Genotypes of Helicobacter pylori isolates in Gambian children and adults

Helicobacter pylori is a globally important and genetically diverse gastric pathogen that infects most people in developing countries. Earlier reports indicated high prevalence of H. pylori colonization, but a low frequency of H. pylori-associated diseases in Africa but recent reviews have shown that gastroduodenal disease is actually common in Africa. Most detailed analyses of H. pylori have used strains from non-African countries, despite the high importance of Africa in the emergence and evolution of humans and their pathogens. There have been far fewer critical studies such as genotypes in association with gastric disease, population genetics and antimicrobial resistance and susceptibility of H. pylori strains from Africa. It is with this background that the genotypes of H. pylori in association with gastroduodenal diseases, antibiotic susceptibility to commonly used drugs and population genetics from ethnic African adults and children in The Gambia were investigated. In this study, it was found that the prevalence of H. pylori is high in dyspeptic patients in The Gambia and that many strains were of the putatively more virulent cagA+, vacAs1 and vacAm1 genotypes. There was a high prevalence of cagA positive strains in patients with overt gastric diseases than those with non-ulcerative dyspepsia; conversely, the co-existence of both cagA+ and cagA- was found to be protective against the development of gastroduodenal disease. Analyses of the sequenced data with the STRUCTURE software indicated that Gambian H. pylori strains were closely related to hspWAfrica than to strains from more distant African regions (hspSAfrica and hpNEAfrica) indicating common ancestral origin. Essentially no traces of European or North African ancestry were found despite Gambia's history of invasion and colonisation by peoples from these regions during the last millennium. Antibiotic susceptibility tests have shown that Gambian strains were found to be highly sensitive to clarithromycin, erythromycin, tetracycline and amoxicillin but found that more than two-thirds of Gambian H. pylori strains were metronidazole resistant. These data indicate caution in use of metronidazole-based therapies in The Gambia. This thesis provides a detailed initial description of a set of H. pylori isolates directly related to a geographically defined West African population. The data presented has answered some relevant questions on H. pylori virulent genes in association with gastro-duodenal diseases and antibiotic susceptibility providing a comprehensive basis for future studies

Exogenous re-infection by a novel Streptococcus pneumoniae serotype 14 as a cause of recurrent meningitis in a child from The Gambia

We report a case of an infant who experienced exogenous re-infection of Streptococcus pneumoniae serotype 14 as a cause of recurrent meningitis after apparently successful antibiotic treatment with ceftriaxone. eBURST analysis revealed that isolates from the two episodes of meningitis belonged to hypervirulent ST63 and ST3321 clonal complexes respectively

Genetic Signatures for \u3cem\u3eHelicobacter pylori\u3c/em\u3e Strains of West African Origin

Helicobacter pylori is a genetically diverse bacterial species that colonizes the stomach in about half of the human population. Most persons colonized by H. pylori remain asymptomatic, but the presence of this organism is a risk factor for gastric cancer. Multiple populations and subpopulations of H. pylori with distinct geographic distributions are recognized. Genetic differences among these populations might be a factor underlying geographic variation in gastric cancer incidence. Relatively little is known about the genomic features of African H. pylori strains compared to other populations of strains. In this study, we first analyzed the genomes of H. pylori strains from seven globally distributed populations or subpopulations and identified encoded proteins that exhibited the highest levels of sequence divergence. These included secreted proteins, an LPS glycosyltransferase, fucosyltransferases, proteins involved in molybdopterin biosynthesis, and Clp protease adaptor (ClpS). Among proteins encoded by the cag pathogenicity island, CagA and CagQ exhibited the highest levels of sequence diversity. We then identified proteins in strains of Western African origin (classified as hspWAfrica by MLST analysis) with sequences that were highly divergent compared to those in other populations of strains. These included ATP-dependent Clp protease, ClpS, and proteins of unknown function. Three of the divergent proteins sequences identified in West African strains were characterized by distinct insertions or deletions up to 8 amino acids in length. These polymorphisms in rapidly evolving proteins represent robust genetic signatures for H. pylori strains of West African origin

