Diphtheria: How PCR testing is improving diagnosis, surveillance in Nigeria

Nigeria’s recent diphtheria outbreak claimed over 600 lives, with over 13,000 confirmed cases recorded across 19 states and the Federal Capital Territory (FCT).

The hardest-hit states were Kano, Yobe, Katsina, Bauchi, Borno and Kaduna, accounting for 95·8% of cases, with 73·6% affecting children aged 1–14 years.

Aside vaccine hesitancy, one of the challenges that bedeviled the country’s response to diphtheria is the time it took to make laboratory diagnosis of the disease.

This is because the country relies exclusively on bacterial microscopy and culturing of clinical samples from suspected diphtheria cases to make diagnosis. This can take several days, and thus delayed diagnosis and treatment.

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Diphtheria is a highly contagious disease caused mainly by bacteria called corynebacterium diphtheria, which can be fatal in 5-10 per cent of cases, with a higher mortality rate in young children.

The bacteria usually spread from person to person through respiratory droplets, often during coughing or sneezing. It can also be transmitted by touching contaminated objects.

For the first time, Nigeria is now introducing a new and more efficient Polymerase Chain Reaction (PCR) test for diagnosing diphtheria, with support from the United States Centers for Disease Control and Prevention (CDC).

The introduction of PCR for diagnosing diphtheria in Nigeria is now changing the narrative. Experts said the PCR method is improving diphtheria diagnosis as well as surveillance and outbreak response in the country.

They said using PCR testing for diphtheria will strengthen public health efforts, leading to better management and control of the disease, and ultimately protecting communities from potential outbreaks.

According to them, the benefits of PCR testing for diphtheria ranged from early detection and diagnosis, reduction in transmission and improved surveillance to effective public health response.

PCR tests are highly sensitive and specific and can detect the DNA of the germ being tested, as well as identify the presence or absence of toxins, which can be critical in confirming whether a patient has a disease like diphtheria.

The challenges with the traditional methods of bacterial microscopy and culturing for diphtheria diagnosis include the cost of maintaining cultures and performing microscopy which can be expensive, especially in resource-limited settings.

Also, microscopy may not always detect low levels of bacteria, leading to incorrect diagnosis.

The PCR testing method will now be used along with the traditionally used methods.

According to the Director of Public Health Laboratories, Nigeria Centre for Disease Control and Prevention (NCDC), Mrs Olajumoke Babatunde, the turnaround time for traditional testing method takes about eight days but results for PCR, take less than 24 hours.

She said, “So that is less than a day. It has had a great impact on disease detection. Early disease detection is very critical when it comes to outbreak response, because if the etiology of a disease is not known on time, you cannot initiate response activities.

“So the PCR method has really increased detection, reduced detection period, and enhanced surveillance. Prompt case detection is very critical to outbreak response.”

Explaining what inspired the introduction of the PCR testing method for diphtheria in Nigeria, the U.S. CDC Nigeria Laboratory Branch Chief, McPaul Okoye, said NCDC requested the U.S. CDC’s technical assistance and support to roll out real-time PCR testing for diphtheria.

He said the last diphtheria outbreak was unprecedented in the sense that in the last four decades, the volume of cases of the disease was huge compared to any other outbreak of diphtheria the country has had.

He said, “So that draws our attention to two things. One is capacity for diagnosis, and two, our uptake of vaccination of diphtheria and effectiveness of the vaccines

“But because our focus is on laboratory, we wanted to be sure that the country has capacity for early detection. So before now, with support from the United Kingdom Health Security Agency (UK HSA), U.S CDC has been supporting the country, working closely with NCDC in the diagnosis of diphtheria, but the primary focus in that approach was the use of microscopy culture  and that takes some time.

“So we thought that given the huge outbreak, there will be need to introduce a method that will enable early detection of the diphtheria cases. So that it can stimulate early detection, early treatment as well as early response.

“The former NCDC director  general, Dr Ifedayo Adetifa, was the one who reached out to the U.S CDC to ask for its support in  introducing the PCR method in other to make it faster,  easier and more efficient  to diagnose diphtheria in the country.

“So he reached out during that last outbreak, and that was when this whole discussion and engagement commenced.”

He said the U.S. CDC provided technical assistance to help build the capacity of the staff at the National Reference Laboratory (NRL), the country’s top laboratory under the NCDC.

He said the U.S. CDC also supported the NRL with lab commodities for PCR testing for diphtheria diagnosis, which include critical PCR testing reagents and commodities, including specific primers, probes and sample collection materials.

He said in the first phase of rolling out PRC testing for diphtheria, U.S. CDC held a week-long virtual training for NRL staff.

The second phase of the training involved a visit from the U.S. CDC Atlanta team and an in-person follow-on training for NRL staff. The training re-enforced standard processes and procedures and reviewed the set up for diphtheria testing.

Nigeria now has the needed capacity for PCR testing for diphtheria at the national level following the completion of the training.

“Following that training, we had them do what is needful to get the system in place, validate the system and be able to test for diphtheria here in the NRL,” he added.

The director of Public Health Laboratories, NCDC, Olajumoke Babatunde, said the conversations for the training started in June last year, with series of meetings with US. CDC.

