Message from the director
What is pneumonia?
What can be done about pneumonia?
Goals of the CRDM
CRDM timeline
Vaccine reducing disease in children and adults
Using a vaccine to reduce antibiotic resistance
Who is most at risk of pneumococcal disease in the pneumococcal vaccine era?
9. HIV-infected individuals and infants <1 year of age are at
increased risk of severe influenza
10. Influenza vaccination is the best way to prevent influenza
11. Emerging respiratory viruses: Middle East Respiratory
Syndrome Coronavirus (MERS-CoV) and avian influenza
12. Ten years of tracking meningococcal meningitis and sepsis
13. Preventing meningococcal disease
14. Burden of respiratory syncytial virus (RSV) in South Africa and risk groups
15. Discovering pertussis in South Africa
16. Staying ahead with advanced diagnostics
17. Sharing skills and experience
18. CRDM surveillance sites
19. Calendar of events for 2012-2014
20. CRDM staff
21. CRDM Publications 2012-2014
22. Contacts and resources
12th November 2014 marks the sixth anniversary
of World Pneumonia Day, an initiative which was
established to advocate for greater attention to be
focused on what is termed by the UNICEF as the
“forgotten epidemic”.
Despite the significant progress in reducing under-five childhood
mortality globally over the past decade, approximately 942,000
children died of pneumonia in 2013. This placed pneumonia as
the leading cause of under-5 childhood mortality, with >95%
of these deaths occurring in low-income countries. Although a
number of bacteria, viruses and fungi have been established to
cause pneumonia, the majority of deaths are thought to occur
due to bacterial infections. In addition, Pneumocystis jirovecii
and cytomegalovirus also contribute to pneumonia deaths
among HIV-infected and other immunocompromised children.
Among the bacterial causes of pneumonia, a large proportion
is attributable to Streptococcus pneumoniae and previously
(prior to widespread immunization) to Haemophilus influenzae
CRDM | 2012-2014
type B (Hib). The fact that these bacteria are among the leading
causes of pneumonia mortality is more an indictment on the
poor health infrastructure which exists in low-middle income
countries, than due to any major challenges related to antibiotic
resistance associated with these bacteria. It has been estimated
that less than one third of children with pneumonia have access
to first-line antibiotic therapy in low-income countries, which if
improved could reduce pneumonia mortality by up to 40-50%
alone. This is a serious indictment of failure to provide basic care
to the most vulnerable in the population. This inequity in access
to health care is further accentuated among those children living
in the poorest economic quintile of the population, and who
suffer disproportionately from pneumonia due to other factors
such as increased exposure to air pollutants and malnutrition.
The ongoing, accelerated introduction of pneumococcal conjugate vaccine (PCV) into public
immunisation programmes of low-income countries, coupled with the recently established widespread
introduction of Hib conjugate vaccine, has the potential for accelerating a decline in pneumonia
hospitalisation and mortality in low-middle income countries. The South African government has been
exemplary in the timeous introduction of HibCV and PCV into its public immunisation programmes,
being the first in Africa to self-fund these vaccines for its public immunisation programme since 1999
and 2009 respectively. Although the impact of these vaccines on childhood mortality is difficult to
quantify in countries such as South Africa, where a number of other changes related to improved
HIV management occurred concurrently with the introduction of these vaccines, the introduction
of these vaccines have likely contributed to the ongoing decline in under-five childhood mortality
in South Africa. In 2013, the under-five childhood mortality was 37 per 1,000 live births, the lowest
rate in the history of the country and almost half of what it was a decade earlier. However, much still
remains to be done in South Africa to prevent children from developing and dying from pneumonia.
Included among these are the strengthening of primary health care to ensure early detection and
timeous treatment with the correct antibiotics, as well as a focus on reducing risk factors such as
indoor pollution and malnutrition, especially in the rural areas of South Africa.
The Centre for Respiratory Diseases and Meningitis (CRDM) at the National Institute for Communicable
Diseases (NICD) has been stalwart in providing epidemiological data on the burden of disease due to
bacterial and viral causes of pneumonia in South Africa. Through its decade-old laboratory-based
and more recently active, hospital-based surveillance, the centre provides burden of disease data
on the causes of childhood and adult pneumonia which are unsurpassed on the African continent.
This has gained it international recognition and also allows for it to contribute to multiple World
Health Organization programmes, and is used as a reference laboratory for training of other African
scientists and a source of isolates to help inform WHO vaccine recommendations on influenza
virus. The activities of the CRDM also contribute to measuring the impact which the introduction
of vaccines has on childhood and adult pneumonia morbidity and mortality. The CRDM, like many
other centres at the NICD, is a national asset whose mission remains to improve the lives of all South
Africans by providing updated epidemiological data to refine treatment strategies and prioritise the
introduction of future vaccines into the public immunization programme of South Africa. Also, its
programme ensures ongoing surveillance to timeously identify any novel viruses, including influenza
viruses with pandemic potential, to inform public health policy and assist the Department of Health
with its programme.
The activities of the centre contribute to the mission of World Pneumonia Day in highlighting the
burden and success of preventative strategies such as vaccination in South Africa. This also provides
a tool for advocacy on pneumonia prevention elsewhere on our continent. The CRDM staff members
are commended for their dedication and the success of their programme on this World Pneumonia
Prof. Shabir Madhi
Executive Director: National Institute for Communicable Diseases
CRDM | 2012-2014
Pneumonia is an infection of the lungs
that is usually caused by bacteria or
viruses, and can also be caused by
Pneumonia is the leading killer of children under five years old
In 2012 alone, 1.1 million children died from this preventable and treatable illness, accounting
for 17-18% of child mortality.
In 2008, there were an estimated 541,000 deaths due to Streptococcus pneumoniae
(pneumococcus) and 203,000 deaths due to Haemophilus influenzae type b (Hib) in children
under five globally.
99% of child pneumonia deaths occur in developing countries.
“Influenza and pneumonia” was the second most common underlying cause of death in South
Africa in 2011, after tuberculosis.
Respiratory syncytial virus is the most common viral cause of childhood pneumonia.
Pneumonia creates an economic burden for families, communities, and governments
Preventing pneumonia averts treatment costs, other losses due to illness and allows children to
become healthy, productive adults.
Scaling up coverage of vaccines against Hib and pneumococcus in the world’s 73 poorest
countries (2011-2020) would avert $51 billion in treatment costs and productivity losses.
This increase in vaccine coverage would also save 2.9 million lives and prevent 52 million cases
of illness.
Global Pneumonia Interventions
Controlling childhood pneumonia requires an integrated package of interventions to protect, prevent and treat the disease.
Fortunately, many of the interventions targeted at pneumonia also help control other childhood diseases, such as diarrhoea,
and should be part of a comprehensive approach to child survival. The Integrated Global Action Plan for the Prevention and Control
of Pneumonia and Diarrhoea (GAPPD) formulated by the World Health Organization (WHO) and the United Nations Children’s
Fund (UNICEF) in 2013 aims to stop preventable childhood deaths from pneumonia and diarrhoea by 2025. Implementation of
this plan by national governments will allow them to achieve the Millennium Development Goal (MDG) to save children under
the age of 5 (MDG4).
Protect Against Pneumonia
Treat Pneumonia
Exclusive breastfeeding during the first six months of life and adequate nutrition
through age five protect babies from pneumonia, diarrhoea, malnutrition and
other diseases.
Regular hand washing, access to clean water and sanitation protect children
against pathogens that cause pneumonia, diarrhoea and other diseases.
Eliminating household air pollution, especially smoke from unsafe cooking stoves
reduces the risk of severe pneumonia in children.
Antibiotics such as amoxicillin can prevent the majority of pneumonia deaths and
cost only about $US 0.21-0.42 per treatment course.
Effective integrated case management strategies ensure that children receive
proper and timely treatment for pneumonia.
