Elevated rates of horizontal gene transfer in the industrialized human microbiome.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.

Helicobacter pylori Diagnosis and Treatment in Africa: The First Lagos Consensus Statement of the African Helicobacter and Microbiota Study Group.

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, aimed 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 a 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.

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.

Progress towards elimination of viral hepatitis: a Lancet Gastroenterology & Hepatology Commission update.

The top 20 highest burdened countries (in disability-adjusted life years) account for more than 75% of the global burden of viral hepatitis. An effective response in these 20 countries is crucial if global elimination targets are to be achieved. In this update of the Lancet Gastroenterology & Hepatology Commission on accelerating the elimination of viral hepatitis, we convene national experts from each of the top 20 highest burdened countries to provide an update on progress. Although the global burden of diseases is falling, progress towards elimination varies greatly by country. By use of a hepatitis elimination policy index conceived as part of the 2019 Commission, we measure countries' progress towards elimination. Progress in elimination policy has been made in 14 of 20 countries with the highest burden since 2018, with the most substantial gains observed in Bangladesh, India, Indonesia, Japan, and Russia. Most improvements are attributable to the publication of formalised national action plans for the elimination of viral hepatitis, provision of publicly funded screening programmes, and government subsidisation of antiviral treatments. Key themes that emerged from discussion between national commissioners from the highest burdened countries build on the original recommendations to accelerate the global elimination of viral hepatitis. These themes include the need for simplified models of care, improved access to appropriate diagnostics, financing initiatives, and rapid implementation of lessons from the COVID-19 pandemic.

The views of African and Middle Eastern Gastroenterologists on the management of mild-to-moderate, non-erosive gastro-esophageal reflux disease (GERD).

INTRODUCTION: Gastro-esophageal reflux disease (GERD) is a common gastrointestinal disorder that occurs when backflow of the gastric contents into the esophagus results in troublesome symptoms. Though GERD has been extensively studied in Western populations, literature on the management of GERD in patients in Africa and Middle East (AME) is scarce. AREAS COVERED: In this review, we provide an overview of the management of mild-to-moderate GERD in AME. Here we focus on the efficacy and safety of currently available treatments for GERD to help physicians and community pharmacists appropriately manage patients with mild-to-moderate GERD in the primary healthcare setting, detailing specific situations and patient scenarios that are relevant to the region, including management of GERD during Ramadan and post-bariatric surgery. EXPERT OPINION: Under-appreciation of the burden of GERD in the region has resulted in a lack of consensus on management. Barriers that currently prevent the adoption of treatment guidelines in the primary healthcare setting may include lack of availability of local guidelines and referral systems, a paucity of region-specific research, and dogmatic adherence to traditional practice. By increasing awareness, strengthening knowledge, and by more effective utilization of resources, physicians and pharmacists could optimize GERD management strategies to better support patients.

Non-alcoholic fatty liver disease and the metabolic syndrome in an urban hospital serving an African community.

BACKGROUND: Liver disease continues to be a major cause of morbidity and mortality in sub-Saharan Africa, including Nigeria, due to the high endemicity of viral hepatitis B. However non-alcoholic fatty liver disease may be an important contributory factor. The impact of fatty liver disease in our region has not been evaluated. AIM: To determine the prevalence of non-alcoholic fatty liver disease (NAFLD) among a population of diabetic (DM) subjects attending the endocrine clinic of LASUTH compared with non-diabetic subjects; ascertain other contributing factors and compare the occurrence of the metabolic syndrome in subjects with and without NAFLD. METHODOLOGY: Consecutive patients who satisfy the study criteria were enrolled. An investigator- administered questionnaire was used to determine symptoms of liver disease, followed by physical examination to obtain anthropometric indices as well as signs of liver disease. Abdominal scan was performed to determine radiologic evidence of fatty liver and fasting blood samples were collected from for the measurement of fasting lipid profile, glucose, liver biochemistry and serology for hepatitis B and C markers. RESULTS: One hundred and fifty subjects, mean age 56 years (standard deviation = 9, range 20-80 yr) and gender ratio (F: M) of 83:67(55%:45%), were recruited. 106 were diabetics and 44 non-diabetics. The overall prevalence of NAFLD amongst all study subjects was 8.7%. The prevalence rate of NAFLD was higher in the DM cases than in the Control subjects but this difference was not statistically significant (9.5 vs. 4.5%, p = 0.2). Only one of the subjects with fatty liver disease had elevated transaminase levels (steatohepatitis) and also had type 2 DM. Central obesity as measured by waist circumference (WC) and SGPT levels were significantly higher in people with fatty liver. The mean body mass index (BMI) of diabetic and non-diabetic patients was similar (31 vs. 30 kg/m(2)). The prevalence of the metabolic syndrome was higher in the subjects with NAFLD than in those without fatty liver disease but this difference was not statistically significant (p = 0.8). CONCLUSION: Non-alcoholic fatty liver disease is present in Africa but is less than what one would expect based on American and European studies.

