Helicobacter pylori diagnosis and treatment in Africa: The First Lagos Consensus Statement of the African Helicobacter and Microbiota Study Group (AHMSG)

BACKGROUND

Helicobacter pylori (H. pylori) infection is the most prevalent type of bacterial infection. Current guidelines from different regions of the world neglect specific African conditions and requirements. The African Helicobacter and Microbiota Study Group (AHMSG), founded in 2022, aims to create an Africa-specific consensus report reflecting Africa-specific issues.

SUMMARY

Eighteen experts from nine African countries and two European delegates supported by nine African collaborators from eight other countries prepared statements on the most important African issues in four working groups: (1) epidemiology, (2) diagnosis, (3) indications and prevention, and (4) treatment. Limited resources, restricted access to medical systems, and underdeveloped diagnostic facilities differ from those of other regions. The results of the individual working groups were presented for the final consensus voting, which included all board members.

KEY MESSAGES

There is need for further studies on H. pylori prevalence in Africa, with diagnosis hinged on specific African situation. Treatment of H. pylori in the African setting should be based on accessibility and reimbursement, while indication and prevention should be defined in specific African countries.

SARS-CoV-2 Variants Genotyping and Diagnostic Performance of a 2-Genes Detection Assay

BACKGROUND

The emergence of the COVID-19 pandemic resulted in the unprecedented expansion of molecular testing technologies. This study aimed at evaluating the performance of the FluoroType® SARS-CoV-2 plus assay for SARS-CoV-2 detection as well as describing the detection of SARS-CoV-2 variants using the FluoroType® SARS-CoV-2 varID Q kit.

METHODS

The study utilized 679 archived nasopharyngeal samples. Analytical performance and the diagnostic performance of the FluoroType® SARS-CoV-2 plus assay were determined using 320 samples and reference material. Variants identification on the FluoroType® SARS-CoV-2 varID Q assay was performed on 359 samples. The study was approved by the Aga Khan University Hospital Institutional Review Board.

RESULTS

The FluoroType® SARS-CoV-2 plus assay's limit of detection was verified as 1.2 copies/µL. The repeatability SD and %CV were 2.45 and 9.8% while reproducibility had an SD and %CV of 1.39 and 5.68%, respectively, for the RdRP gene. The positive and negative percent agreement were determined to be 99.4% (95% CI; 98.1%-100%) and 99.4% (95% CI; 98.2%-100%) respectively. In the variants identification, samples from the original wave had no mutations identified while 12.3%, 49%, and more than 90% of the samples during the Alpha, Delta, and Omicron waves, respectively, had detectable mutations.

CONCLUSIONS

The FluoroType® SARS-CoV-2 plus assay demonstrated analytical performance comparable to the reference method with a diagnostic sensitivity and specificity of >99%. The FluoroType® SARS-CoV-2 varID Q assay achieved rapid detection of circulating variants.

Child deaths caused by Klebsiella pneumoniae in sub-Saharan Africa and south Asia: a secondary analysis of Child Health and Mortality Prevention Surveillance (CHAMPS) data

BACKGROUND

Klebsiella pneumoniae is an important cause of nosocomial and community-acquired pneumonia and sepsis in children, and antibiotic-resistant K pneumoniae is a growing public health threat. We aimed to characterise child mortality associated with this pathogen in seven high-mortality settings.

METHODS

We analysed Child Health and Mortality Prevention Surveillance (CHAMPS) data on the causes of deaths in children younger than 5 years and stillbirths in sites located in seven countries across sub-Saharan Africa (Ethiopia, Kenya, Mali, Mozambique, Sierra Leone, and South Africa) and south Asia (Bangladesh) from Dec 9, 2016, to Dec 31, 2021. CHAMPS sites conduct active surveillance for deaths in catchment populations and following reporting of an eligible death or stillbirth seek consent for minimally invasive tissue sampling followed by extensive aetiological testing (microbiological, molecular, and pathological); cases are reviewed by expert panels to assign immediate, intermediate, and underlying causes of death. We reported on susceptibility to antibiotics for which at least 30 isolates had been tested, and excluded data on antibiotics for which susceptibility testing is not recommended for Klebsiella spp due to lack of clinical activity (eg, penicillin and ampicillin).

