Shigella infection in children under 5 years old in western French Guiana.

French Guiana, a tropical country, is characterised by a young and multi-ethnic population. Difficulties in accessing safe water sources lead to outbreaks of gastroenteritis. The objectives of this study were (1) to describe the microbiological profile of shigella strains isolated in western French Guiana, including antimicrobial susceptibility and the distribution of strains in terms of species and serotypes and (2) to estimate the incidence of shigellosis in children under 5 years old. A retrospective observational study was conducted of 213 cases of shigellosis diagnosed in the biology department of the hospital centre for western French Guiana between 2000 and 2012 in children under 5 years old. The serogroups (formerly known as species) that predominates in French Guiana was Shigella flexneri. No resistance was observed to fluoroquinolones or to third-generation cephalosporins. The average incidence of shigellosis in children under 5 years old in western French Guiana was estimated at 189.6 cases per 100 000 inhabitants per year. Shigellosis is a public health problem in western French Guiana. These infections suggest the difficulties in accessing safe water sources and the lack of public sanitation. A quadrivalent vaccine containing Shigella sonnei and three serotypes of S. flexneri (S. flexneri 2a, 3a and 6) could provide broad coverage against shigella infections.

High rate of faecal carriage of extended-spectrum ß-lactamase-producing Enterobacteriaceae in healthy children in Bangui, Central African Republic.

The aim of this study was to estimate the prevalence of extended-spectrum ß-lactamase-producing Enterobacteriaceae (ESBL-E) in faeces of healthy children aged 0-59 months in Bangui (Central African Republic). Stool samples of 134 children, recruited for a matched case-control study, were cultured on a commercial ESBL-selective chromogenic medium (CHROMagar ESBL, France). The phenotypic resistance patterns of isolated strains were investigated, as well as the genetic basis for antibiotic resistance. The factors associated with increased risk for ESBL-E carriage were also studied. The prevalence of ESBL-E carriage was 59% (79/134), one of the highest reported worldwide. The only factor found to be associated with carriage was living in a highest-income family (p=0.03). In all, 83 ESBL-E were recovered as simultaneous carriage of two strains was detected in four children. blaCTX-M-15 was found in all strains except two, frequently associated with qnr (54/81, 66%) and aac(6')-Ib-cr (35/81, 43%) genes. Escherichia coli, the most commonly recovered species (51/83, 61%), was assigned mainly to the pandemic B2-O25b-ST131 group (39/51, 76%). Resistance transfer, which was studied in 20 randomly selected ESBL-E strains, was successful in 13 (13/20, 65%) isolates. In eight of these isolates (8/13, 62%), blaCTX-M-15 genes were found in incompatibility group FIb conjugative plasmids. We found one of the highest prevalence rates of faecal carriage of ESBL-E reported worldwide, highlighting the need to improve control of the distribution of antibiotics in limited-resource countries.

Dormant phages of Helicobacter pylori reveal distinct populations in Europe.

Prophages of Helicobacter pylori, a bacterium known to co-evolve in the stomach of its human host, were recently identified. However, their role in the diversity of H. pylori strains is unknown. We demonstrate here and for the first time that the diversity of the prophage genes offers the ability to distinguish between European populations, and that H. pylori prophages and their host bacteria share a complex evolutionary history. By comparing the phylogenetic trees of two prophage genes (integrase and holin) and the multilocus sequence typing (MLST)-based data obtained for seven housekeeping genes, we observed that the majority of the strains belong to the same phylogeographic group in both trees. Furthermore, we found that the Bayesian analysis of the population structure of the prophage genes identified two H. pylori European populations, hpNEurope and hpSWEurope, while the MLST sequences identified one European population, hpEurope. The population structure analysis of H. pylori prophages was even more discriminative than the traditional MLST-based method for the European population. Prophages are new players to be considered not only to show the diversity of H. pylori strains but also to more sharply define human populations.

The levels of antibodies to Panton-Valentine leukocidin (PVL) vary with PVL prevalence along a north-to-south gradient.