Health-care provision and policy for non-alcoholic fatty liver disease in sub-Saharan Africa.

Sub-Saharan Africa, which has a population of more than 1 billion people, carries 24% of the global burden of disease and spends the least on health care of any region, relying heavily on international development assistance to deliver health care for HIV, tuberculosis, and malaria. The demographic and epidemiological transitions occurring in sub-Saharan Africa, with rising prevalences of obesity and diabetes, enhance the risk of non-alcoholic fatty liver disease (NAFLD), yet this remains an unrecognised complication of metabolic syndrome. There are no guidance documents on NAFLD from sub-Saharan Africa, and non-communicable disease (NCD) guidance documents do not include the associated burden of fatty liver disease. Combating the health and socioeconomic burden of NAFLD requires an integrated liver health approach, with task-shifting to primary health care. Using clear guidance documents to link education and management of HIV, viral hepatitis, NAFLD, and associated NCDs is also crucial to an integrated approach to infectious diseases and NCDs, which requires targeted funding from both governments and international development agencies.

Hepatitis C viral load and genotypes among Nigerian subjects with chronic infection and implication for patient management: a retrospective review of data.

INTRODUCTION: Hepatitis C Virus (HCV) is highly infectious with no currently available vaccine. Prior to treatment, it is recommended to confirm HCV infection with either quantitative or qualitative nucleic acid test. Access to these assays in Nigeria is limited but for effective management of patients, HCV viral load (VL) prior to therapy is required and genotype may be needed in some instances. This study aimed at reviewing the pattern of HCV viral load and genotype in the country, and its implication in patient management. METHODS: this was a retrospective study that involved data abstraction from an electronic database of an accredited laboratory between June 2013 and May 2017. De-linked data were abstracted from records of adult subjects with HCV VL and genotype results, these were analysed using Microsoft Excel 2010 and SPSS v20. RESULTS: within the study period, 346 subjects had baseline VL and 134 (38.7%) had genotype results available. Of these, 202/346 (58.4%) had detectable VL results with higher prevalence in males (64.7%) and ≥51years (42.5%) age group. The median VL among 202 subjects was 407,430 (IQR: 96,388 - 1,357,012) IU/mL. Distribution of genotypes showed that genotypes 1 and 4 had prevalence of 63.2% and 16.8% respectively. CONCLUSION: genotypes 1 and 4 have the highest prevalence. A greater proportion of subjects had VL values ≤800,000 IU/mL, an indication that they are more likely to respond well to available antiviral therapy hence, access to these antivirals will greatly improve management of HCV infection in Nigeria.

Helicobacter pylori patient isolates from South Africa and Nigeria differ in virulence factor pathogenicity profile and associated gastric disease outcome.

Helicobacter pylori is a gram-negative, spiral-shaped bacterial pathogen and the causative agent for gastritis, peptic ulcer disease and classified as a WHO class I carcinogen. While the prevalence of H. pylori infections in Africa is among the highest in the world, the incidence of gastric cancer is comparably low. Little is known about other symptoms related to the H. pylori infection in Africa and the association with certain phenotypes of bacterial virulence. We established a network of study sites in Nigeria (NG) and South Africa (ZA) to gain an overview on the epidemiological situation. In total 220 isolates from 114 patients were analyzed and 118 different patient isolates examined for the presence of the virulence factors cagA, vacA, dupA, their phylogenetic origin and their resistance against the commonly used antibiotics amoxicillin, clarithromycin, metronidazole and tetracycline. We report that H. pylori isolates from Nigeria and South Africa differ significantly in their phylogenetic profiles and in their expression of virulence factors. VacA mosaicism is intensive, resulting in m1-m2 vacA chimeras and frequent s1m1 and s1m2 vacA subtypes in hpAfrica2 strains. Gastric lesions were diagnosed more frequent in Nigerian versus South African patients and H. pylori isolates that are resistant against one or multiple antibiotics occur frequently in both countries.

