest level of emergency medical patient care, treatment and

transport (fixed wing ‘planes, helicopters or road ambulances) from any location in the

state to the most appropriate medical facility.9

59

Prologue

My role

I was tasked with designing and creating the first state-wide descriptive South Australian

Trauma Registry (SATR) Annual Report, 1 July 2015 to 30 June 2016. Whilst preparing

the report, I was able to identify SATR data quality issues within the system and to

highlight these issues in preparation for the planned implementation of an on-line SATR

database in January 2018, in addition to providing feedback to stakeholders. Preparation

of the annual report provided me with an opportunity to explore the complexities

involved in communicating the results of data analysis via a report format which can both

meet the expectations of the report audience and comply with SA Health formal

communication standards.

Lessons learned

• It is important to understand the dataset to be analysed, including data dictionary

definitions, any changes to how the data has been recorded during the reporting

period, any variations to how the data is being recorded at different sites and, reasons

for any missing data items.

• It is important to tailor the planned analysis and report content and format to the

anticipated report audience and, if possible, to facilitate two-way open

communication with stakeholders regarding the planned report.

• It is important to be aware that:

o the intended report audience might vary in their individual expectations of the

required report,

o some audience expectations might not be clearly communicated,

o one single report content and format might not be suitable for both professional

and lay audiences, and

o available resources are likely to impact on the ability to meet audience

expectations of the final report

• As far as possible, users of a report should actively participate in the design of the

report on an on-going basis so that there is a shared and realistic perception during the

report planning stage of the extent to which the report will meet various expectations.

60

• How to use IBM SPSS Statistics 24 software syntax for reproducible data cleaning,

re-coding and analysis and how to use of STATA (version 15) statistical software for

statistical significance testing.

• Organisations may have specific requirements for the format of their reports in terms

of fonts, styles, colours and report layouts; these requirements serve multiple

functions including ease of readability and recognition of the organisation’s brand.

Impact of the work

This data analysis:

• Provided a baseline summary and identified trends in trauma events in

South Australia for the South Australian State Trauma Committee (SASTC) and the

Department for Health and Wellbeing (‘SA Health’). The SASTC provides

governance for the South Australian Trauma Registry (SATR) and includes the

clinical heads and senior trauma nurses from Adelaide metropolitan trauma services

together with SA Health central office personnel from the Emergency Management

Unit and the Prevention and Population Health Branch (PPH).

• Identified aspects of the SATR that require quality improvement as SA implements a

new on-line SATR in January 2018; in response, an initial monthly quality assurance

report was introduced by PPH in September 2018.

• Provided a template for future SATR annual reports and facilitated the SASTC’s

shared understanding of what should be included in future annual reports; both, in

terms of the content/format included in the annual report produced and, in terms of

the content and format changes which the SASTC would like to include in future

reports.

• Progressed compliance with the SA Health Strategic Plan 2017-2020, which affirms

that evidence and information is presented in a meaningful way and underpins

clinical service design.10

Acknowledgements

I wish to acknowledge Helen Thomas, Manager of the SA Health Prevention and

Population Health Branch Data Warehouse, who provided valuable technical advice, in

particular, explanation regarding aspects of the SATR database. PPH Principal

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Statistician, Kamalesh Venugopal, provided guidance regarding statistical significance

testing and, PPH Communications Advisor, Karli Borresen, provided advice regarding

formatting the report in accordance with the SA Health Communications Protocol Policy

Directive.11 Dr Tambri Housen provided guidance regarding the writing of this chapter.

Lastly, I wish to acknowledge the SA Nurse Trauma Coordinators who resolved data

queries and clarified aspects of how the data should be interpreted, ensuring that the

report made sense from a clinical perspective.

Master of Philosophy in Applied Epidemiology core activity

requirement

This chapter is written in fulfilment of the field placement core activity requirement to

analyse a public health dataset such as surveillance data.

