Genomic history of the seventh pandemic of cholera in Africa.

The seventh cholera pandemic has heavily affected Africa, although the origin and continental spread of the disease remain undefined. We used genomic data from 1070 Vibrio cholerae O1 isolates, across 45 African countries and over a 49-year period, to show that past epidemics were attributable to a single expanded lineage. This lineage was introduced at least 11 times since 1970, into two main regions, West Africa and East/Southern Africa, causing epidemics that lasted up to 28 years. The last five introductions into Africa, all from Asia, involved multidrug-resistant sublineages that replaced antibiotic-susceptible sublineages after 2000. This phylogenetic framework describes the periodicity of lineage introduction and the stable routes of cholera spread, which should inform the rational design of control measures for cholera in Africa.

Characterisation of class 3 integrons with oxacillinase gene cassettes in hospital sewage and sludge samples from France and Luxembourg.

In this study, antibiotic resistance class 3 integrons in Gram-negative bacteria isolated from hospital sewage and sludge and their genetic contents were characterised. Two samples of hospital effluent from France and Luxembourg and one sample of sludge from a wastewater treatment plant in France were collected in 2010 and 2011. Bacteria were cultured on selective agar plates and integrons were detected in colonies by quantitative PCR. Integron gene cassette arrays and their genetic environments were analysed by next-generation sequencing. Three class 3 integron-positive isolates were detected, including Acinetobacter johnsonii LIM75 (French hospital effluent), Aeromonas allosaccharophila LIM82 (sludge) and Citrobacter freundii LIM86 (Luxembourg hospital effluent). The gene cassettes were all implicated in antibiotic (aminoglycoside and ß-lactam) or antiseptic resistance. An oxacillinase gene cassette (blaOXA-10, blaOXA-368 or blaOXA-2) was found in each integron. All of the class 3 integrons were located on small mobilisable plasmids. This study highlights the role of class 3 integrons in the dissemination of clinically relevant antibiotic resistance genes, notably oxacillinase genes, in hospital effluent.

The Lake Chad Basin, an Isolated and Persistent Reservoir of Vibrio cholerae O1: A Genomic Insight into the Outbreak in Cameroon, 2010.

The prevalence of reported cholera was relatively low around the Lake Chad basin until 1991. Since then, cholera outbreaks have been reported every couple of years. The objective of this study was to investigate the 2010/2011 Vibrio cholerae outbreak in Cameroon to gain insight into the genomic make-up of the V. cholerae strains responsible for the outbreak. Twenty-four strains were isolated and whole genome sequenced. Known virulence genes, resistance genes and integrating conjugative element (ICE) elements were identified and annotated. A global phylogeny (378 genomes) was inferred using a single nucleotide polymorphism (SNP) analysis. The Cameroon outbreak was found to be clonal and clustered distant from the other African strains. In addition, a subset of the strains contained a deletion that was found in the ICE element causing less resistance. These results suggest that V. cholerae is endemic in the Lake Chad basin and different from other African strains.

Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.

We identified 3 lineages among multidrug-resistant (MDR) Salmonella enterica serotype Typhi isolates in the Gulf of Guinea region in Africa during the 2000s. However, the MDR H58 haplotype, which predominates in southern Asia and Kenya, was not identified. MDR quinolone-susceptible isolates contained a 190-kb incHI1 pST2 plasmid or a 50-kb incN pST3 plasmid.

Multiple contaminations of chickens with Campylobacter, Escherichia coli and Salmonella in Yaounde (Cameroon).

INTRODUCTION: Food-borne diseases associated with Campylobacter, Escherichia coli, and Salmonella are mainly caused by the consumption of raw or undercooked poultry meat. The objective of this study was to evaluate the prevalence of Campylobacter, Escherichia coli, and Salmonella in chickens. METHODOLOGY: One hundred and fifty chickens collected from eight retail markets in Yaounde were examined for the presence of Campylobacter, Escherichia coli, and Salmonella using standard bacteriological procedures. RESULTS: Of the 150 chickens collected, 135 (90%) were contaminated with Campylobacter (68.9% C. coli and 31.1% C. jejuni). All the chickens were positive for E. coli. Among the 150 isolates, 17 (11.3%) were enteropathogenic E. coli (EPEC). Additionally, 103 Salmonella strains were recovered from 90 chickens. Salmonella Enteritidis (45.6%) and Salmonella Hadar (28.1%) were the most frequent serotypes. Multiple contamination was found in 142 chickens (94.6%), of which 83 (55.3%) were concurrently contaminated with Campylobacter, Escherichia coli, and Salmonella. CONCLUSION: These results show that chickens in Cameroon are highly contaminated with Campylobacter, Escherichia coli, and Salmonella. The multiple contaminations of chickens is a potential risk of infection for consumers and highlights the necessity of public awareness for food safety.