Duodenal ulcer promoting gene (DupA), plasticity region genes and sigma factors in H. pyloristrains from Nigeria.

INTRODUCTION: Helicobacter pylori is a principal cause of gastric cancer. The aim of this study was to determine the prevalence and contribution of duodenal ulcer promoting gene A (dupA), the plasticity region genes and sigma factors in relation to their pathological expression of H. pylori infections in the Nigerian population. METHODOLOGY: Polymerase Chain Reaction was used to analyze a total of forty-nine H. pylori strains isolated from patients attending various endoscopic units in tertiary hospitals in Nigeria for complete dupA (G27 variant), jhp0917, jhp0918, other plasticity region genes jhp 914/917, jhp0914, jhp0940 and sigma factors. RESULTS: PCR results indicated that the prevalence of complete dupA (G27 variants), jhp0917, jhp0918 and other plasticity region genes jhp0914, jhp0914/0917 and jhp0940 in the H. pylori strains were 4%, 53%, 88%, 73%, 12% and 0% respectively. The prevalence values of the sigma factors were 96%, 92%, 80% for rpoN,  fliA and rpoD respectively. However, the endoscopic findings showed that erosion, normal mucosal, ulcer, hyperaemic stomach, mucosal atrophy and oedematous stomach in the patients where the H. pylori strains were isolated were 40.8%, 32.7%, 10.2%, 8.2%, 2.0% and 6.1% respectively. There was significant association between jhp0917, jhp914/917 and G27 variant and the endoscopic findings, while other plasticity genes showed no association with the endoscopic findings. CONCLUSION: These results suggest that the presence of jhp0917, jhp0914/917 and G27 variant could be used as marker to predict the pathological effect of severity in Nigeria patients with H. pylori infection.

The Prevalence of Occult Hepatitis B Infection among Blood Donors in Lagos, Nigeria.

BACKGROUND: In occult hepatitis B virus (HBV) infection, the HBV DNA is present in the blood or liver tissue in patients negative for hepatitis B surface antigen (HBsAg) with or without anti-HBV antibodies. Thus, the absence of HBsAg in the blood only reduces the risk of transmission and is not sufficient enough to ensure the absence of HBV infection. AIM: This study was aimed at determining the prevalence of occult HBV infection among blood donors in Lagos. STUDY DESIGNS: A cross-sectional study was done among 101 consenting blood donors at Lagos State University Teaching Hospital, Ikeja, between November 2016 and January 2017. MATERIALS AND METHODS: HBV DNA analysis and viral load were done at the Molecular Laboratory of National Sickle Cell Centre, Idi Araba, Lagos, for all the HBsAg negative blood donors screened by rapid kit at Ikeja. RESULTS: The prevalence of occult HBV DNA among the participants was 3% consisting of 3% prevalence of HBV DNA surface antigen and 0% prevalence for precore and core of the HBV DNA. CONCLUSION: The low prevalence (3%) of occult HBV seen in our study does not make it cost-effective to routinely screen blood donors or the general population for HBV infection using DNA polymerase chain reaction.

Prevalence of Helicobacter pylori infection among dyspeptic patients with and without type 2 diabetes mellitus in Nigeria.

BACKGROUND: This multicenter study was undertaken to determine the prevalence of Helicobacter pylori (H. pylori) infection among dyspeptic patients with and without type 2 diabetes mellitus (T2DM). METHODS: Patients with dyspepsia were recruited from tertiary teaching hospitals, three in the South-West and one in the South-South regions of Nigeria, between November 2016 and August 2017. The participants had breath samples analyzed for H. pylori by the Urea Breath Test (UBT) following manufacturer's instructions. Dyspeptic patients who were diagnosed previously with T2DM were recorded. Crosstab using chi-square and correlation analyses were used to test (hypothesis) variables. RESULTS: The entire cohort included 471 dyspeptics, 19 (4%) of whom had T2DM. H. pylori infection was reported in 232/471 (49.3%) dyspeptics and 13/19 T2DM patients, without significant difference between diabetics and nondiabetics. The majority (84.6%) of those positive for UBT and T2DM were in the age group 52-71 years, while none was in the age group 72-91 years. There was no statistical significance (P>0.05) between the age group, UBT and T2DM positive. CONCLUSIONS: Our study showed that, in Nigeria, there is no difference in prevalence of H. pylori in dyspeptic patients with and without T2DM.