Recent research on Staphylococcus aureus vaccine development has focused on active immunization against Panton-Valentine leukocidin (PVL), a potent leukotoxin associated with both superficial and severe deep-seated infections. PVL prevalence is highly variable worldwide, but it is unknown to what extent immunity to PVL varies between patients from geographic areas with different PVL-positive S. aureus prevalences. We conducted a retrospective multicentric study of anti-PVL and anti-alpha-toxin (Hla) antibody levels in uninfected adult patients from France (low PVL prevalence; n = 200), Algeria (moderate prevalence; n = 143), and Senegal (high prevalence; n = 228). The antibody levels were quantified by an enzyme-linked immunosorbent assay (ELISA) procedure. Because Hla is present in virtually all S. aureus strains, its corresponding antibody levels were considered to reflect population exposure to S. aureus. Compared with French participants, the average anti-PVL antibody levels were 2.5-fold and 8.2-fold higher in Algerian and Senegalese participants, respectively (p < 0.001). Conversely, anti-Hla antibody levels did not differ between participants from the three countries, suggesting that the observed differences in anti-PVL antibody levels were not biased by variations in population exposure to S. aureus. Hence, anti-PVL antibody levels in the general populations of France, Algeria, and Senegal vary widely and match variations in PVL-positive S. aureus strain prevalence, with an increasing north-to-south gradient. To conclude, immunity to PVL in a given population correlates with local PVL prevalence. This finding can help to inform PVL vaccine strategies.

Staphylococcus aureus nasal and pharyngeal carriage in Senegal.

Nasal and pharyngeal swabs were collected from 132 patients admitted to the Principal Hospital in Dakar (Senegal), in January and February 2012. The prevalence of Staphylococcus aureus carriage was 56.1% (n = 74): 40.2% for pharyngeal samples and 36.4% for nasal samples. None of the isolates was methicillin-resistant. Carriage was independently associated with being female (p <0.01) and large households (≥15 members) (p 0.04). The luk-PV genes encoding Panton-Valentine leukocidin (PVL) were present in 26.2% of the isolates. These data highlight the importance of the oropharynx as a site of colonization, and the high prevalence of PVL-positive isolates in Senegal as compared with industrialized countries.

Prevalence and characterization of extended-spectrum ß-lactamase-producing clinical Salmonella enterica isolates in Dakar, Senegal, from 1999 to 2009.

A total of 1623 clinical isolates of Salmonella belonging to 229 serotypes were received by the Senegalese Reference Center for Enterobacteria from January 1999 to December 2009. The most common serotypes were Enteritidis (19% of the isolates), Typhi (8%), Typhimurium (7%) and Kentucky (4%). A significant increase in the prevalence of resistance to amoxicillin (0.9% in 1999 to 11.1% in 2009) and nalidixic acid (0.9% in 1999 to 26.7% in 2009) was observed in non-typhoidal Salmonella serotypes. For critically important antibiotics, notably ciprofloxacin and extended-spectrum cephalosporins (ESCs), the rates of resistance were low: 0.3% and 0.5%, respectively. Seven ESC-resistant Salmonella strains and three additional ESC-resistant strains from Senegal (1990) and Mali (2007) were studied to identify the genetic basis of their antibiotic resistance. All ESC-resistant strains produced an extended-spectrum ß-lactamase (ESBL). These were CTX-M-15 (n = 6; 2000-2008), SHV-12 (n = 3; 2000-2001) and SHV-2 (n = 1; 1990). A large IncHI2 ST1 pK29-like plasmid was found in six strains (three producing SHV-12 and three CTX-M-15), whereas IncN and IncF plasmids were found in three strains and one strain, respectively. The association of plasmid-mediated quinolone resistance (PMQR) genes qnrB1 and aac(6')-Ib-cr was found in four ESBL-producing strains, leading to decreased susceptibility and even full resistance to ciprofloxacin (MIC range 0.75-2 mg/L) despite the absence of mutations in the quinolone resistance-determining region (QRDR) of gyrA, gyrB, parC and parE. This association of ESBL and multiple PMQR mechanisms within the same strains is therefore a serious concern as it hampers the use of both ESCs and fluoroquinolones for severe Salmonella infections.

Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258.