Improving access to services and increasing awareness and demand for services
within communities is crucial to controlling pneumonia as only around 30% of
children with bacterial pneumonia receive the antibiotics they need.
Prevent Pneumonia
Vaccines against pneumococcus, Hib, pertussis, influenza and measles can
prevent a significant portion of pneumonia cases.
The Hib vaccine was introduced into the South African Expanded Programme on
Immunization (EPI) in 1999 and the pneumococcal conjugate vaccine in 2009. The
measles vaccine is also given as part of the EPI.
Annual influenza vaccination is recommended for everyone ≥6 months of age in
South Africa.
Other preventative strategies include: adequate nutrition, zinc supplementation
for children with diarrhoea, prevention of HIV infection in children and antibiotic
prophylaxis for HIV-infected or -exposed children.
Efavirenz-based programmes for the prevention of mother-to-child transmission
of HIV were rolled out in South Africa from April 2012 and cotrimoxazole
prophylaxis for HIV-infected children is recommended.
Addressing socioeconomic and environmental factors associated with increased
risk to contract pneumonia emphasises personal hygiene practices like regular
hand washing with soap and implementing measures to reduce household air
CRDM | 2012-2014
In 2012, the NICD was restructured and the Centre for Respiratory Diseases and Meningitis
(CRDM) was formed. Our goals are:
To conduct surveillance for communicable respiratory diseases and meningitis within South Africa in order to
provide data on the burden, severity and seasonality.
To characterise pathogens contributing to respiratory diseases and meningitis in order to understand the
contribution of genetic factors to the cause and transmission of disease, and guide vaccine development,
treatment and prevention policy.
To monitor trends in antiviral and antibacterial drug resistance in respiratory and meningeal pathogens in
order to inform empiric treatment guidelines.
To monitor the impact and effectiveness of interventions to reduce
respiratory diseases and meningitis.
To provide reference laboratory functions for specialised organism
identification and characterisation related to respiratory diseases
and pathogens causing meningitis nationally and regionally.
To identify and characterise novel respiratory and meningeal
pathogens with potential to cause outbreaks and to assist with
response to respiratory disease outbreaks.
To be a source of local and regional expertise on respiratory
diseases and meningitis.
CRDM | 2012-2014
To engage in directed and relevant research to answer questions
related to regional respiratory disease and meningitis disease
problems and their surveillance and management.
To build local and regional capacity in epidemiology and
laboratory diagnostics for respiratory diseases and meningitis.
CRDM | 2012-2014
Pneumococcal conjugate vaccine (PCV) introduced into the Expanded Programme on Immunisation (EPI)
Haemophilus influenzae serotype b (Hib) vaccine booster at nine months introduced into the EPI
Pertussis vaccine changed from whole cell to acellular pertussis vaccine in the EPI
Syndromic surveillance programme for Severe Acute Respiratory Illness (SARI) started in three provinces to test for pneumococcus,
influenza, respiratory syncytial virus and eight other common respiratory viruses
New molecular diagnostic assays implemented to detect and serogroup/type Streptococcus pneumoniae, Neisseria meningitidis,
Haemophilus influenzae and ten respiratory viruses
First laboratory-confirmed case of pandemic influenza A(H1N1)pdm09 identified in South Africa
First edition of the annually updated “Healthcare Workers Handbook on Influenza” published
Enhanced viral watch programme for surveillance of hospitalised patients in all nine provinces introduced
SARI surveillance site in Klerksdorp-Tshepong started enrolling patients
Case definition for SARI surveillance expanded at Edendale and Klerksdorp-Tshepong sites to
include chronic cases
Case-control study initiated to evaluate effectiveness of PCV-7 in routine use through the EPI
13-valent PCV replaced 7-valent vaccine in the EPI
Avian influenza A(H7N1) outbreak in ostriches in the Western Cape
Guidelines published for the Management, Prevention and Control of Meningococcal Disease in South Africa
CRDM | 2012-2014
Healthcare utilisation survey conducted in Pietermaritzburg
Multi-year study of household transmission of influenza in HIVinfected and -uninfected individuals started
CRDM biosafety level 3 laboratory established
Nature; Vol. 312, Aug, 2014
Centre for Respiratory Diseases and Meningitis established
Expanded testing to include atypical bacterial causes of pneumonia, pertussis, tuberculosis and Pneumocystis jirovecci at Edendale and Klerksdorp-Tshepong SARI sites
Molecular diagnostic assays implemented for detection of Bordetella pertussis, Mycoplasma pneumoniae,
Chlamydia pneumoniae and Legionella species
Healthcare utilisation surveys conducted in Soweto and Klerksdorp
Surveillance for influenza-like illness implemented at Edendale and Klerksdorp-Tshepong sites
Avian influenza A(H7) outbreak in ostriches in the Western and Eastern Cape areas
CRDM appointed as WHO/AFRO (World Health Organization Regional Office for Africa) Regional Reference
Laboratory for vaccine-preventable invasive bacterial diseases (VP-IBD) for the southern and eastern African
Scientists have struggled to explain the erratic
behaviour of the binary star η Carinae, which
brightened unexpectedly in the 1840s and
again more recently.
Visual apparent magnitude*
*Lower numbers represent greater brightness.
CRDM featured in the journal “Nature” for the work being done
on monitoring the impact of the pneumococcal vaccine in
South Africa. Nature; Vol. 312, Aug., 2014; News in Focus
SARI surveillance implemented at Rahima Moosa Mother and
Child and Helen Joseph Hospitals
A nurse prepares to immunize a young child with pneumococcal and rotavirus vaccines in Ghana.
Hidden bonus
from vaccination
Immunization against pneumococcus in Africa also reduces
levels of antibiotic resistance.
his summer, Eritrea, Côte d’Ivoire and
Niger will join a growing list of countries where infants receive a vaccine
to prevent pneumonia, meningitis and other
deadly diseases caused by the pneumococcus bacterium (Streptococcus pneumoniae).
Pneumonia is a leading killer of young children in low-income countries; vaccinations
from 2010 to the end of this year are estimated
to have averted 500,000 deaths, according to
the GAVI Alliance in Geneva, an international
organization that facilitates vaccination.
Data from South Africa also point to another
benefit of vaccination: stemming a rising tide
of antibiotic resistance in the developing
world. The country’s introduction of a pneumococcal conjugate vaccine (PCV) in 2009 has
not only reduced the overall incidence of invasive pneumococcal disease by about two-thirds
in infants (the age group vaccinated) and in
adults, but has also reduced penicillin-resistant
infections in both groups.
This is the first time such benefits have
been observed outside the developed world.
X-ray production peaked in mid-July
and has since plummeted to near zero —
probably as the colliding winds, where
the X-rays are born, have become entirely
unstable and collapsed.
The Hubble Space Telescope and other
instruments are also tracking dramatic
changes in the chemical-element signatures
found in η Carinae’s light spectrum. The
interaction between the two approaching
stars can strip electrons from elements such
as iron and helium, ionizing them more
strongly than in normal celestial environments. “You have these bare helium nuclei
— that’s awfully hard to make in normal
circumstances,” says Gull. Watching this
process over time helps to reveal how the
stellar winds are interacting.
At the Pico dos Dias Observatory in
southern Brazil, astronomer Augusto
Damineli has been spending every night
since 25 July trying to catch a glimpse of
η Carinae through the winter clouds. On
29 July, his team finally caught a brief opening and managed to gather data showing that
a helium spectral line is dropping in just the
pattern that Damineli expected. “TOUCHDOWN!” he wrote in an e-mail.
In 2009, when η Carinae had its most
recent close encounter, the system’s X-ray
production plunged and then shot back up
in half the time it did in 2003. That could be
because the primary star’s winds are slowing down, so it takes less time for the whole
system to recover. If the wind speeds have
continued to drop, X-ray emissions might
shoot up even faster than last time.