Clinical and Socio- Demographic Risk Factors for Acquisition of Helicobacter pylori Infection in Nigeria

Background: The aim of the study was to assess clinical and socio-demographic characteristics as well as prior drug usage as risk factors for Helicobacter pylori (H. pylori) infection in Nigeria. Methods: A total of 347 respondents were surveyed by assessing their clinical and socio-demographic characteristics in comparison with the non-invasive gold standard for H. pylori diagnosis, the urea breath test (UBT). Chi-square test and odds ratio analyses were conducted in order to assess if variables such as socio-demographic factors, drug intake, and history of ulcer/gastritis/ gastric cancer within the family significantly predicted test results. Results: A total of 130 (37.5%) respondents were positive for H. pylori by the UBT. Living with more than three people in an apartment and a history of ulcer/gastritis within the family were significantly associated with H. pylori (p ≤0.05), as well as current antibiotic intake (p ≤0.05). Nationality, stay outside Nigeria, level of education, main occupation, smoking and drinking habits, sources of drinking water, number of children and history of gastric cancer had no significant association with H. pylori infection (p ≥ 0.05). Conclusion: The results of the questionnaire revealed that most socio-demographic characteristics of the respondents had no significant association with H. pylori. Overcrowding, having siblings/parents with history of ulcer/gastritis as well as prior antibiotic usage had a significant association.

Helicobacter pylori strains from a Nigerian cohort show divergent antibiotic resistance rates and a uniform pathogenicity profile.

Antibiotic resistance in Helicobacter pylori is a factor preventing its successful eradication. Particularly in developing countries, resistance against commonly used antibiotics is widespread. Here, we present an epidemiological study from Nigeria with 111 isolates. We analyzed the associated disease outcome, and performed a detailed characterization of these isolated strains with respect to their antibiotic susceptibility and their virulence characteristics. Furthermore, statistical analysis was performed on microbiological data as well as patient information and the results of the gastroenterological examination. We found that the variability concerning the production of virulence factors between strains was minimal, with 96.4% of isolates being CagA-positive and 92.8% producing detectable VacA levels. In addition, high frequency of bacterial resistance was observed for metronidazole (99.1%), followed by amoxicillin (33.3%), clarithromycin (14.4%) and tetracycline (4.5%). In conclusion, this study indicated that the infection rate of H. pylori infection within the cohort in the present study was surprisingly low (36.6%). Furthermore, an average gastric pathology was observed by histological grading and bacterial isolates showed a uniform pathogenicity profile while indicating divergent antibiotic resistance rates.

Characteristics, management, and outcomes of patients with hepatocellular carcinoma in Africa: a multicountry observational study from the Africa Liver Cancer Consortium.

BACKGROUND: Hepatocellular carcinoma is a leading cause of cancer-related death in Africa, but there is still no comprehensive description of the current status of its epidemiology in Africa. We therefore initiated an African hepatocellular carcinoma consortium aiming to describe the clinical presentation, management, and outcomes of patients with hepatocellular carcinoma in Africa. METHODS: We did a multicentre, multicountry, retrospective observational cohort study, inviting investigators from the African Network for Gastrointestinal and Liver Diseases to participate in the consortium to develop hepatocellular carcinoma research databases and biospecimen repositories. Participating institutions were from Cameroon, Egypt, Ethiopia, Ghana, Ivory Coast, Nigeria, Sudan, Tanzania, and Uganda. Clinical information-demographic characteristics, cause of disease, liver-related blood tests, tumour characteristics, treatments, last follow-up date, and survival status-for patients diagnosed with hepatocellular carcinoma between Aug 1, 2006, and April 1, 2016, were extracted from medical records by participating investigators. Because patients from Egypt showed differences in characteristics compared with patients from the other countries, we divided patients into two groups for analysis; Egypt versus other African countries. We undertook a multifactorial analysis using the Cox proportional hazards model to identify factors affecting survival (assessed from the time of diagnosis to last known follow-up or death). FINDINGS: We obtained information for 2566 patients at 21 tertiary referral centres (two in Egypt, nine in Nigeria, four in Ghana, and one each in the Ivory Coast, Cameroon, Sudan, Ethiopia, Tanzania, and Uganda). 1251 patients were from Egypt and 1315 were from the other African countries (491 from Ghana, 363 from Nigeria, 277 from Ivory Coast, 59 from Cameroon, 51 from Sudan, 33 from Ethiopia, 21 from Tanzania, and 20 from Uganda). The median age at which hepatocellular carcinoma was diagnosed significantly later in Egypt than the other African countries (58 years [IQR 53-63] vs 46 years [36-58]; p<0·0001). Hepatitis C virus was the leading cause of hepatocellular carcinoma in Egypt (1054 [84%] of 1251 patients), and hepatitis B virus was the leading cause in the other African countries (597 [55%] of 1082 patients). Substantially fewer patients received treatment specifically for hepatocellular carcinoma in the other African countries than in Egypt (43 [3%] of 1315 vs 956 [76%] of 1251; p<0·0001). Among patients with survival information (605 [48%] of 1251 in Egypt and 583 [44%] of 1315 in other African countries), median survival was shorter in the other African countries than in Egypt (2·5 months [95% CI 2·0-3·1] vs 10·9 months [9·6-12·0]; p<0·0001). Factors independently associated with poor survival were: being from an African countries other than Egypt (hazard ratio [HR] 1·59 [95% CI 1·13-2·20]; p=0·01), hepatic encephalopathy (2·81 [1·72-4·42]; p=0·0004), diameter of the largest tumour (1·07 per cm increase [1·04-1·11]; p<0·0001), log α-fetoprotein (1·10 per unit increase [1·02-1·20]; p=0·0188), Eastern Cooperative Oncology Group performance status 3-4 (2·92 [2·13-3·93]; p<0·0001) and no treatment (1·79 [1·44-2·22]; p<0·0001). INTERPRETATION: Characteristics of hepatocellular carcinoma differ between Egypt and other African countries. The proportion of patients receiving specific treatment in other African countries was low and their outcomes were extremely poor. Urgent efforts are needed to develop health policy strategies to decrease the burden of hepatocellular carcinoma in Africa. FUNDING: None.