This she said was followed with an assessment of  labs, particularly  the labs in Kano and Yobe states. “Kano being the epicentre of the outbreak. We needed to also decentralize testing, because most of the samples at the initial stage were transported to NRL.

“As earlier mentioned, the culture method takes minimum of eight days. And even at that, but the movement from the states to the NRL lab takes another minimum of, like, two, three days. So we had a lot of a very long turnaround time.

“So we did assessment of the labs in the two states so we can provide support in terms of equipment and human capacity building.”

She further explained that the U.S CDC team started the capacity building through online training initially.

“Because of the time, you know, it was an emergency and they needed to get some clearance from the home government. After the online training we did the physical training at the NRL.”

U.S. CDC Nigeria Laboratory Branch Chief, McPaul Okoye, explained that, “Our focus first is to make sure that capacity is built here at the NRL. Then subsequently, the NCDC team will cascade the capacity building to states. So the NCDC NRL, can detect diphtheria using PCR method. NCDC will also train staff at the labs in the state, to be able to do so.”

Olajumoke of NCDC said, “We have started also using the PCR method for most of the samples that we receive. The next phase is to roll out the training in Kano and Yobe and expand to other states over time.

“We have about 29 laboratories across 29 states in our laboratory network.”

Asked if the use of PCR method would not overburden the health system, considering the diverse disease outbreaks the method is being used for, the U.S. CDC Nigeria Laboratory Branch chief, McPaul Okoye, said “that’s also why we, as U.S CDC and other partners, are here in Nigeria to support the country.

“That is what we are doing at the moment, despite the fact that we are experiencing multiple outbreaks at the same time. We do so taking full advantage of the molecular laboratory network across the country.

“We have developed molecular network for HIV, TB and many other diseases. We also, with leadership of NCDC, have network for yellow fever. So rather than developing new network each time there’s an outbreak, we ensure integrated disease testing and surveillance leveraging the investment that already exists, and the molecular labs come handy, because you can test multiple diseases on the same equipment.

“All you need do is to have the needed reagents,  the probes, the primers etc and also have trained and skilled lab scientists to do that. That’s exactly the direction NCDC is headed, and that’s what we are supporting them to be able to do. “

He  said every state had built PCR capacity for COVID-19, adding that  the country is also  leveraging on previous and ongoing investment to address current outbreaks.

Mrs Olajumoke said the U.S CDC support has had a great impact on the country’s health system beyond diphtheria PCR testing including enhanced surveillance, early disease detention, and early response activities.

She said with enhanced local surveillance, Nigeria has strengthened its ability to detect diphtheria in communities and prevent future outbreaks.

She said, “you know, government funding is very limited. We take a lot of competing activities, and so sometimes it’s always very difficult even for us to be able to procure some of these reagents when needed. But with the support from U.S. CDC, when there is no reagent we turn to the international reagent resource, IRR managed by U.S CDC.

“We place requests to IRR, from time to time and obtain reagents free of charge. No matter the number of equipment we have in the lab, once you don’t have appropriate critical reagents to use for diagnosis, the lab becomes useless.

So U.S CDC has really supported us in many areas; provision of commodities, provision of reagents and consumables, and also this capacity building, which, like I said, has led to so many impacts.”

She also said strengthening laboratory capacity is very critical to the NCDC.

“We have a mandate, and that mandate is prevention, detection and response to diseases of public health importance. Most importantly, you cannot even respond when you have not detected, and that is where laboratory stands out.

“So without the support from U.S. CDC and other partners, I don’t think we would have been able to achieve our mandate as a public health institute in the country. So like Oliver Twist we are partners in progress, and we also believe that it’s going to be a continuous thing. The collaboration is very fruitful.”

Okoye said the interest of U.S CDC, is for Nigeria to rapidly respond and prevent the continued spread of diseases. He said this includes building public health laboratory capacity.

“That’s the kind of capacity we are building. And all of this rests on a very robust and functional laboratory network. Laboratory capacity is critically essential, because without it, you are like flying in the dark.

“The laboratory provides the direction for every response, and that’s what we want the country to have ability detect disease as rapidly as possible and responding to it efficiently. That’s the summary of what we’re doing, and it cuts across HIV, diphtheria, TB, yellow fever, measles, meningitis, and other priority diseases.”

He recommended that states and local governments should appropriate funding for disease outbreak preparedness and response.

“They have to all take responsibility in making sure that there is appropriate lab infrastructure, appropriate surveillance system to routinely monitor any disease outbreak so that we can collectively detect it early and respond efficiently to prevent needless deaths.”

He said  U.S. CDC would continue to work with NCDC to provide ongoing support and assistance as the country rolls out the new method of confirming diphtheria cases.

“The US CDC has been supporting  the Government of Nigeria since 2004  in establishing robust laboratory networks for diseases of public health importance, upgrading laboratory facilities in the country, enhancing high-quality laboratory systems and instituting quality management systems and improvement processes leading to the certification or accreditation of laboratories in Nigeria by national and international accreditation bodies.

“It helped develop core laboratory diagnostic capacity to test for COVID-19, mpox, yellow fever, measles, Lassa fever, cholera and cerebrospinal meningitis, and now, for the first time we are supporting the country in using PCR for diagnosing diphtheria.”