Seeing such big differences from one
close encounter to the next is “what everyone is waiting for”, says Andrea Mehner,
an astronomer at the European Southern
Observatory in Santiago, Chile, who is
monitoring η Carinae with Hubble. “We
cannot make the star do something exciting if it doesn’t want to.” ■
1 4 | NAT U R E | VO L 5 1 2 | 7 AUG U S T 2 0 1 4
© 2014 Macmillan Publishers Limited. All rights reserved
CRDM | 2012-2014
decline in IPD
was almost
70 %
In 2009, all infants in South Africa started receiving the pneumococcal conjugate vaccine as part
of the government’s immunisation programme. Because we had documented levels of severe
pneumococcal disease as part of our national surveillance programme before the vaccine was
rolled out to all children (von Gottberg et al., Vaccine, 2013), we were able to monitor the changes
in disease as a result of bringing this vaccine into all South African vaccination clinics. In 2010, we
already noticed some declines in disease at a very young age (<2 years of age), but by 2012, disease
due to the serotypes contained in the vaccine had decreased by almost 90% and even invasive
pneumococcal disease overall (including all the other serotypes that are not included in the vaccine)
showed a decline of almost 70%.
CRDM | 2012-2014
Although only infants are receiving this vaccine, due to the fact that this age group spreads disease
to other age groups, disease has declined across all age groups. This was not an unexpected finding,
as this protection for adults has been seen in countries such as the United States and England. It is
the first time however, that such additional protection in age groups not vaccinated has now also
been documented in a low- or middle-income country.
Our centre started an additional research study to measure the effectiveness of this vaccine more
carefully and we were able to confirm more accurately that this vaccine prevented disease due to the
serotypes that it was designed to prevent by approximately 75% in HIV-uninfected children (Cohen
et al., Clin Infect Dis, 2014). We were not able to show clear protection in HIV-infected children, but
these children are also benefiting from the overall reduced transmission of this organism.
In South Africa, we are fortunate in that we can monitor antibiotic resistance among pneumococcal
isolates - the most important bacterium to cause pneumonia in children, as part of the national
surveillance programme. Throughout the country, laboratories that receive clinical specimens from
sick patients who may have pneumonia or meningitis, and that grow this bacterium during the
processing of these specimens, are then requested to send these isolates to our laboratory so that
we can characterise the isolates and monitor antibiotic resistance. As a result, more than 40,000
cases have been recorded on our database since 2003 and many of these cases have isolates saved
for further testing.
Approximately 40% of pneumococcal isolates causing severe disease in all ages were penicillin
resistant when the CRDM reviewed data from 2003 through 2008 (Crowther-Gibson et al., Antimicrob
Agents Chemother, 2012). This type of antibiotic resistance was more common among isolates
causing disease in children (~60% resistance). Approximately 20% of isolates were so-called multidrug resistant, in that they were classified as resistant to a few antibiotic groups. This further limits
choices of antibiotics for treatment.
Due to resistance being more common among children, it is also more common among the
serotypes that cause disease in children, which are also the serotypes specifically targeted by the
pneumococcal conjugate vaccines currently being used in South Africa. By reducing these childhood
serotypes, we have effectively also reduced the more resistant pneumococcal strains, and antibiotic
resistance has declined substantially among the isolates that we are subsequently receiving in our
laboratory. So far we have been able to measure more than 80% reduction in penicillin-resistant
and multi-drug-resistant disease among very young children (<2 years) following introduction of
pneumococcal conjugate vaccines.
CRDM | 2012-2014
Who is most at risk of pneumococcal disease in the pneumococcal vaccine era?
As part of our research study to monitor vaccine effectiveness in routine practice (Cohen et al.,
Clin Infect Dis, 2014), we examined groups of children who were at highest risk of contracting
pneumococcal disease with and without vaccination (von Mollendorf et al., Antimicrob Agents
Chemother, 2014). We found that children who were HIV-uninfected and had disease caused
by any serotypes, were at higher risk if they had young siblings, underlying medical conditions,
poorer socio-economic backgrounds, were not up-to-date for vaccination and had been exposed
to HIV perinatally. In contrast HIV-infected children who were ill, i.e. malnourished, diagnosed
with tuberculosis and not on antiretroviral therapy were more likely to get pneumococcal
Due to improvement in programmes to reduce the perinatal transmission of HIV from mothers
to their children, there are a growing number of children who are HIV-exposed but uninfected.
We showed that these children are at increased risk of being hospitalised with pneumococcal
disease as well as dying from pneumococcal disease if they are very young (<6 months of age)
when they fall ill.
HIV-infected individuals and infants <1 year of age are at increased risk of severe influenza
It is important to know who is at highest risk of severe influenza in order to decide who to
target with vaccination campaigns. The CRDM analysed national mortality and surveillance
statistics and combined this with modelling approaches to address this important question. We
estimated that influenza causes 2,500 - 5,700 respiratory deaths and 17,000 - 22,000 respiratory
hospitalisations in South Africa each year (Tempia et al., Clin Infect Dis, 2014). Children aged
<1 year have the highest risk of being admitted to hospital or dying from influenza (Tempia
et al., Clin Infect Dis, 2014 and Cohen et al., Clin Infect Dis, 2014). Analysis of data from more
CRDM | 2012-2014
than 10,000 people enrolled into the pneumonia surveillance programme demonstrated that
HIV-infected individuals are three to six times more likely to be admitted to hospital with severe
influenza than HIV-uninfected individuals (Cohen et al., Clin Infect Dis, 2014). Once admitted to
hospital, HIV-infected individuals also stay in hospital for longer and are more likely to die.
CRDM | 2012-2014
Vaccination with the trivalent influenza vaccine (TIV) is the best way to prevent influenza infection.
The NICD publishes annual recommendations for the risk groups which should be targeted for
influenza vaccination (Walaza, S Afr Med J, 2014). The main risk groups include pregnant women
(including the first two weeks of the post-partum period), infants and young children (particularly <2
years of age), persons with chronic diseases (including HIV) and persons aged ≥65 years.
The National Department of Health started providing influenza vaccines to the target groups in
2010 and before this time, South African citizens could access the influenza vaccine from private
practitioners and pharmacies at a cost. Each year, before the start of the influenza season, the CRDM
assists the Department of Health with the training of health care workers in preparation for the
delivery of the influenza vaccine. To help raise awareness among health practitioners about the
importance of influenza vaccination, the CRDM hosts the annual influenza symposium before the
start of the influenza season. The health care worker’s handbook on influenza, published annually,
also provides guidance on clinical management and treatment considerations for patients with
respiratory illness during the influenza season.
CRDM | 2012-2014
Influenza vaccine effectiveness depends on the characteristics of the person being vaccinated (age
and health) and on whether there is a good match between the circulating viruses and the viruses
contained in the vaccine. In general, influenza vaccines work best among children >2 years and
healthy adults. Recent studies using data from the Viral Watch influenza surveillance programme
which is coordinated by the CRDM, have generated annual estimates of the effectiveness of the
influenza vaccine as administered in South Africa (Ntshoe et al., PLoS One, 2014). In 2013, TIV was
estimated to be 87% effective against laboratory-confirmed influenza. This study showed that the
vaccine was significantly protective in 2010, 2011 and 2013, but not in 2012 when the circulating
A(H3N2) strain showed genetic drift. A recent study conducted in South Africa showed that influenza
vaccination of pregnant HIV-infected and-uninfected women was safe and effective. In addition it
provided protection to HIV-unexposed infants up to 24 weeks of age (Madhi et al., N Engl J Med,
2014). The effectiveness in infants is important because the influenza vaccine is not licensed for
children aged <6 months and this group is at high risk of influenza-associated hospitalisation and
Middle East Respiratory Syndrome Coronavirus
(MERS-CoV) and avian influenza A(H7N9)
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was identified in 2012 as the cause
of severe acute respiratory syndrome cases in Saudi Arabia. All cases of MERS have been linked
to countries in and near the Arabian Peninsula and travel history to those countries. The source of
human infection with MERS-CoV is still unknown, although the virus has been found in some camels.