Bacterial Isolates and Antibiotic Sensitivity among Gambian Children with Severe Acute Malnutrition

Background. Establishing the pattern of infection and antimicrobial sensitivities in the local environment is critical to rational use of antibiotics and the development of management algorithms. Methods. Morbidity history and physical examination of 140 children with severe acute malnutrition were recorded. Their blood, stool, and urine samples were cultured and antibiotic sensitivity patterns determined for any bacterial pathogens isolated. Results. Thirty-eight children had a pathogen isolated from blood culture, 60% of which were considered contaminants. Coagulase negative staphylococcus was the predominant contaminant, while the major causes of bacteraemia were nontyphoidal Salmonella (13%), S. pneumoniae (10%), and E. coli (8%). E. coli accounted for 58% of the urinary isolates. No pathogen was isolated from stool. In vitro sensitivity by disk diffusion showed that 87.5% of the isolates were sensitive to ampicillin and/or gentamicin and 84.4% (27/32) to penicillin and/or gentamicin. Conclusions. A combination of ampicillin and gentamicin provides adequate antibiotic cover for severely malnourished children in The Gambia

PCR-based genotyping of Helicobacter pylori of Gambian children and adults directly from biopsy specimens and bacterial cultures

<p>Abstract</p> <p>Background</p> <p><it>Helicobacter pylori </it>is an important agent of gastroduodenal disease in Africa and throughout the world. We sought to determine an optimum method for genotyping <it>H. pylori </it>strains from children and adults in The Gambia, West Africa.</p> <p>Results</p> <p>Virulence genes were amplified in 127 of 190 cases tested (121 adults and 6 children); each of 60 bacterial cultures, and 116 from DNA extracted directly from biopsies. The proportion of biopsies that were <it>cagA</it>+, the ratio of <it>vacAs1</it>/<it>s2</it>, and <it>vacAm1</it>/<it>m2</it>, and the proportion of mixed strain populations in individual subjects changed with age. Strains lacking virulence <it>cagA </it>and <it>vacA </it>genes and with apparently homogeneous (one predominant strain) infections were more common among infants than adults.</p> <p>Conclusions</p> <p>In order to detect the range of bacterial genotypes harbored by individual patients, direct PCR proved slightly superior to isolation of <it>H. pylori </it>by biopsy culture, but the techniques were complementary, and the combination of both culture and direct PCR produced the most complete picture. The seemingly higher virulence of strains from adult than infant infections in The Gambia merits further analysis.</p

Incidence of macrolide-lincosamide-streptogramin B resistance amongst beta-haemolytic streptococci in The Gambia.

BACKGROUND: In West Africa, penicillin, macrolide and lincosamide resistance among beta-haemolytic streptococci (BHS) isolates has rarely been described. However, such data are critical to detect and track the emergence of antibiotic resistance. METHODS: Beta-haemolytic streptococci were cultured from clinical specimens from patients attending the clinic at the Medical Research Council Unit The Gambia (n = 217) and kept at -70 °C. Of these, 186 were revived and tested for penicillin susceptibility by disc diffusion and E-test methods, and the D-test for determination of constitutive and inducible macrolide-lincosamide (MLSB) resistance phenotypes. RESULTS: The majority of BHS isolates from infections were group A streptococci (GAS) (126/186, 67.7%). Of these, 16% were from invasive disease (30/186). Other BHS isolated included lancefield groups B (19, 10.2%); C (9/186, 4.8%), D (3/186, 1.6%), F (5/186, 2.7%), G (16/186, 8.6%) and non-typeable (8/186, 4.3%). Prevalence of BHS isolated from blood cultures ranges from 0% (2005) to 0.5% (2010). Most (85, 45.7%) of the isolates were from wound infections. Of the 186 BHS isolates, none was resistant to penicillin and 14 (6.1%) were resistant to erythromycin. Of these, 8 (4.3%) demonstrated constitutive MLSB resistance, and 5 (2.7%) were inducible MLSB resistant. All the inducible MLSB isolates were GAS, and majority of the constitutive MLSB isolates (6/8, 75.0%) were non-GAS. CONCLUSIONS: Beta-haemolytic streptococci, predominantly GAS are associated with a wide range of infections in The Gambia. It is reassuring that macrolide and lincosamide resistance is relatively low. However, monitoring of MLSB resistance is necessary with the global spread of resistant BHS strains