FINDINGS

Among 2352 child deaths with cause of death assigned, 497 (21%, 95% CI 20-23) had K pneumoniae in the causal chain of death; 100 (20%, 17-24) had K pneumoniae as the underlying cause. The frequency of K pneumoniae in the causal chain was highest in children aged 1-11 months (30%, 95% CI 26-34; 144 of 485 deaths) and 12-23 months (28%, 22-34; 63 of 225 deaths); frequency by site ranged from 6% (95% CI 3-11; 11 of 184 deaths) in Bangladesh to 52% (44-61; 71 of 136 deaths) in Ethiopia. K pneumoniae was in the causal chain for 450 (22%, 95% CI 20-24) of 2023 deaths that occurred in health facilities and 47 (14%, 11-19) of 329 deaths in the community. The most common clinical syndromes among deaths with K pneumoniae in the causal chain were sepsis (44%, 95% CI 40-49; 221 of 2352 deaths), sepsis in conjunction with pneumonia (19%, 16-23; 94 of 2352 deaths), and pneumonia (16%, 13-20; 80 of 2352 deaths). Among K pneumoniae isolates tested, 121 (84%) of 144 were resistant to ceftriaxone and 80 (75%) of 106 to gentamicin.

INTERPRETATION

K pneumoniae substantially contributed to deaths in the first 2 years of life across multiple high-mortality settings, and resistance to antibiotics used for sepsis treatment was common. Improved strategies are needed to rapidly identify and appropriately treat children who might be infected with this pathogen. These data suggest a potential impact of developing and using effective K pneumoniae vaccines in reducing neonatal, infant, and child deaths globally.

FUNDING

Bill & Melinda Gates Foundation.

Development, roll-out and implementation of an antimicrobial resistance training curriculum harmonizes delivery of in-service training to healthcare workers in Kenya

Background

Antimicrobial resistance (AMR) is an increasingly severe threat to global public health that requires action across different sectors. Selection of appropriate antimicrobials is an urgent challenge due to the emergence of drug resistance. In 2017, Kenya developed an AMR policy and National Action Plan to drive prevention and containment of AMR. A priority activity under AMR surveillance strategic objective was to develop a national AMR training curriculum for in-service healthcare workers. In this paper we discuss the development process, gains achieved through implementation across the country and lessons learned.

Methods

An initial stakeholders' forum was convened to brainstorm on the process for developing the curriculum and some issues deliberated upon include the design approach, development roadmap, curriculum outline and scope, delivery, and evaluation methodologies. A dedicated team of subject matter experts (SMEs), drawn from the project and government ministries, compiled the initial draft of the curriculum and later the training materials. A series of other stakeholders' meetings were convened to review these materials. The National Antimicrobial Stewardship Interagency Committee (NASIC) of the MOH in Kenya identified a team of experts from academia, research, and government to work with the SMEs in reviewing and providing valuable inputs to the curriculum. Additionally, principles of adult learning and a One Health approach for development were considered as AMR has drivers and impacts across sectors. A validation workshop was held to finalize the documents with a formal launch conducted during the World Antibiotics Awareness Week of 2020.

Results

A multisectoral AMR surveillance training curriculum and facilitator and trainee manuals were developed and endorsed by MOH and Ministry of Agriculture, Livestock, Fisheries and Cooperatives within one year. Over 500 healthcare workers in 19 counties were trained, with overwhelming adoption by other stakeholders in Kenya and beyond.

Conclusion

This curriculum was developed to standardize training for AMR detection and surveillance. The central role played by the MOH ensured expeditious development and roll-out of this curriculum. The in-service curriculum, now available on an e-learning platform, provides a ready opportunity to build capacity of healthcare professionals. Additional resources are needed to standardize and scale these efforts to reach all healthcare workers.

Helicobacter pylori Infection in Africa: Update of the Current Situation and Challenges

BACKGROUND

The burden of Helicobacter pylori infection (HPI) in Africa remains high with varying levels of prevalence among children and adults reported in different regions of the continent. Persistent and uneradicated HPI could result in gastric cancer, although less severe pathological outcomes have been reported among Africans - the so-called "African enigma."

SUMMARY

Analysis of endoscopic findings of the upper gastrointestinal tract demonstrates similarities with that of patients from the West. Thus, it could be asserted that the true picture of HPI in Africa is yet to be unveiled due to several challenges including inadequate health-care system, lack of treatment guidelines and standardized protocol for diagnosis, and lack of data. This review explores the prevalence, diagnosis, treatment, and health-care system in Africa as it relates to HPI, thus providing an update and highlighting the need for an African HPI guideline.

KEY MESSAGES

There is high prevalence of Helicobacter pylori infection (HPI) in Africa with an increasing burden of antibiotic resistance. Various methods including invasive and noninvasive methods are deployed in the diagnosis of HPI in Africa. There is a need for consensus on diagnosis and treatment of HPI in Africa.

Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses

Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. aurisIMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology.

Prospective Cohort Study on Timing of Antimicrobial Prophylaxis for Post-Cesarean Surgical Site Infections

Background: Sepsis is the leading cause of maternal death in sub-Saharan Africa (SSA), a region that sees some of the highest rates of maternal death and morbidity in the world. As one of the most commonly performed surgical procedures in SSA and a proved risk factor for surgical site infection (SSI), cesarean section (CS) is an important operation to target because of its massive impact on maternal and neonatal health. There is currently insufficient published data available on the patient and facility-based context around SSI after CS to establish a true and clear understanding of this infectious category. The objective of this study was to collect accurate and valid data on the incidence of SSI after CS and the circumstances around SSI in two Kenyan hospitals. Hypothesis: Our primary analysis focused on the consequences of timing of peri-operative antimicrobial prophylaxis. We hypothesized that patients who were given antibiotics pre-operatively would show lower SSI rates than those given the agents post-operatively. Methods: This was an Institutional Review Board-approved observational study of 609 women who had CS operations at two Kenyan hospitals from September to December 2015. Thika provided antimicrobial prophylaxis prior to incision for all patients, and Kiambu provided only post-operative prophylaxis. It should be noted that this difference was the result of a previous intervention at Thika and not a part of this observational study. Results: Patients at the two hospitals had similar pre-operative characteristics indicating a relatively healthy population. The median age was 26 ± 6 years (range 18-43) at Thika and 26 ± 5 (18-44) at Kiambu. Median parity was 1 ± 1 (range 0-7) at Thika and 1 ± 1 (0-10). Patients also went through a comparable number of antenatal care visits (median 4 ± 1 at both hospitals). The number of patients with prolonged rupture of the membranes was 103 (34.4%) at Thika and 99 (32.9%) at Kiambu. There was a slightly higher number of patients with meconium-stained liquor at Kiambu Hospital (115) than at Thika (74). The SSI rate was 4.0% (12/299; 11 superficial, 1 deep) at Thika and 9.3% (28/301; 18 superficial, 7 deep, 3 organ/space) at Kiambu. Conclusions: The data show a striking difference between SSI rates in patients who were given properly timed pre-operative antibiotics and patients who were given only post-operative antibiotics. Administration of post-operative antibiotics is currently the norm in much of SSA, and there is strong evidence that many of the infectious problems encountered in this population would be reduced by the provision of antibiotic prophylaxis prior to the incision.

Streptococcus pneumoniae serotype epidemiology among PCV-10 vaccinated and unvaccinated children at Gertrude's Children's Hospital, Nairobi County: a cross-sectional study

Background:Streptococcus pneumoniae (SP n) serotype replacement and emergence of multidrug resistant SP n has exacerbated the need for continuous regional serotype surveillance. We investigated SP n serotypes circulating among children ≤5 years in Nairobi County. Methods:Streptococcus pneumoniae stocks stored at -70°C in brain heart infusion medium were thawed at room temperature for 30 minutes. In total, 10 µl of the stored SP n cells were suspended in 50 µl PBS and gently vortexed. About 10 µl of the suspended cells were added on to a glass slide and mixed with 10 µl pooled antisera. The glass slide was swirled gently while observing for any reaction. The process was repeated with individual groups under various antisera pools. Those serotypes that did not belong to any pool were typed directly until a positive agglutination reaction was observed. The cells/PBS/serotype-specific antisera mixture on the glass slide were covered with a coverslip and observed under a phase contrast microscope at ×100 objective lens with oil emulsion. Results: Out of the 206 subjects sampled, 20.39% (n=42) were found to be carriers of SP n. About 52% (n=22) of the SP n carriers had received the recommended dose of PCV-10, while 48% (n=20) of the carriers had not. Almost all (n=41; 19.90% of subjects) isolates contained non-vaccine type SP n serotypes, while n=1 of the serotypes (in 0.49% of subjects) were untypeable. Serotypes 28F, 6A, 11A, 3 and 7C were prevalent in both vaccinated and unvaccinated children, whereas serotypes 23A, 17F, 35F, 48, 13 and 35B, and 23B, 20, 19B, 21, untypeable, 15B and 39 were found among unvaccinated and vaccinated groups, respectively. Conclusions: All SP n serotypes isolated from the subjects sampled were non PCV-10 vaccine type. Therefore Kenyan children receiving PCV-10 vaccine are not protected.