62

Executive Summary

The South Australian Trauma Registry (SATR) Annual Report includes data for trauma

events managed and recorded in the SATR by the three South Australian (SA) Major

Trauma Service hospitals; the Royal Adelaide Hospital, Flinders Medical Centre and, the

Women’s and Children’s Hospital.

This is the first South Australian state-wide descriptive annual report of the SATR data.

Prior to this report, ongoing analysis of the trauma data was performed within individual

hospitals for quality improvement and trauma audit activities but, analysis at the state-

wide level was limited to a number of defined trauma clinical indicators only.

Data for injuries that occurred between 1 July 2015 and 30 June 2016 are the focus of the

annual report. For the purpose of comparison, data for the preceding four year period,

1 July 2011 to 30 June 2015, have also been included in the analysis. The report has been

produced in consultation with the SA State Trauma Committee and the SA Trauma

Registry Sub-Committee.

Key Findings

In the year 1 July 2015 to 30 June 2016:

• In total, 3,035 trauma events were recorded in the SA Trauma Registry; a 35%

increase since the year 1 July 2011 to 30 June 2012 (2,244 events).

• The injury rate per 100,000 South Australians was 178.6; this rate has risen from a

rate of 136.9 in the year 1 July 2011 to 30 June 2012, a 30.5% increase.

• At the time of discharge from the Major Trauma Services, the proportion of people

with trauma events known to have survived was 97.7% (2,945 out of 3,015).

• Sixty-two trauma-related deaths occurred at the Major Trauma Services during the

episode of care for the trauma event. The majority of deaths occurred in trauma

events with a New Injury Severity Score (NISS) of greater than 12.

• The overall rate of trauma-related deaths was 3.6 per 100,000 South Australians. The

highest rate of deaths occurred in people aged 80 years and over; 23.3 deaths per

100,000.

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• The majority of trauma events occurred in males (66.7%) and in metropolitan areas

(63.5%).

• The highest rate of trauma occurred in people aged 15-19 years; the age-specific

injury rate for this age-group was 327.4 trauma events per 100,000 South Australians.

• There has been an upward trend in the annual rate of trauma events in all age groups

since the year 1 July 2011 to 30 June 2012; the largest increase occurred in the age-

group 0-15 years with the rate of injury rising 66.3% from 119 to 198 trauma events

per 100,000 South Australians in this age-group.

• Just over half of the trauma events that occurred were road transport related (1,651

events, 54.4%).

• Trauma events in pedal cyclists rose to 22.0% (363) of all transport-related events,

increasing from 13.8% (172) in the year 1 July 2011 to 30 June 2012, an 8.2%

increase.

• Falls were the cause of 22.3% (678) of trauma events but accounted for 40.3% (25) of

trauma-related deaths.

• The proportion of trauma events not admitted to the Major Trauma Service hospital

has risen each year from 24.5% (549 events) in the year 1 July 2011 to 30 June 2012

to 34.8% (1,051) in the year 1 July 2015 to 30 June 2016.

• The proportion of trauma events transferred directly to a Major Trauma Service (not

treated at other hospitals en-route) increased slightly from 73% in the year 1 July

2011 to 30 June 2012 to 79% in the year 1 July 2015 to 30 June 2016.

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Introduction

Physical injury to the body (or “trauma”) is the sixth leading cause of death worldwide.12

Nearly 8% of reported deaths in Australia are due to injuries with higher rates reported in

men and in the oldest age group, 65 years and older.13 Injury is the leading cause of death

in people under the age of 45 years.14

In addition to the risk of death, the costs associated with injury include the cost of

emergency department visits, hospital admissions and the added cost of significant

human and societal burden with many injury survivors never returning to school, work, or

their regular lives.15 ‘Years Lived with Disability’ (YLD) is a measure of the years of

what could have been a healthy life but were instead spent in states of less than full health

(Refer Box 1).16 Based on calculations of YLD, the Australian Burden of Disease Study:

impact and causes of illness and death in Australia 2011 report states “