Setting research priorities for global pandemic preparedness: An international consensus and comparison with ChatGPT's output

Background

In this priority-setting exercise, we sought to identify leading research priorities needed for strengthening future pandemic preparedness and response across countries.

Methods

The International Society of Global Health (ISoGH) used the Child Health and Nutrition Research Initiative (CHNRI) method to identify research priorities for future pandemic preparedness. Eighty experts in global health, translational and clinical research identified 163 research ideas, of which 42 experts then scored based on five pre-defined criteria. We calculated intermediate criterion-specific scores and overall research priority scores from the mean of individual scores for each research idea. We used a bootstrap (n = 1000) to compute the 95% confidence intervals.

Results

Key priorities included strengthening health systems, rapid vaccine and treatment production, improving international cooperation, and enhancing surveillance efficiency. Other priorities included learning from the coronavirus disease 2019 (COVID-19) pandemic, managing supply chains, identifying planning gaps, and promoting equitable interventions. We compared this CHNRI-based outcome with the 14 research priorities generated and ranked by ChatGPT, encountering both striking similarities and clear differences.

Conclusions

Priority setting processes based on human crowdsourcing - such as the CHNRI method - and the output provided by ChatGPT are both valuable, as they complement and strengthen each other. The priorities identified by ChatGPT were more grounded in theory, while those identified by CHNRI were guided by recent practical experiences. Addressing these priorities, along with improvements in health planning, equitable community-based interventions, and the capacity of primary health care, is vital for better pandemic preparedness and response in many settings.

Molecular surveillance of arboviruses in Nigeria

Arboviral infections are fast becoming a global public health concern as a result of its high fatality rate and sporadic spread. From the outbreak of Zika virus in the Americas, the endemicity of Yellow fever in West Africa and South America, outbreaks of West Nile virus in South Africa to the year-round and national risk of Dengue fever in Mainland China and India. The war against emerging and re-emerging viral infection could probably lead to the next pandemic. To be above the pending possible arboviral pandemic, consistent surveillance of these pathogens is necessary in every society. This study was aimed at conducting a surveillance for Yellow fever virus, Zika virus, Chikungunya virus, Dengue virus and Rift Valley fever virus in four states in Nigeria using molecular techniques. A cross-sectional study involving 1600 blood samples collected from febrile patients in Lagos, Kwara, Ondo and Delta States between 2018 and 2021 was conducted using Real time polymerase chain reaction for detection of the pathogens. Extraction and purification of viral RNA were done using Qiagen Viral RNA Mini Kit. Samples were analyzed using One Step PrimeScript III RT-PCR mix (Takara Bio) alongside optimized primers and probes designed in-house. Positive samples were sequenced on MinION platform (Nanopore technologies). Bioinformatic and phylogenetic analysis were performed with DNASTAR Lasergene 17.3. All the RNA extracted from samples collected from the four states were negative for ZIKV RNA, RVFV RNA, CHIKV RNA and DENV RNA. However, twelve of the samples (2%) tested positive for YFV RNA. Three full genomes of sizes 10,751 bp, 10,500 bp and 10,715 bp were generated and deposited in GenBank with accession numbers: ON323052, ON323053 and ON323054 respectively. Phylogenetic analysis shows clustering within lineage 3 of West African genotype. This result shows an active spread of Yellow fever in Delta State, Nigeria. However, there is no emergence of a new genotype There is a need for an intense surveillance of Yellow fever virus in Nigeria to avert a major outbreak.

Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria

BACKGROUND

Salmonella infections remain an important public health issue worldwide. Some serovars of non-typhoidal Salmonella (NTS) have been associated with bloodstream infections and gastroenteritis, especially in children in Sub-Saharan Africa with circulating S. enterica serovars with drug resistance and virulence genes. This study identified and verified the clonal relationship of Nigerian NTS strains isolated from humans, animals, and the environment.