Streptococcus pneumoniae Serotype Epidemiology among PCV-10 Vaccinated and Unvaccinated Children at Gertrude's Children's Hospital, Nairobi County: A Cross-Sectional Study

Background: Serotype replacement and emergence of multidrug resistant S. pneumoniae has exacerbated the need for continuous regional serotype surveillance especially in the developing world. We investigated S. pneumoniae serotypes circulating among vaccinated and unvaccinated children ≤5 years in Nairobi County post PCV10 era. Methods: A total of 206 vaccinated and unvaccinated children attending Gertrude's Children's Hospital (GCH) were recruited for this study. Nasopharyngeal swabs collected using Copan Flocked Swabs were the main study specimen. Culturing and isolation of S. pneumoniae was done on BA with gentamicin and BA plates respectively at the GCH main laboratory. Serotyping was done using the Quellung reaction at the KEMRI-Wellcome Trust, Kilifi.  Results: Out of the 206 subjects sampled, 20.39% (42) were found to be carriers of S. pneumoniae. About 52% (n=22) of the S. pneumoniae carriers had received the recommended dose of PCV-10, while 48% (n=20) of the carriers had not. Almost all (n=41; 19.90% of subjects) isolates contained non-vaccine type S. pneumoniae serotypes, while n=1 of the serotypes (in 0.49% of subjects) were untypeable. Serotypes 28F, 6A, 11A, 3 and 7C were prevalent in both vaccinated and unvaccinated children, whereas serotypes 23A, 17F, 35F, 48, 13 and 35B, and 23B, 20, 19B, 21, untypeable, 15B and 39 were found among unvaccinated and vaccinated groups, respectively. Conclusions: All S. pneumoniae serotypes isolated from the subjects sampled were non PCV-10 vaccine type. These results therefore highlight the importance of monitoring and evaluation to provide epidemiological information to determine the effectiveness of PCV10 in Kenya's Public health services.

Developing core elements and checklist items for global hospital antimicrobial stewardship programmes: a consensus approach

OBJECTIVES

With increasing global interest in hospital antimicrobial stewardship (AMS) programmes, there is a strong demand for core elements of AMS to be clearly defined on the basis of principles of effectiveness and affordability. To date, efforts to identify such core elements have been limited to Europe, Australia, and North America. The aim of this study was to develop a set of core elements and their related checklist items for AMS programmes that should be present in all hospitals worldwide, regardless of resource availability.

METHODS

A literature review was performed by searching Medline and relevant websites to retrieve a list of core elements and items that could have global relevance. These core elements and items were evaluated by an international group of AMS experts using a structured modified Delphi consensus procedure, using two-phased online in-depth questionnaires.

RESULTS

The literature review identified seven core elements and their related 29 checklist items from 48 references. Fifteen experts from 13 countries in six continents participated in the consensus procedure. Ultimately, all seven core elements were retained, as well as 28 of the initial checklist items plus one that was newly suggested, all with ≥80% agreement; 20 elements and items were rephrased.

CONCLUSIONS

This consensus on core elements for hospital AMS programmes is relevant to both high- and low-to-middle-income countries and could facilitate the development of national AMS stewardship guidelines and adoption by healthcare settings worldwide.

Pattern of pathogens and their sensitivity isolated from surgical site infections at the Aga Khan University Hospital, Nairobi, Kenya

BACKGROUND

In low income countries, surgical site infections (SSIs) are costly and impose a heavy and potentially preventable burden on both patients and healthcare providers. This study aimed to determine the occurrence of SSI, pathogens associated with SSI, the antibiogram of the causative pathogens and specific risk factors associated with SSI at the hospital.

METHODS

Two hundred and sixty-eight respondents admitted for general surgical procedures (other than neurological and cardiothoracic surgeries) at the Aga Khan University Hospital were eligible to take part in the study. Post-surgery patients were observed for symptoms of infection. Follow ups were done through the consulting clinics, breast clinic and casualty dressing clinic by a team of surgeons. In cases of infection, pus swabs were collected for culture.

RESULTS

SSI incidence rate was 7.0%, pathogens isolated from SSI included gram negative enteric bacilli and S. aureus which was the most prevalent bacterial isolate. Only one isolate of MRSA was found and all staphylococci were susceptible to Vancomycin. Preoperative stay ≥ 2 days and wound class were the risk factors associated with SSI.

CONCLUSION

The SSI incidence rates (7.0%) observed in this study were relatively lower than the ones documented in other studies in Kenya. S. aureus is the most prevalent pathogen associated with SSI. Similar to findings from other studies done in the region; prolonged hospital stay and dirty wounds were the risks associated with postsurgical sepsis at the hospital.