The molecular epidemiology of third-generation cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in developing countries is poorly documented. From February 2007 to March 2008, we collected 135 3GC-R K. pneumoniae isolates from seven major towns in Maghreb (Morocco), West Africa (Senegal, Côte d'Ivoire), Central Africa (Cameroon), East Africa (Madagascar) and Southeast Asia (Vietnam). Their genetic diversity, assessed by multilocus sequence typing, was high (60 sequence types), reflecting multiclonality. However, two major clonal groups, CG15 (n = 23, 17% of isolates) and CG258 (n = 18, 13%), were detected in almost all participating centres. The two major clonal groups have previously been described in other parts of the world, indicating their global spread. The high diversity of enterobacterial repetitive intergenic consensus sequence-PCR banding patterns at the local level indicates that most isolates were epidemiologically unrelated. The isolates were characterized by the presence of multiple resistance determinants, most notably the concomitant presence of the aac(6')-Ib-cr, qnr and blaCTX-M-15 genes in 61 isolates (45%) belonging to 31 sequence types. These isolates were detected across a large geographical area including Cameroon (n = 1), Vietnam (n = 4), Madagascar (n = 10), Côte d'Ivoire (n = 12), Morocco (n = 13) and Senegal (n = 21). These results have major implications for patient management and highlight a potential reservoir for resistance determinants.

Clinical relevance of cagA and vacA gene polymorphisms in Helicobacter pylori isolates from Senegalese patients.

The molecular epidemiology of Helicobacter pylori in Africa is poorly documented. From January 2007 to December 2008, we investigated 187 patients with gastric symptoms in one of the main tertiary hospitals in Dakar, Senegal. One hundred and seventeen patients were culture-positive for H. pylori. Polymorphisms in vacA and cagA status were investigated by PCR; the 3'-region of cagA was sequenced, and EPIYA motifs were identified. Bacterial heterogeneity within individuals was extensively assessed by using an approach based on vacA and cagA heterogeneity. Fourteen per cent of H. pylori-positive patients displayed evidence of mixed infection, which may affect disease outcome. Patients with multiple vacA alleles were excluded from subsequent analyses. Among the final study population of 105 patients, 29 had gastritis only, 61 had ulcerated lesions, and 15 had suspicion of neoplasia based on endoscopic findings. All cases of suspected neoplasia were histologically confirmed as gastric cancer (GC). The cagA gene was present in 73.3% of isolates. CagA proteins contained zero (3.7%), one (93.9%) or two (2.4%) EPIYA-C segments, and all were western CagA. Most of the isolates possessed presumed high-vacuolization isotypes (s1i1m1 (57.1%) or s1i1m2 (21.9%)). Despite the small number of cases, GC was associated with cagA (p 0.03), two EPIYA-C segments in the C-terminal region of CagA (p 0.03), and the s1 vacA allele (p 0.002). Multiple EPIYA-C segments were less frequent than reported in other countries, possibly contributing to the low incidence of GC in Senegal.

Epidemiology of methicillin-susceptible Staphylococcus aureus lineages in five major African towns: high prevalence of Panton-Valentine leukocidin genes.

The epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in Africa is poorly documented. From January 2007 to March 2008, 555 S. aureus isolates were collected from five African towns in Cameroon, Madagascar, Morocco, Niger, and Senegal; among these, 456 unique isolates were susceptible to methicillin. Approximately 50% of the MSSA isolates from each different participating centre were randomly selected for further molecular analysis. Of the 228 isolates investigated, 132 (58%) belonged to five major multilocus sequence typing (MLST) clonal complexes (CCs) (CC1, CC15, CC30, CC121 and CC152) that were not related to any successful methicillin-resistant S. aureus (MRSA) clones previously identified in the same study population. The luk-PV genes encoding Panton-Valentine leukocidin (PVL), present in 130 isolates overall (57%), were highly prevalent in isolates from Cameroon, Niger, and Senegal (West and Central Africa). This finding is of major concern, with regard to both a source of severe infections and a potential reservoir for PVL genes. This overrepresentation of PVL in MSSA could lead to the emergence and spread of successful, highly virulent PVL-positive MRSA clones, a phenomenon that has already started in Africa.

Epidemiology of methicillin-resistant Staphylococcus aureus lineages in five major African towns: emergence and spread of atypical clones.

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Africa is poorly documented. From January 2007 to March 2008, we collected 86 MRSA isolates from five African towns, one each in Cameroon, Madagascar, Morocco, Niger and Senegal. Although one or two major clones, defined by the sequence type and staphylococcal cassette chromosome mec type, predominated at each site, genetic diversity (ten clones) was relatively limited in view of the large geographical area studied. Most of the isolates (n = 76, 88%) belonged to three major clones, namely ST239/241-III, a well-known pandemic clone (n = 34, 40%), ST88-IV (n = 24, 28%) and ST5-IV (n = 18, 21%). The latter two clones have only been sporadically described in other parts of the world. The spread of community-associated MRSA carrying the Panton-Valentine leukocidin genes is a cause for concern, especially in Dakar and possibly throughout Africa.