Challenges in the management of chronic HBV infection in West Africa: The clinician's perspective.

BACKGROUND: Hepatitis B infection has become a public health issue in recent years. Approximately 350 million of the world's population are chronically infected reaching endemic proportions in West Africa. Guidelines for treatment are continuously improving but are becoming more complex. AIM: To determine the challenges hepatologists experience in the management of patients with chronic hepatitis B. METHODS: This was a cross-sectional descriptive study conducted among hepatologists in West Africa during a regional hepatitis conference in 2013. RESULTS: Forty-six hepatologists completed the questionnaire. When evaluating a patient for chronic hepatitis B, the preferred investigations were: LFT (100%); abdominal ultrasound (93.5%); HBeAg (93.5%); HBV DNA (78%); HBsAg measure (22%); HBV genotype (15.2%); and liver biopsy (34.8%). Most had their patients on nucleoside/nucleotide analogue but follow-up visits after 1 year were problematic. CONCLUSION: The majority of hepatologists had good intentions regarding the evaluation of their patients, but only a small percentage of patients are properly investigated.

Hepatitis C Virus (HCV) Prevalence in Special Populations and Associated Risk Factors: A Report From a Tertiary Hospital.

BACKGROUND: With the advent of highly effective anti-hepatitis C virus (HCV) drugs, efforts to identify infected cases, high-risk groups, and associated risk factors have become the focus of current control measures. OBJECTIVES: To determine the prevalence of the HCV antibody among diabetics and patients with lymphoproliferative disorders (LPD) who presented to the outpatient clinics of a university hospital and its associated risk factors. PATIENTS AND METHODS: Consecutively consenting patients who had been previously diagnosed with diabetes mellitus and LPD at the outpatient department of the Lagos State University teaching hospital were recruited. A case record form was used to extract their demographics and physical examination findings as well as any risk factors for HCV infection; blood was also drawn to run a serological assay for the HCV antibody. All data were collated and analyzed using the Statistical Package for the Social Sciences version 20. Student T-test, Chi square, and logistic regression were some of the inferential statistics used in addition to descriptive statistics. RESULTS: In all, 438 patients (405 diabetics and 33 patients with LPD) were recruited. Their ages ranged from 17 - 87 years with a mean + Standard deviation of 59.61 + 11.859 years. The prevalence of hepatitis C among the diabetic subgroup was 0.7%, while the antibody was present in 9.1% of the LPD patients. The occurrence of the HCV antibody was, however, not significantly associated with age, sex, educational level, or marital status (P > 0.05). Having multiple sexual partners was identified as the only significant risk factor for hepatitis C (OR = 9.148; P = 0.017). CONCLUSIONS: This survey suggested that a higher HCV prevalence exists in this population than is currently reported in the general population, and having sex with multiple partners was a risk factor for HCV infection.