METHODS

In total, 2,522 samples were collected from patients, animals (cattle and poultry), and environmental sources between December 2017 and May 2019. The samples were subjected to a standard microbiological investigation. All the isolates were identified using Microbact 24E, and MALDI-TOF MS. The isolates were serotyped using the Kauffmann-White scheme. Antibiotic susceptibility testing was conducted using the disc diffusion method and the Vitek 2 compact system. Virulence and antimicrobial resistance genes, sequence type, and cluster analysis were investigated using WGS data.

RESULTS

Forty-eight (48) NTS isolates (1.9%) were obtained. The prevalence of NTS from clinical sources was 0.9%, while 4% was recorded for animal sources. The serovars identified were S. Cotham (n = 17), S. Give (n = 16), S. Mokola (n = 6), S. Abony (n = 4), S. Typhimurium (n = 4), and S. Senftenberg (n = 1). All 48 Salmonella isolates carried intrinsic and acquired resistant genes such as aac.6…Iaa, mdf(A), qnrB, qnrB19 genes and golT, golS, pcoA, and silP, mediated by plasmid Col440I_1, incFIB.B and incFII. Between 100 and 118 virulence gene markers distributed across several Salmonella pathogenicity islands (SPIs), clusters, prophages, and plasmid operons were found in each isolate. WGS revealed that strains of each Salmonella serovar could be assigned to a single 7-gene MLST cluster, and strains within the clusters were identical strains and closely related as defined by the 0 and 10 cgSNPs and likely shared a common ancestor. The dominant sequence types were S. Give ST516 and S. Cotham ST617.

CONCLUSION

We found identical Salmonella sequence types in human, animal, and environmental samples in the same locality, which demonstrates the great potential of the applied tools to trace back outbreak strains. Strategies to control and prevent the spread of NTS in the context of one's health are essential to prevent possible outbreaks.

Efficacy of silver nanoparticles against multidrug resistant clinical Staphylococcus aureus isolates from Nigeria

Multidrug resistant (MDR) S. aureus infections continue to account for excess mortality in hospital and community settings and constitute a rising global health problem. However, data on the efficacy and mechanism of actions of alternative solutions like silver nanoparticles in developing countries are lacking. This study investigated anti-staphylococcal activity of silver nanoparticles (AgNP) against local strains from Nigeria. A total 119 clinical isolates of S. aureus from five Nigerian laboratories categorized as MRSA (n = 52) and MSSA (n = 67) by PCR were studied. The MIC of AgNP produced by chemical reduction method and characterized by surface plasmon resonance absorbance and size equivalence by scanning electron microscopy was determined by microbroth dilution method. Its effect on protease activity and plasmids were also investigated. Baseline characteristics of the isolates revealed MDR phenotype of the isolates, carriage of diverse plasmids (15-32 kb) among the MDR MSSA, and mean extracellular protease activity of 24.8-55.7 U/mL. The chemically synthesized AgNP had a peak absorbance at 400 nm with a size equivalence of 4.58 nm. The MICs of AgNP against the isolates were 4.7 μg/mL and 4.9 μg/mL, respectively, for MRSA and MSSA (P > 0.05). The bactericidal effect of AgNP at 2.5-5 μg/mL on the MSSA and MRSA isolates was observed at 2.7-5.5 h post exposure in vitro. Further analysis revealed plasmid eviction in the MDR MSSA isolates exposed to 5 μg/mL AgNP and dose-dependent reduction in extracellular protease activity by 84.6-93.1%. Hemolysis of human erythrocytes by AgNP was not observed at the MIC range. Conclusion: This study revealed safety and efficacy of AgNP against clinical MDR S. aureus isolates from Nigeria, using plasmid eviction and protease inhibition as mechanisms of action.