Persons at highest risk to develop severe MERS include people with diabetes, kidney failure, chronic
lung disease, and people whose immune systems are compromised such as transplant and HIVinfected individuals.
Human infections with a new avian influenza A(H7N9) virus were first reported in China in March 2013.
Most human infections are believed to result from exposure to infected poultry or contaminated
environments such as live bird markets in China. This virus is defined as a low pathogenic avian strain
as it does not cause disease symptoms in poultry and may continue unnoticed. The possibility that
H7N9 could gain the ability to spread sustainably among people should not be ignored.
Human-to-human transmission of MERS-CoV and avian influenza A(H7N9) is through close contact
with confirmed cases, but no evidence of sustained spread between humans has been reported.
For emerging infectious agents of concern, all countries should have the ability to quickly identify
potential cases as part of their pandemic preparedness planning.
South Africa conducts active surveillance for imported cases of MERS-CoV and influenza A(H7N9).
Case definitions are updated regularly and are published on the NICD webpage. The CRDM offers
diagnostic testing for MERS-CoV and influenza A(H7N9) as well as a number of additional influenza
types and subtypes which have been identified in animals. Support for diagnostic testing is also
offered to neighbouring countries that do not have in-country ability to test for emerging viruses. No
cases of MERS-CoV or influenza A(H7N9) have been identified in South Africa to date.
CRDM | 2012-2014
Even though meningococcal infection occurs infrequently in the population (incidence on average
of 1 per 100,000 persons), it is a devastating illness with a sudden onset of severe symptoms that
can be life-threatening, even to previously healthy individuals. Meningococcal disease is endemic to
South Africa and has the potential to cause outbreaks in crèches, schools, university residents, and
on the mines. Since 1999, the CRDM has been conducting surveillance for all laboratory-confirmed
cases of meningococcal disease in South Africa.
Ten years of meningococcal surveillance data from South Africa were presented at the 16th
International Congress of Infectious Diseases, held in Cape Town in 2014. These data clearly show the
cyclical nature of the disease as it waxes and wanes over a ten-year period. Currently disease rates
are at a nadir, therefore South Africa should be on the alert for a possible upsurge of meningococcal
disease over the next few years.
CRDM | 2012-2014
Much work has been done to characterise the molecular make-up of the meningococcal isolates
causing disease in South Africa by multilocus sequence typing (MLST) and comparing them to
isolates from other countries with isolates registered on the global database (http://pubmlst.org/
neisseria/). Meningococci causing disease in South Africa have been characterised and these data
have been published in various peer-reviewed journals (du Plessis et al., J Clin Microbiol, 2012;
Moodley et al., J Clin Microbiol, 2012; du Plessis et al., J Infect, 2014 and Ndlangisa et al., PLoS One,
Meningococcal vaccine uptake in South Africa is minimal, however with the recent registration of
conjugate meningococcal vaccines CRDM staff have participated in various expert advisory groups
in preparation for the use of these new vaccines. The unit is also undertaking a cost-effectiveness
analysis to determine potential approaches for routine quadrivalent conjugate meningococcal
vaccination introduction in South Africa. Seventy-five percent of the meningococcal cases occurring
in South Africa would be prevented by these vaccines which are targeted at preventing disease due
to serogroups A, C, Y and W. Potential options for routine vaccination would be to target infants,
where disease burden is highest, or teenagers, a group where nasopharyngeal carriage is highest
and who contribute most to ongoing transmission.
Vaccines based on outer-membrane proteins (OMP) of meningococci have been developed,
particularly targeting serogroup B strains which account for a large proportion of disease in
developed countries and almost 25% of meningococcal disease in South Africa. Altough this vaccine
is targeted at preventing serogroup B disease, it may protect against other serogroups. We have
described the distribution of vaccine antigens in isolates from other meningococcal serogroups
(Mothibeli et al., Vaccine, 2011). This knowledge should help guide decision makers whether these
new OMP vaccines would be of benefit to our population.
The CRDM will continue to use the surveillance data to describe the epidemiology of laboratoryconfirmed, invasive disease and to monitor for emerging antimicrobial resistance of the isolates. It
will also advocate, where necessary, for the prevention of disease through vaccination. Molecular
characterisation will continue in a effort to better understand the lineages that commonly cause
disease as we commit to fighting meningococcal disease on a global scale.
CRDM | 2012-2014
CRDM | 2012-2014
Respiratory syncytial virus (RSV) is the most common cause of viral pneumonia in children and most
children will have been infected by the age of two years. Many children will have a mild common
cold-like infection, and re-infection with RSV is common.
Surveillance for RSV in hospitalised individuals in South Africa has demonstrated that during the
annual RSV season 50-60% of all respiratory admissions in children are due to RSV. The RSV season in
South Africa begins in early February until mid May/early June each year. This season precedes the
influenza season in South Africa.
times more likely to die from RSV infection than HIV-uninfected children. The only prophylaxis and
treatment available for RSV is a very expensive monoclonal antibody called palivizumab. Although
palivizumab is not available in the public health care sector, when used it is usually given to children
at risk of severe illness and given just prior to the RSV season. There are several candidate vaccines
in development.
In South Africa children under the age of one year admitted to hospital are three times more likely
to have RSV-associated pneumonia than non-RSV pneumonia. HIV-infected children are three to
five times more likely to be admitted to hospital with RSV pneumonia compared to HIV-uninfected
children (Moyes et al., J Infect Dis, 2013). In addition, hospitalised HIV-infected children are 30
Pertussis, commonly known as whooping cough, is caused by the bacterium Bordetella pertussis. It
is a highly infectious disease caused by person-to-person spread of infectious respiratory droplets.
Bordetella pertussis can cause severe disease in neonates and infants, as well as in older children
and adults. It is a vaccine-preventable disease and use of the vaccine has significantly reduced the
burden of disease globally. However, in countries with high vaccine coverage, the disease still occurs
in neonates and infants that have not received the full primary vaccination schedule. In addition,
countries such as the United States, that have replaced the whole-cell pertussis vaccine with the
acellular pertussis vaccine are observing an increase in disease in adolescents, potentially due to
waning immunity.
In South Africa, the whole-cell pertussis vaccine was introduced in 1950 and was replaced by the
acellular vaccine in 2009. However, there are limited data on the prevalence of pertussis in South
Africa. We have established laboratory methods for the identification of Bordetella species from clinical
specimens. We provide specialised diagnostics for suspected cases of pertussis in South Africa and
report all cases to the Department of Health. In 2012, we initiated ongoing surveillance for pertussis
and are collecting data on the epidemiology of pertussis disease to increase our understanding
of pertussis in South Africa, detect outbreaks and advise on policy. We are currently performing
surveillance at three sites in Gauteng, KwaZulu-Natal and North West. In 2015, surveillance will be
expanded to Mpumalanga and the Western Cape.
CRDM | 2012-2014
Molecular diagnostics
We have developed highly sensitive and specific molecular diagnostic assays for the detection and
characterisation of respiratory and meningeal pathogens including Streptococcus pneumoniae,
Haemophilus influenzae, Neisseria meningitidis (Wang et al., J Clin Microbiol, 2012), Bordetella
pertussis, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella species, parainfluenza virus
1-3, respiratory syncytial virus, influenza virus A and B, enterovirus, human metapneumovirus,
adenovirus and rhinovirus (Pretorius et al., J Infect Dis, 2012). These real-time PCR assays enable us
to perform rapid diagnostics from clinical specimens, and particularly culture-negative specimens.