Evaluation of the Kudoh method for mycobacterial culture: Gambia experience

AbstractObjective/backgroundTo evaluate the Kudoh swab method for improving laboratory diagnosis of tuberculosis (TB) in Gambia.MethodsA total of 75 sputa (50 smear positive and 25 smear negative) were examined. Sputum samples were collected from leftover routine samples from the Medical Research Council Unit, Gambia TB Diagnostic Laboratory. The samples were processed using the standard N-acetyl-l-cysteine-NaOH (NALC-NaOH) methods currently used and Kudoh swab method. These were cultured on standard Lowenstein Jensen (LJ) and Modified Ogawa media, respectively, and incubated aerobically at 36±1°C for mycobacterial growth. To determine if the decontamination and culture methods compared could equally detect the Mycobacterium tuberculosis complex (MTBC) highly commonly isolated in Gambia, spoligotyping was done.ResultsIn total, 72% (54/75) of MTBC were recovered by both LJ and Modified Ogawa methods. The LJ method recovered 52% (39/75) and Modified Ogawa recovered 56% (42/75) of the MTBC, respectively. Spoligotyping showed Euro-American 35% (19/54), Indo-Oceanic 35% (19/54), Mycobacterium africanum (West African type 2) 26% (14/54), Beijing 2% (1/54), and M. africanum (West African type 1) 2% (1/54).ConclusionThe Kudoh method is simpler and cheaper than the NALC-NaOH method. There was no significant difference in recovery between the methods. The Kudoh method is ideal in overburdened TB laboratories with poor resources in developing countries. The predominant lineages were Euro-American and Indo-Oceanic, followed by M. africanum (West African type 2)

Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes

Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such “Sel1-like repeat” (SLR) genes (“slr genes”). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, dN/dS = ω > 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (ωJ > 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations

Etiology of severe childhood pneumonia in the Gambia, West Africa, determined by conventional and molecular microbiological analyses of lung and pleural aspirate samples.

Molecular analyses of lung aspirates from Gambian children with severe pneumonia detected pathogens more frequently than did culture and showed a predominance of bacteria, principally Streptococcus pneumoniae, >75% being of serotypes covered by current pneumococcal conjugate vaccines. Multiple pathogens were detected frequently, notably Haemophilus influenzae (mostly nontypeable) together with S. pneumoniae

Seasonality and outbreak of a predominant Streptococcus pneumoniae serotype 1 clone from The Gambia: Expansion of ST217 hypervirulent clonal complex in West Africa

BACKGROUND: Streptococcus pneumoniae serotype 1 causes > 20% of invasive disease, among all age groups combined, in The Gambia. In contrast, it is rarely detected in carriage studies. This study compares the molecular epidemiology of S. pneumoniae serotype 1 causing invasive disease in The Gambia between 1996 and 2005 to those carried in the nasopharynx between 2004 and 2006. RESULTS: A total of 127 invasive and 36 nasopharyngeal carriage serotype 1 isolates were recovered from individuals of all age groups and were analyzed by serotyping, antibiotic susceptibility testing and MLST. MLST analysis revealed 23 different sequence types (STs), 18 of which were novel. The most prevalent clone among the 163 isolates was ST618 (70.5%), followed by ST3575 (7.4%), ST2084 (2.5%) and ST612 (2.5%). A single ST (ST618), previously shown to belong to the ST217 hypervirulent clonal complex, was frequent among carriage (61.1%) and invasive (72.7%) serotype 1 isolates. ST618 causing both paediatric and adult disease peaked annually in the hot dry season and caused outbreak in 1997 and 2002. CONCLUSION: For over a decade, isolates of ST618 have been the dominant lineage among serotype 1 carriage and disease isolates circulating in the Gambia. This lineage shows similar epidemiological features to those of the meningococcus in the African meningitis belt being able to cause outbreaks of disease