Typhoid Fever: Tracking the Trend in Nigeria

Typhoid fever continues to pose a serious health challenge in developing countries. A reliable database on positive blood cultures is essential for prompt interventions. To generate reliable data on Salmonella enterica serovar Typhi (S. Typhi)–positive blood culture trends in typhoidal Salmonella in Nigeria alongside changing contextual factors and antimicrobial resistance patterns, a retrospective cohort study was conducted in two hospitals in Lagos between 1993 and 2015. Medical records of typhoid patients were reviewed for positive culture and antibiogram, using standard procedures and analyzed. Additional data were retrieved from a previous study in seven facilities in Abuja and three hospitals in Kano from 2008 to 2017 and 2013 to 2017, respectively. A declining trend in percent positivity of S. Typhi was observed in Abuja with more erratic trends in Lagos and Kano. In Lagos, more than 80% of the isolates from the entire study period exhibited multiple drug resistance with a generally increasing trend. Of the chosen contextual factors, improvements were recorded in female literacy, access to improved water supply, diarrheal mortality in children younger than 5 years, gross domestic product, and poverty while access to improved sanitation facilities decreased over time nationally. Typhoid fever still poses a serious health challenge in Nigeria and in antibiotic resistance, and is a major health security issue. A combined approach that includes the use of typhoid vaccines, improvements in sanitation, and safe water supply is essential.

Occurrence of extended-spectrum and AmpC β-lactamases in multiple drug resistant Salmonella isolates from clinical samples in Lagos, Nigeria

PURPOSE

Salmonella spp. are important foodborne pathogens exhibiting increasing resistance to antimicrobial drugs. Resistance to broad-spectrum β-lactams, mediated by extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase enzymes is fast spreading and has had negative impacts on the clinical outcomes, particularly on third-generation cephalosporins. This study investigated the carriage of AmpC gene among multidrug-resistant Salmonella spp. from Lagos, Nigeria.

METHODS

Forty Salmonella spp. from clinical samples (S. typhi = 13; S. typhimurium = 10; S. enteritidis = 8; S. choleraesuis = 5; S. paratyphi = 4) were subjected to in vitro susceptibility test by disk diffusion methods. Isolates that were resistant to cefoxitin and third-generation cephalosporins were screened for ESBL (Double Disk Synergy Test Method) and AmpC enzyme (AmpC disk test) production. Detection of AmpC fox gene was carried out by polymerase chain reaction.

RESULTS

Thirty-two (80%) of the Salmonella isolates were cefoxitin resistant. Plasmid-mediated AmpC β-lactamase and ESBL enzymes were recorded in 10/40 (25%) and 16/40 (40%) of the Salmonella isolates, respectively. Specifically, 16/40 (40%) of the Salmonella isolates possessed 380 bp AmpC fox gene, with the highest occurrence found in S. typhi strains (43.8%) followed by S. typhimurium (25%). There was no AmpC fox gene detected in S. paratyphi strains. Interestingly, coproduction of enzymes occurred in some of the isolates, raising fears of resistance to a multitude of antibiotics in the treatment of bacterial infections.

CONCLUSION

Emergence of AmpC β-lactamase-producing Salmonella isolates in our environment was recorded for the first time, raising concern on increased antibiotic resistance among strains of Salmonella serovars in Lagos. Further genotypic study of the isolates could answer the questions on strain sources, clonal relatedness, and mechanism of spread.

A retrospective study of community-acquired Salmonella infections in patients attending public hospitals in Lagos, Nigeria

Introduction: A retrospective cohort study on Salmonella-associated diseases (SADs) was conducted in 14 public hospitals across Lagos State, Nigeria, between 1999 and 2008. Methodology: Medical records of clinically diagnosed patients with confirmed Salmonella infections were reviewed for the 10-year period. Laboratory diagnosis of typhoid fever cases in all the hospitals were first based on Widal agglutination tests then followed by culture, while non-typhoidal Salmonella infections were based on culture technique. Results: A total of 85,187 confirmed cases of SADs were found, of which 880 deaths were recorded (case-fatality rate = 1.03% / 10 years). The mean incidence of SADs in Lagos State for the 10-year period was estimated at 45 cases per 100,000 persons/year, while that of typhoid fever alone was 16 cases per 100,000 persons/year. During the studied period, the number of deaths due to typhoid fever was significantly (P < 0.05) higher than deaths due to gastroenteritis except in 2003 and 2004. Risk associated with typhoidal deaths was 4 to 11 times greater when compared to gastroenteritis deaths between 2000 and 2002. Salmonella-associated diseases were most prevalent in adults 21 -to30 years of age (49.49%). Cases of patients with invasive Salmonella-associated gastroenteritis were observed mainly in children under five years of age. Conclusion: The current surveillance data indicated high incidence of SADs in areas exposed to environmental contaminations. This study revealed that infections caused by Salmonella enterica serovars are endemic in our environment thus poses a serious threat to public health. Constant public health education is essential to avert undue epidemics.