CRDM | 2012-2014
To ensure reliable and accurate results, we participate in internal and external quality assessment
programmes including the United Kingdom National External Quality Assessment Service (UK
NEQAS), Quality Control for Molecular Diagnostics (QCMD), exchange programmes with the
Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO). The
use of molecular diagnostics and multi-pathogen detection platforms for both bacteria and viruses
enables the identification of co-infections and is increasing our understanding of multi-pathogen
infections and pathogen interactions.
Emerging viral pathogens
TaqMan Array Card (TAC)
The National Influenza Centre (NIC) is a WHO reference laboratory for influenza surveillance and
research that is housed within our centre and continues to provide data on circulating influenza
strains to WHO collaborating centres for annual updating of the southern hemisphere vaccine, as
well as data on influenza strains that cannot be typed or emerging respiratory viruses.
We are conducting studies to evaluate the TaqMan Array Card (TAC) technology. TAC functions as a
multiple-pathogen detection system using an array of vessels for the amplification of nucleic acids
using real-time PCR. Individual wells of the card contain lyophilised primers and probes to detect
pathogen-specific targets. TAC is currently being used in the Sepsis Aetiology in Neonates in South
Africa (SANISA) study to detect and identify pathogens causing early-onset neonatal sepsis and
community-acquired sepsis in infants at Chris Hani Baragwanath Hospital, as well as in the TAC-KID
study, a multi-centre study to determine the cause of pneumonia in children less than 5 years of age
in South Africa, India, Peru and Malawi.
The following techniques have been established:
Influenza virus isolation using MDCK-SIAT1 cell lines;
Re-establishing the use of embryonated eggs for virus isolation, to increase our ability to
generate viable viruses of which representative isolates are sent to the WHO collaborating
Real-time reverse-transcription PCR assays for the diagnosis of infections caused by H5, H7 and
H9 avian influenza viruses in order to monitor virus transmission at the animal-human interface;
Serum-based haemagglutination inhibition, to investigate evidence of virus trans mission to
humans after avian influenza virus outbreaks in 2011 and 2012;
Full genome sequencing of influenza viruses from clinical samples; and
Real-time RT-PCR testing of the novel Middle East Respiratory Syndrome Coronavirus (MERS-CoV).
CRDM | 2012-2014
The CRDM was appointed as a Southern African Regional Reference
Laboratory for the Global WHO Vaccine-Preventable Invasive Bacterial
Diseases network
CRDM is a South African National Accreditation System (SANAS) accredited
laboratory since 2008, and complies with the quality management
requirements of ISO 15189 (Facility accreditation number M0029G and
The centre undertakes teaching and training activities for laboratory and
clinical staff. The centre also assists with training of among others medical
technologists, medical scientists, epidemiologists, public health and
microbiology registrars and SA-FELTP residents. Regular surveillance site visits
provide training opportunities to engage with laboratory and hospital staff
participating in national surveillance.
CRDM | 2012-2014
In 2012, the CRDM was appointed as a Southern African Regional Reference
Laboratory for the Global WHO Vaccine-Preventable Invasive Bacterial
Diseases network and contributes by providing training and technical support
to African laboratories in order to improve laboratory capacity and expertise
in these countries.
Workshops and training interventions hosted by CRDM at the NICD, as well as
throughout South Africa and Africa, have provided participants with skills to
enhance surveillance and monitoring of respiratory and meningitis pathogens.
CRDM | 2012-2014
Enhanced GERMS sites
SARI sites
Enhanced GERMS and
SARI sites
CRDM | 2012-2014
Enhanced GERMS sites
Addington, King Edward and RK Khan Hospitals, Durban, KwaZulu-Natal
Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, Gauteng
Dr George Mukhari Hospital, Pretoria, Gauteng
Greys Hospital and Northdale Hospital, Pietermaritzburg, KwaZulu-Natal
Kimberley Hospital, Kimberley, Northern Cape
Natalspruit Hospital, Johannesburg, Gauteng (only cryptococcus surveillance and invasive pneumococcal
disease case-control study)
Nelson Mandela Academic Hospital and Mthatha Provincial Hospital, Mthatha, Eastern Cape
Polokwane and Mankweng Hospitals, Polokwane, Limpopo
Red Cross Children’s Hospital and Tygerberg Hospital, Cape Town, Western Cape
Rob Ferreira and Themba Hospitals, Nelspruit, Mpumalanga
Rustenberg Hospital, Rustenberg, North West (closed in 2013)
Steve Biko (Pretoria Academic Hospital) and Tshwane Hospital, Pretoria, Gauteng
Universitas and Pelonomi Hospitals, Bloemfontein, Free State
SARI sites
Mapulaneng and Matikwana Hospitals (Agincourt Site), Nelspruit, Mpumalanga
Enhanced GERMS and SARI sites
Chris Hani Baragwanath Academic Hospital, Soweto, Gauteng (for SARI 2009-2013)
Edendale Hospital, Pietermaritzburg, KwaZulu-Natal
Helen Joseph Hospital and Rahima Moosa Mother and Child Hospital, Johannesburg, Gauteng
Klerksdorp Tshepong Hospital Complex, Klerksdorp, North West
CRDM | 2012-2014
EVENTS 2012-2014
Conferences hosted
National and international
Annual Influenza Symposium, NICD, Johannesburg in March each year.
3rd Annual African Network for Influenza Surveillance and
Epidemiology (ANISE) Meeting, Nairobi, Kenya, 1 - 3 March 2012.
8th International Symposium on Pneumococci and Pneumococcal
Diseases (ISPPD), Iguaçu Falls, Brazil, 11 - 15 March 2012.
East African Paediatric Conference: Pre-conference meeting on
rotavirus, Mombasa, Kenya, 14 April 2012.
Southern African Society for Veterinary Epidemiology and
Preventative Medicine conference, Farm Inn Hotel, Pretoria,
1 - 2 August 2012.
13th Conference of the International Society for Veterinary
Epidemiology and Economics, Maastricht, Netherlands, 20 - 24 August 2012.
11th Biennial Conference of the Society for Tropical Veterinary
Medicine (STVM) and the final meeting of the EU-funded project
Arbo-Zoonet, Orvieto, Italy, 19 - 22 September 2012.
Joint Conference on emerging and re-emerging epidemics
affecting Global Health, Ovieto, Italy, 19 - 22 September 2012.
15th Annual Meeting of the European Society for Clinical Virology
and Joint Meeting with the European Society for Veterinary
Virology, Madrid, Spain, 4 - 7 September 2012.
18th International Pathogenic Neisseria Conference (IPNC),
Würzburg, Germany, 9 - 14 September 2012.
8th International Annual Respiratory Syncytial Virus Symposium,
Santa Fe, New Mexico, USA, 26 - 30 September 2012.
1st International African Vaccinology Conference (IAVC), Lagoon
Beach Hotel, Cape Town, South Africa, 9 - 11 October 2012.
1st International Conference of the African Society for Laboratory
Medicine (ASLM), Cape Town, South Africa, 1 - 7 December 2012.
CRDM | 2012-2014
The African Influenza and Emerging Respiratory Virus
Preparedness Meeting, Westin Hotel, Cape Town,
4 September 2013.
4th African Network for Influenza Surveillance and Epidemiology
(ANISE) Meeting, Cape Town, South Africa, 5 - 6 December 2014 .
International Conference of the Association of Institutes for
Tropical Veterinary Medicine, Johannesburg, South Africa, 25 - 29 August 2013.
Options for the Control of Influenza VIII conference (Options),
International Convention Centre, Cape Town, 5 - 9 September 2013.
5th Federation of Infectious Diseases Societies of Southern
Africa (FIDSSA) Congress, Champagne Sports Resort
Drakensberg, KwaZulu-Natal, South Africa, 10 - 12 October 2013.