[Helicobacter pylori and gastroduodenal lesions in Dakar, Senegal]. / Helicobacter pylori et pathologie gastroduodenale a Dakar (Sénégal).

INTRODUCTION: The bacteriological characteristics of Helicobacter pylori (HP) vary in function of time and place. The aim of this study was to update histological and bacteriological feature of HP infection in patients presenting gastroduodenal lesions in Dakar, Senegal. PATIENTS AND METHOD: This prospective study included patients with gastroduodenal lesions managed over a 6-month period in a digestive endoscopy center in Dakar. In all cases gastric biopsy was performed to obtain specimens for histological diagnosis according Sydney modified classification and HP culture with antibiogram. RESULTS: A total of 158 patients were included. Mean patient age was 48.7 years and the sex-ratio was 1.2. Endoscopic lesions were ulcer in 88 cases, gastritis in 54 cases and tumors in 16. Histological examination demonstrated chronic gastritis in 100% of cases, inflammatory activity in 79.1%, metaplasia in 78.5%, gastric atrophy in 41.1%, adenocarcinoma in 7.6%, dysplasia in 5.7%, and MALT lymphoma in 2.5% with presence of HP in 72.8% of cases. Cultures were positive for HP in 65.8% of cases. Antibiograms indicated that HP was sensitive to amoxicilline in 100% of cases, clarithromycine in 96.6%, ciprofloxacine in 84.1%, and métronidazole in 29.5%. CONCLUSION: Chronic gastritis is a constant feature of gastroduodenal lesions in Dakar. Histology combined with culture showed HP infection in 78.5% of cases. The antibiotic sensitivity of HP in Dakar has changed over the past decade.

Antimicrobial Resistance in Outpatient Escherichia coli Urinary Isolates in Dakar; Senegal

Background: Data regarding the evolution of antimicrobial resistance are needed to suggest appropriate empirical treatment of urinary tract infections (UTI) in developing countries. To assess the antimicrobial susceptibility of Escherichia coli; the predominant pathogen in community-acquired UTI; a prospective multicenter study was carried out in Dakar; Senegal. Methodology: From February 2004 to October 2006; 1010 non-duplicate E. coli strains were collected from four centres. Antimicrobial susceptibility testing was performed using disk diffusion method according to the recommendations of the CA-SFM (2004). Results: Most of the isolates were resistant to amoxicillin (73.1); amoxicillin- clavulanic acid (67.5); cephalothin (55.8); and trimethoprim/sulfamethoxazole (68.1). Extended spectrum beta-lactamase was detected in 38 strains. The overall resistance rates to nalidixic acid; norfloxacin and ciprofloxacin were 23.9; 16.4and 15.5; respectively. Most of the strains were susceptible to gentamicin; nitrofurantoin and fosfomycin (respective susceptibility rates; 93.8; 89.9; and 99.3). During this period; a significant decrease in sensitivity was observed for cephalothin; fluoroquinolones and trimethoprim/sulfamethoxazole (p0.001). Conclusions: These data suggest that trimethoprim/sulfamethoxazole may no longer be used as empirical treatment for community- acquired UTI in Dakar. In order to preserve the activity of fluoroquinolones for future years; alternatives such as fosfomycin or nitrofurantoin should be considered

[Evaluation of toxoplasmosis seroprevalence among 2416 women of childbearing age followed at the Pasteur Institute of New Caledonia]. / Estimation de la séroprevalence de la toxoplasmose chez 2 416 femmes en âge de procréer suivies à l'Institut Pasteur de Nouvelle-Calédonie.

Evaluation of Toxoplasmosis seroprevalence was conducted in 2416 women of childbearing age by Pasteur Institute of New-Caledonia. The estimated seroprevalence was 56.7%, significantly higher in the North-East part of the territory (79.1%), area characterized by strong precipitations, and in the Melanesian ethnic group (62.1%). The habits of this population could enhance contamination by ingestion of oocysts during childhood or adolescence, particularly in the North-East territory. Melanesian women living in the North-East and being not immunized against toxoplasmosis represent the population with the highest risk for Toxoplasma gondii infection.