Application of phage typing and pulsed-field gel electrophoresis to analyse Salmonella enterica isolates from a suspected outbreak in Lagos, Nigeria

INTRODUCTION

Inadequate potable water supply and poor sanitation predispose to food- and water-borne diseases associated with Salmonella enterica serovars in developing countries. In this study the possible source of an unprecedented upsurge of Salmonella-associated community gastroenteritis was traced using both phage-typing and pulsed-field gel electrophoresis (PFGE).

METHODOLOGY

Nineteen Salmonella Typhimurium (three sporadic isolates included) and 13 Salmonella Enteritidis isolates from clinical, animal, and environmental samples were subjected to antimicrobial susceptibility testing, phage-typing, and PFGE analysis using standard procedures.

RESULTS

Eleven (68.8%) of the 16 outbreak-related multidrug resistant S. Typhimurium belonged to DT 71 phage type with cluster PFGE type X3, representing the most prevalent strain identified among human, animal, and environmental isolates. The remaining five (31.2%) outbreak-related strains  reacted but did not conform with clear phage types (RDNC) with cluster PFGE types X1 and X2 (96.8% similarity). Sporadic strains were untypable and belonged to X4 PFGE type. However, the evaluated S. Enteritidis strains that were multidrug resistant without a definite phage type belonged to PFGE cluster type X1e and were identified among the water and human strains. None of the Typhimurium and Enteritdis isolates was resistant to the fluoroquinolone antibiotics that were evaluated.

CONCLUSION

This study emphasizes the epidemiological usefulness of PFGE typing in the detection of emerging strains of multipledrug resistant Salmonella, particularly S. Typhimurium DT71, that pose serious health implications in our environment. The study provides epidemiological links between environmental reservoirs and human infection in this community.

Multidrug resistance in Salmonella enterica serovar typhi isolated from patients with typhoid fever complications in Lagos, Nigeria

OBJECTIVE

The aim of this study was to determine the prevalence of Salmonella enterica serovar typhi in patients with pyrexia of unknown origin (PUO), and antimicrobial resistance in strains isolated from patients with S. typhi in Lagos, Nigeria.

STUDY DESIGN

In total, 103 patients were included in this study, subdivided into two categories. Category A comprised 74 patients presenting with PUO, and Category B comprised 29 patients harbouring S. typhi who did not respond to initial treatment.

METHODS

Blood samples were cultured for bacterial isolates and identified by standard procedures. Susceptibility testing was performed according to the National Committee for Clinical Laboratory Standards. Plasmid DNA extraction was performed using the alkaline lysis method with Escherichia coli v517 used as the standard. Conjugation and transformation experiments were performed using standard methods. For the latter, E. coli K12 HB 101 (ara-14, galK2, hsd 520, lacyl, leu, mtl-1, Pro A2, rec A13, rps L20, sup E44, thii xyl-5) was used as the recipient and plasmid PBR 322 was used as the positive control.

RESULTS

The prevalence of S. typhi in PUO was 16.2% (12/74). In all, 25 of 41 (61.0%) cases were multidrug resistant (MDR) with phenotypic-resistant patterns: ACoCT, ACTCeS, ACTCoCe and ACTS were commonly encountered among the strains. Interestingly, four of the strains harbouring similar plasmid DNA were isolated from patients with hepatosplenomegaly, and a strain harbouring a large transferable plasmid of 81.2MDa was isolated from a psychosis patient.