RSVVW 2013 - RSV Vaccines for the World Conference, Porto, Portugal, 14 - 16 October 2013.
8th World Congress of the World Society for Paediatric
Infectious Disease (WSPID) Conference, Cape Town, South
Africa, 19 - 22 November 2013.
9th International Symposium on Pneumococci and Pneumococcal
Diseases (ISPPD), Hyderabad, India, 9 - 13 March 2014.
16th International Congress on Infectious Diseases conference
Cape Town, South Africa, 2 - 5 April 2014.
5th African Pneumococcal Paediatric Summit, Zimbali Lodge,
KwaZulu-Natal, South Africa, 2 August 2014.
UNIPATH Conference, Pretoria, South Africa, 19 - 21 September 2014.
North West Provincial Research conference, South Africa, 1 - 2 October 2014.
19th International Pathogenic Neisseria Conference (IPNC),
Asheville, North Carolina, USA, 12 - 17 October 2014.
9th International RSV Symposium, Stellenbosch, South Africa,
9 - 13 November 2014.
2nd International Conference of the African Society for Laboratory
Medicine (ASLM), Cape Town, South Africa, 30 November - 3
December 2014.
CRDM | 2012-2014
EVENTS 2012-2014
Workshops and meetings
CRDM | 2012-2014
SARIMA (Southern African Research and Innovation Management
Administration) workshop on the role of research managers, Farm
Inn, Pretoria, South Africa, 4 - 6 June 2012.
Workshop on Health and Economic Impact of Influenza, Intercontinental Hotel, Bali, Indonesia, 5 - 7 June 2012.
The Second Southern African Postgraduate Student Symposium,
Pretoria, South Africa, 16 - 18 September 2012.
The Global Meeting on Immunization Monitoring and Surveillance,
Washington DC, United States of America, 9 - 11 October 2012.
The Invasive Bacterial Vaccine-Preventable Disease (IB-VPD)
Laboratory Technical Working Group, Washington DC, United States of
America, 12 October 2012.
1st NICD Pneumococcal Surveillance Workshop, NICD,
Johannesburg, South Africa, 17 - 19 October 2012.
The Pfizer SA Pneumococcal Disease at the Media Master class
meeting, Sandton, Johannesburg, South Africa, 29 October 2012.
The Vaccine Effectiveness Methods meeting, Hilton Paddington,
London, United Kingdom, 28 - 29 November 2012.
2013 2013
The Consortium for the Standardization of Influenza
Seroepidemiology (CONCISE) regional influenza
seroepidemiology expert meeting, Hong Kong University,
Hong Kong SAR, China, 22 - 23 January 2013.
International Pneumococcal Disease Expert Panel (Pfizer
International Corporation), Johannesburg, South Africa, 11 February 2013.
The Pfizer Pneumococcal Expert Summit, Cape Town, South
Africa, 16 - 17 March 2013.
The Meningitis Expert Forum: A focus on MenACWY-CRM,
convened by Novartis, Milan, Italy 28 May 2013.
The Global meeting on Implementing New and Under-utilized
Vaccines, meeting convened by WHO, Dominican Republic,
4 - 6 June 2013.
Sanofi Pasteur Advisory Board Meeting, Radisson Gautrain
Hotel, Sandton, Johannesburg, South Africa, 31 August 2013.
Consortium for Standardization of Influenza Seroepidemiology
(CONSISE) international meeting, Westin Hotel, Cape Town,
South Africa, 3 - 5 September 2013.
New and Underutilised Vaccines Implementation (NUVI)
strategic Review meeting, Geneva, Switzerland,
16 - 20 September 2013.
The Respiratory Syncytial Virus Global Estimates Network,
Edinburgh, Scotland, 4 - 6 November 2013.
Laboratory Technical Working Group (TWG) for WHO IB-VPD
Surveillance Network (Invasive Bacterial Vaccine Preventable
Disease), Bangkok, Thailand, 13 – 14 November 2013.
A Pfizer Advisory Board Meeting on Pneumococcal Vaccination
in Adults, Hilton Hotel, Cape Town, South Africa, 16 November 2013.
The 2nd GMI (Global Meningococcal Initiative) summit meeting,
Cape Town, South Africa, 17 - 18 November 2013.
The Influenza Expert meeting, WHO, Geneva, Switzerland, 10 - 13 December 2013.
The Academy of Family Practice/ Sandton Clinic CPD Meeting,
Bryanston Country Club, Johannesburg, South Africa, 15 February 2014.
The 9th Annual Sequencing, Finishing, and Analysis in the Future
Meeting, Santa Fe, New Mexico, 28 - 30 May 2014.
The 12th regional meeting of The Fogarty International Centerinitiated Multinational Influenza Seasonal Mortality Study
(MISMS), an Influenza Research Workshop, Washington DC,
United States of America, 30 June - 3 July 2014.
Sanofi Pasteur Advisory Board Meeting, Sandton Convention
Centre, Sandton, Johannesburg, South Africa, 12 July 2014.
National Influenza Surveillance Vaccine Effectiveness meeting
at Red Cross Children’s Hospital, Cape Town, South Africa,
22 - 24 July 2014.
Good Emergency Management Practice workshop:
“Strengthening capacity to respond to animal diseases
emergencies” The workshop was held at St George’s Hotel, South Africa, 25 - 29 August 2014.
Meningitis Expert Panel Meeting, Rhodes Memorial Restaurant,
Cape Town, South Africa, 1 September 2014.
The First South African Pertussis Interest Group Meeting, Protea
Hotel North Warf, Cape Town, South Africa, 2 September 2014.
Global IB VPD Sentinel Surveillance meeting (iTAG and TWG),
Geneva, Switzerland, 27 - 30 October 2014.
CRDM | 2012-2014
CRDM | 2012-2014
Dr. Anne
von Gottberg
Centre head
Ms. Linda
de Gouveia
Dr. Mignon du Plessis
Senior medical scientist
Dr. Nicole Wolter
Senior medical scientist
Medical scientists (x7)
Ms. Olga Hattingh
Medical technologist
Ms. Happy Skosana
Medical technologist
Medical technologists (x2)
Data clerks (x2)
Medical technicians (x2)
Dr. Florette
Centre head
Ms. Orienka
Medical scientist
scientists (x4)
Dr. Ziyaad
Senior medical
Intern medical scientist
Ms. Amelia Buys
technologists (x4)
Dr. Sibongile
Dr. Cheryl
Centre head
Dr. Claire von
Dr. Jocelyn Moyes
assistants (x2)
Nurse epidemiologist
Field project co-ordinator
Surveillance officers (x9)
Research assistants (x3)
Medical officer
Data manager
Data analyst
Data clerks (x10)
Surveillance officer
Research assistant
Allam, Mushal
Baloyi, Keitumetsi
Buthelezi, Nelisiwe
Buys, Amelia
Carrim, Maimuna
Bacteriology unit (Bioinformatician)
Epidemiology unit (Surveillance officer)
Epidemiology unit (Surveillance officer)
Virology unit (Medical technologist)
Bacteriology unit (Medical scientist)
Cohen, Cheryl
de Gouveia, Linda
Dlamini, Wesley
Duma, Noluthando
du Plessis, Mignon
Epidemiology unit (Centre head)
Bacteriology unit (Laboratory manager)
Virology unit (Medical technician)
Bacteriology unit (Medical technologist)
Bacteriology unit (Medical scientist)
Fourie, Cardia
Ganesh, Karistha
Harvey, Lynn
Hattingh, Olga
Hellferscee, Orienka
Virology unit (Medical technologist)
Bacteriology unit (Medical Scientist)
Virology unit (Laboratory assistant)
Bacteriology unit (Medical technologist)
Virology unit (Medical scientist)
CRDM | 2012-2014
Hyde, Phyllis
Khasane, Pontsho
Lengana, Sarona
Letlape, Boitumelo
Makamba, Wanga
Bacteriology unit (Administrator)
Epidemiology unit (Administrator)
Epidemiology unit (Medical officer)
Epidemiology unit (Database administrator)
Epidemiology unit (Data clerk)
not available
Makhele, Lifuo
Malapane, Julia
Malinga, Nhlakanipho
Mamorobela, Ernest
Mampa, Nthabiseng
Bacteriology unit (Medical technician)
Epidemiology unit (Research assistant)
Epidemiology unit (Research assistant)
Virology unit (Medical technologist)
Epidemiology unit (Data clerk)
Manaka, Mokupi
Maraka, Dimakatso
Mashaba, Theresa
Matshogo, Seipati
McAnerney, Jo
Epidemiology unit (Field project coordinator)
Epidemiology unit (Data clerk)
Virology unit (Laboratory assistant)
Epidemiology unit (Research assistant)
Epidemiology unit (Nurse epidemiologist)
CRDM | 2012-2014
not available
Mdluli, Cleopatra
Mgidlana, Kholiwe
Mhlarhi, Shirley
Miller, Beulah
Moerdyk, Alexandra
Epidemiology unit (Data clerk)
Epidemiology unit (Research assistant)
Epidemiology unit (Data clerk)
Virology unit (Medical technologist)
Virology unit (Medical technologist)
not available
Mogale, Dineo Judith
Mohale, Thabo
Moleleki, Malefu
Moodley, Anna Alleta
Moosa, Fahima
Bacteriology unit (Medical technologist)
Bacteriology unit (Medical scientist)
Bacteriology unit (Medical scientist)
Epidemiology unit (Surveillance officer)
Bacteriology unit (Medical scientist)
Moremi, Myrah
Motsepe, Kelebogile
Moyes, Jocelyn
Mthembu, Thembi
Mthembu, Thulisile
Epidemiology unit (Surveillance officer)
Epidemiology unit (Data clerk)
Epidemiology unit (Medical epidemiologist)
Bacteriology unit (Data clerk)
Epidemiology unit (Surveillance officer)
CRDM | 2012-2014
Mtshali, Senzo
Musetha, Robert
Naicker, Dshanta
Naidoo, Prabha
Ncwana, Bekiwe
Virology unit (Medical scientist)
Epidemiology unit (Data clerk)
Virology unit (Medical scientist)
Bacteriology unit (Medical technician)
Epidemiology unit (Surveillance officer)
Ndlangisa, Kedibone
Ngubane, Wendy
Nguweneza, Athermon
Ntoyi, Mpho
Papo, Makatisane
Bacteriology unit (Medical scientist)
Epidemiology unit (Surveillance officer)
Epidemiology unit (Data analyst)
Epidemiology unit (Data clerk)
Epidemiology unit (Data manager)
not available
Phalatse, Louisa
Rangunwala, Azeeza
Salie-Bassier, Yusrah
Sambo, Andrina
Sekhula, Pertunia
Epidemiology unit (Surveillance officer)
Virology unit (Medical scientist)
Virology unit (Intern medical scientist)
Epidemiology unit (Surveillance officer)
Epidemiology unit (Data clerk)
CRDM | 2012-2014
not available
Seleka, Mpho
Shangase, Khadija
Skosana, Happy
Treurnicht, Florette
Tshabalala, Judith
Virology unit (Medical scientist)
Epidemiology unit (Surveillance officer)
Bacteriology unit (Medical technologist)
Virology unit (Acting centre head)
Bacteriology unit (Data clerk)
von Mollendorf, Claire
Walaza, Sibongile
Valley-Omar, Ziyaad
Venter, Marietjie
von Gottberg, Anne
Virology unit (Medical scientist)
Virology unit (Centre head 2009- March 2014)
Bacteriology unit (Centre head)
Wolter, Nicole
Bacteriology unit (Medical scientist)
CRDM | 2012-2014
Epidemiology unit (Medical epidemiologist) Epidemiology unit (Medical epidemiologist)
Abrahams, M. R., F. K. Treurnicht, N. K. Ngandu, S. A. Goodier, J. C. Marais, H. Bredell, R. Thebus, R. D. de Assis, K. Mlisana, C. Seoighe, S. A. Karim, C. M. Gray, and C. Williamson. 2013. Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression. AIDS. 27:507-518.
Adler, D., F. Laher, M. Wallace, K. Grzesik, H. Jaspan, L.-G. Bekker, G. Gray, Z. Valley-Omar, B. Allan, and A.-L. Williamson. 2013. High rate of multiple concurrent human papillomavirus infections among HIV-uninfected South African adolescents. J Immunol Tech Infect Dis 2:1.
Ampofo, W. K., S. Al Busaidy, N. J. Cox, M. Giovanni, A. Hay, S. Huang, S. Inglis, J. Katz, T. Mokhtari-Azad, M. Peiris, V. Savy, P. Sawanpanyalert, M. Venter, A. L. Waddell, G. Wickramasinghe, W. Zhang, and T.
Ziegler. 2013. Strengthening the influenza vaccine virus selection and development process: outcome of the 2nd WHO Informal Consultation for Improving Influenza Vaccine Virus Selection held at the Centre
International de Conferences (CICG) Geneva, Switzerland, 7 to 9 December 2011. Vaccine 31:3209-3221.
Archer, B. N., G. A. Timothy, C. Cohen, S. Tempia, M. Huma, L. Blumberg, D. Naidoo, A. Cengimbo, and B. D. Schoub. 2012. Introduction of 2009 pandemic influenza A virus subtype H1N1 into South Africa:
clinical presentation, epidemiology, and transmissibility of the first 100 cases. J Infect Dis 206 Suppl 1:S148-53.
Archer, B. N., S. Tempia, L. F. White, M. Pagano, and C. Cohen. 2012. Reproductive number and serial interval of the first wave of influenza A(H1N1)pdm09 virus in South Africa. PLoS One 7:e49482.
Cockeran, R., H. C. Steel, N. Wolter, L. de Gouveia, A. von Gottberg, K. P. Klugman, A. T. Leanord, D. J. Inverarity, T. J. Mitchell, C. Feldman, and R. Anderson. 2012. Effects of clarithromycin at sub-minimum
inhibitory concentrations on early ermB gene expression, metabolic activity and growth of an ermB-expressing macrolide-resistant strain of Streptococcus pneumoniae. Open J Respir Dis 2 :1-8.
Cohen, A. L., O. Hellferscee, M. Pretorius, F. Treurnicht, S. Walaza, S. Madhi, M. Groome, H. Dawood, E. Variava, K. Kahn, N. Wolter, A. von Gottberg, S. Tempia, M. Venter, and C. Cohen. 2014. Epidemiology of
influenza virus types and subtypes in South Africa, 2009-2012. Emerg Infect Dis 20:1162-1169.
Cohen, C., C. von Mollendorf, L. de Gouveia, N. Naidoo, S. Meiring, V. Quan, V. Nokeri, M. Fortuin-deSmit, B. Malope-Kgokong, D. Moore, G. Reubenson, M. Moshe, S. A. Madhi, B. Eley, U. Hallbauer, R.
Kularatne, L. Conklin, K. L. O’Brien, E. R. Zell, K. Klugman, C. G. Whitney, and A. von Gottberg. 2014. Effectiveness of 7-valent pneumococcal conjugate vaccine against invasive pneumococcal disease in HIVinfected and -uninfected children in South Africa: a matched case-control study. Clin Infect Dis 59:808-818.
Cohen, C., L. Simonsen, J. Sample, J. W. Kang, M. Miller, S. A. Madhi, M. Campsmith, and C. Viboud. 2012. Influenza-related mortality among adults aged 25-54 years with AIDS in South Africa and the United
States of America. Clin Infect Dis 55:996-1003.