CONCLUSIONS

Our study confirmed the circulation of MDR S. typhi in Lagos, Nigeria. Periodic review of antibiotics used in hospitals is essential as the efficacies of chloramphenicol, ampicillin and cotrimoxazole are now doubtful. Ciprofloxacin and ofloxacin are effective drugs for treatment of typhoid fever, but with current trends of drug abuse in Nigeria, resistance is likely to develop. These results, therefore, provide an early warning signal for the prudent use of fluoroquinolone antimicrobials to preserve their usefulness.

Screening of some medicinal plants used in south-west Nigerian traditional medicine for anti-Salmonella typhi activity

Ten Nigerian medicinal plants used traditionally for the treatment of several ailments of both microbial and non-microbial origins were tested on multi-drug resistant S. typhi (MDR) strains of which six of them were active. The results revealed that both the aqueous and ethanol extracts of Terminalia avicennioides, Momordica balsamina, Combretum paniculatum and Trema guineensis were effective on the MDR-S. typhi strains with minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values ranging from 9.60 to 14 mcg/ml and 24 to 33 mcg/ml, respectively. Whereas, only the aqueous extracts of Morinda lucida and Ocimum gratissimum were found to be active against this pathogen with MIC and MBC values of 9.60 and 24 mcg/ml for M. lucida, 40 and 55 mcg/ml for O. gratissimum, respectively. There was no statistical significant difference (P > 0.05) between the activity of each plant extract and the decoctions prepared from them. All the six active plants showed positive reactions to alkaloids, tannins, flavonoids and anthraquinones but in variable degrees. All but M. balsamina, indicated the presence of saponin.

Prevalence of multi-drug resistant Salmonella typhi among clinically diagnosed typhoid fever patients in Lagos, Nigeria

A total of 635 clinically diagnosed typhoid fever patients were bled from three different health institutions in the metropolis of Lagos, Nigeria over a period of 15 months, May 1997 to July 1998. Out of the total blood cultured, 101 (15.9%) isolates of Salmonella species were isolated of which 68 (67.3%) were S. typhi, 17 (16.8%) and 16 (15.8%) were S. paratyphi A. and S. arizonae respectively. The overall isolation rate of S. typhi among patients is 10.7%, with most isolates 45.9% found among the severely-ill young adults, age group 16-30 years. All isolates were subjected to anti-microbial susceptibility testing using 12 different antibiotics: chloramphenicol, ampicillin, cotrimoxazole, gentamicin, colistin sulfate, nalidixic acid, nitrofurantoin, cefotaxime, tetracycline, streptomycin, ofloxacin and ciprofloxacin. All the S. typhi and S. paratyphi A isolates showed resistance to two or more of the 10 of 12 antibiotics tested particularly the 3-first-line antibiotics commonly used (chloramphenicol, ampicillin and cotrimoxazole) in the treatment of typhoid fever in Nigeria. No isolate showed resistance to ofloxacin and ciprofloxacin, however, nalidixic acid and gentamicin showed a moderate and appreciable inhibition to most of our isolates.

Escherichia coli in patients with acute gastroenteritis in Lagos, Nigeria

Over a period of 12 months, a total of 852 stool samples from patients (both children and adults) with acute diarrhoeal diseases attending some public and government recognised health institutions in Lagos metropolis were screened for diarrhoeagenic bacterial agents. One hundred and eighty two bacterial isolates were found out of which 83 (45.6%) were Escherichia coli, 38 (20.9%) Shigella spp, 31 (17%) Salmonella spp, 16 (8.8%) Klebsiella spp, eight (4.4%) Aeromonas spp, while there were only six (3.3%) isolates for Plesiomonas spp. Of the 83 isolates for E. coli group, 49 (59%) were enteropathogenic (EPEC), 17 (20.5%) enterotoxigenic (ETEC), 10 (12.1%) enteroinvasive (EIEC) and seven (8.4%) enterohaemorrhagic (EHEC). The EPEC strains particularly serotype 055, were mostly encountered in children aged over five years. On the other hand, EIEC and ETEC strains were found mainly in adults while EHEC O157: H7 strains occurred in all the age groups studied. This study further stresses the important role of EIEC and ETEC in acute diarrhoeal diseases and the possible implication of EHEC in acute gastroenteritis, especially in children in Lagos, Nigeria.