10. Cohen, C., J. Moyes, S. Tempia, M. Groome, S. Walaza, M. Pretorius, H. Dawood, M. Chhagan, S. Haffejee, E. Variava, K. Kahn, A. Tshangela, A. von Gottberg, N. Wolter, A. L. Cohen, B. Kgokong, M. Venter,
and S. A. Madhi. 2013. Severe influenza-associated respiratory infection in high HIV prevalence setting, South Africa, 2009-2011. Emerg Infect Dis 19:1766-1774.
11. Cohen, C., S. Walaza, J. Moyes, M. Groome, S. Tempia, M. Pretorius, O. Hellferscee, H. Dawood, M. Chhagan, F. Naby, S. Haffejee, E. Variava, K. Kahn, S. Nzenze, A. Tshangela, A. von Gottberg, N. Wolter, A. L.
Cohen, B. Kgokong, M. Venter, and S. A. Madhi. 2014. Epidemiology of Viral-Associated Acute Lower Respiratory Tract Infection among Children <5 Years of Age in a High HIV Prevalence Setting, South Africa,
2009-2012. Pediatr Infect Dis J. In Press.
12. Crowther-Gibson, P., C. Cohen, K. P. Klugman, L. de Gouveia, and A. von Gottberg. 2012. Risk factors for multidrug-resistant invasive pneumococcal disease in South Africa, a setting with high HIV prevalence,
in the prevaccine era from 2003 to 2008. Antimicrob Agents Chemother 56:5088-5095.
CRDM | 2012-2014
13. Dangor, Z., A. Izu, D. P. Moore, M. C. Nunes, F. Solomon, N. Beylis, A. von Gottberg, J. M. McAnerney, and S. A. Madhi. 2014. Temporal association in hospitalizations for tuberculosis, invasive pneumococcal disease and influenza virus illness in South African children. PLoS One 9:e91464.
14. du Plessis, M., C. Moodley, K. M. Mothibeli, A. Fali, K. P. Klugman, and A. von Gottberg. 2012. Population snapshot of invasive serogroup B meningococci in South Africa from 2005 to 2008. J Clin Microbiol. 50:2577-2584.
15. du Plessis, M., N. Wolter, P. Crowther-Gibson, H. J. Hamstra, K. Schipper, C. Moodley, C. Cohen, D. van de Beek, P. van der Ley, A. von Gottberg, and A. van der Ende. 2014. Meningococcal serogroup Y lpxL1
variants from South Africa are associated with clonal complex 23 among young adults. J Infect 68:455-461.
16. Feikin, D. R., E. W. Kagucia, J. D. Loo, R. Link-Gelles, M. A. Puhan, T. Cherian, O. S. Levine, C. G. Whitney, K. L. O’Brien, and M. R. Moore. 2013. Serotype-specific changes in invasive pneumococcal disease after
pneumococcal conjugate vaccine introduction: a pooled analysis of multiple surveillance sites. PLoS Med 10:e1001517.
17. Frean, J., O. Perovic, V. Fensham, K. McCarthy, A. von Gottberg, L. de Gouveia, B. Poonsamy, L. Dini, J. Rossouw, K. Keddy, W. Alemu, A. Yahaya, A. Pierson, V. Dolmazon, S. Cognat, and J. B. Ndihokubwayo.
2012. External quality assessment of national public health laboratories in Africa, 2002-2009. Bull World Health Organ 90:191-199A.
18. Gumede, N., O. Lentsoane, C. C. Burns, M. Pallansch, E. de Gourville, R. Yogolelo, J. J. Muyembe-Tamfum, A. Puren, B. D. Schoub, and M. Venter. 2013. Emergence of vaccine-derived polioviruses, Democratic
Republic of Congo, 2004-2011. Emerg Infect Dis 19:1583-1589.
19. Haynes, A. K., A. P. Manangan, M. K. Iwane, K. Sturm-Ramirez, N. Homaira, W. A. Brooks, S. Luby, M. Rahman, J. D. Klena, Y. Zhang, H. Yu, F. Zhan, E. Dueger, A. M. Mansour, N. Azazzy, J. P. McCracken, J. P.
Bryan, M. R. Lopez, D. C. Burton, G. Bigogo, R. F. Breiman, D. R. Feikin, K. Njenga, J. Montgomery, A. L. Cohen, J. Moyes, M. Pretorius, C. Cohen, M. Venter, M. Chittaganpitch, S. Thamthitiwat, P. Sawatwong,
H. C. Baggett, G. Luber, and S. I. Gerber. 2013. Respiratory syncytial virus circulation in seven countries with Global Disease Detection Regional Centers. J Infect Dis 208 Suppl 3:S246-54.
20. Hunt, G. M., J. Ledwaba, A. E. Basson, J. Moyes, C. Cohen, B. Singh, S. Bertagnolio, M. R. Jordan, A. Puren, and L. Morris. 2012. Surveillance of transmitted HIV-1 drug resistance in Gauteng and KwaZulu-Natal
Provinces, South Africa, 2005-2009. Clin Infect Dis 54 Suppl 4:S334-8.
21. Keddy, K. H., A. Sooka, P. Crowther-Gibson, V. Quan, S. Meiring, C. Cohen, T. Nana, C. Sriruttan, S. Seetharam, A. Hoosen, P. Naicker, E. Elliott, S. Haffejee, A. Whitelaw, and K. P. Klugman. 2012. Systemic
shigellosis in South Africa. Clin Infect Dis 54:1448-1454.
22. Liu, M. K., N. Hawkins, A. J. Ritchie, V. V. Ganusov, V. Whale, S. Brackenridge, H. Li, J. W. Pavlicek, F. Cai, M. Rose-Abrahams, F. Treurnicht, P. Hraber, C. Riou, C. Gray, G. Ferrari, R. Tanner, L. H. Ping, J. A.
Anderson, R. Swanstrom, M. Cohen, S. S. Karim, B. Haynes, P. Borrow, A. S. Perelson, G. M. Shaw, B. H. Hahn, C. Williamson, B. T. Korber, F. Gao, S. Self, A. McMichael, and N. Goonetilleke. 2013. Vertical T cell
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CRDM | 2012-2014
Contact information
Centre for Respiratory Diseases and Meningitis
National Institute for Communicable Diseases, division of the National Health Laboratory Service
1 Modderfontein Road, Sandringham, Johannesburg
Tel: 27-11 386 6400 Fax: 27-11 882 0596
E-mail: [email protected] Website: www.nicd.ac.za
Centre Heads
Anne von Gottberg (Bacteriology)
Tel: 27-11 555 0316 E-mail: [email protected]
Cheryl Cohen (Epidemiology)
Tel: 27-11 386 6593 E-mail: [email protected]
Florette Treurnicht (Virology)
Tel: 27-11 386 6392 E-mail: [email protected]
CRDM | 2012-2014
Resource information
World pneumonia day website: http://worldpneumoniaday.org/
WHO Integrated Global Action Plan for the Prevention and Control of Pneumonia and Diarrhoea (GAPPD):
UNICEF Ending Preventable Child Deaths from Pneumonia and Diarrhoea by 2025: The integrated Global Action Plan for Pneumonia and Diarrhoea (GAPPD):
UNICEF Pneumonia and diarrhoea: Tackling the deadliest diseases for the world’s poorest children, 2012:
UNICEF Committing to Child Survival: A Promise Renewed Progress Report 2013:
United Nations Foundation. Every Woman, Every Child. Commission on Life-Saving Commodities 2012:
PATH Tackling the deadliest diseases for the world’s poorest children 2012:
Pneumonia: Open Access Journal: https://pneumonia.org.au/
IVAC Pneumonia and Diarrhea Progress Report 2013:
Centers for Disease Control and Prevention website: http://www.cdc.gov/pneumonia/
National Institute for Communicable Diseases annual reports and publications:
CRDM | 2012-2014