Prevalence and antimicrobial resistance of Salmonella serotypes in chickens from retail markets in Yaounde (Cameroon).

From February 2006 to January 2007, 150 chickens were collected from eight retail markets in Yaounde, and 90 (60%) tested positive for Salmonella. Seventy-nine chickens were contaminated with only one Salmonella serotype, 10 with two different serotypes, and 1 with four serotypes. The most prevalent serotypes were Enteritidis (47 strains) and Hadar (29 strains). The isolates were tested for their susceptibilities to amoxicillin, amoxicillin/clavulanic acid, cefoxitin, cefotaxime, gentamicin, streptomycin, tetracycline, chloramphenicol, sulfonamides, nalidixic acid, ciprofloxacin, and trimethoprim/sulfamethazole by disk diffusion assay. Minimum inhibitory concentrations of ampicillin, streptomycin, tetracycline, sulfonamides, and nalidixic acid were determined for the resistant strains by agar dilution method. Eleven isolates (10.7%) of the 103 tested were susceptible to all antimicrobials. Resistance was most observed to tetracycline (84.5%), streptomycin (44.7%), and nalidixic acid (34%). Forty-one isolates (39.8%) were multidrug resistant (resistant to three or more antimicrobials from different classes), of which 68.3% were Hadar and 21.9% Enteritidis. The most frequent resistant pattern in Hadar was streptomycin-tetracycline-nalidixic acid. These results highlight once more the need for surveillance of Salmonella contamination in poultry.

Antimicrobial resistance and molecular characterization of Vibrio cholerae O1 during the 2004 and 2005 outbreak of cholera in Cameroon.

There was an outbreak of cholera in Cameroon during 2004 and 2005; the epidemic began in Douala in January 2004 and spread throughout the south of the country. The World Health Organization (WHO) reported 8005 cases in 2004 and 2847 cases in 2005. Five hundred eighty-nine stool samples were received in the Pasteur Centre of Cameroon and 352 were microbiologically confirmed to be positive for Vibrio cholerae O1. Isolated strains were tested for their antimicrobial susceptibilities. All the strains were multidrug resistant and predominantly showed a common resistance pattern at the beginning of the outbreak. Tetracycline, recommended by the WHO for treating cholera in adults, was effective against all the strains tested. Cotrimoxazole (trimethoprim/sulfamethoxazole), previously a first-line treatment in children, was ineffective in vitro for all the clinical isolates and was quickly replaced by amoxicillin. Ampicillin resistance emerged at the end of 2004 and was the leading resistance pattern observed in the second half of 2005. This therefore represented the second major resistance pattern. These two major resistance profiles were not associated with patient characteristics (sex and age) or to the geographic origin of strains. However, there was a highly significant relationship between resistance patterns and the year of isolation (p < 0.001). The strains possessed genes ctxA and ctxB encoding the two cholera toxin subunits and were very closely related, irrespective of their antimicrobial resistance patterns. They were not differentiated by molecular typing methods and gave similar ribotyping and pulsed-field gel electrophoresis patterns.

Restriction endonuclease patterns of the omp1 gene of reference Chlamydia trachomatis strains and characterization of isolates from Cameroonian students.

Eighteen reference strains of Chlamydia trachomatis were differentiated by omp1 PCR- and nested PCR-based RFLP analysis, using two restriction digestions, one with AluI and the other with the three enzymes HpaII, EcoRI and HinfI. AluI digestion allowed the differentiation of 12 different profiles after CT1/CT5 PCR and 13 different profiles after the nested PCR. The triple hydrolysis permitted the identification of 15 different patterns. In all, 16/18 reference strains were clearly identified. These reference patterns were successfully used to genotype 34 of 35 (28 strains and 7 clinical specimens) samples from infected students, collected during a screening programme in Yaounde (Cameroon). Genotypes D, Da, E, F, G and J were found. The most prevalent omp1 genotype was E (n = 14; 40 %), followed by F (n = 7; 20 %). As RFLP patterns of reference strains are essential for typing clinical isolates, they will greatly facilitate C. trachomatis characterization in many resource-limited laboratories.

Screening of volunteer students in Yaounde (Cameroon, Central Africa) for Chlamydia trachomatis infection and genotyping of isolated C. trachomatis strains.

The prevalence of Chlamydia trachomatis infection was 3.78% out of 1,277 volunteer students screened by direct fluorescence assay and Cobas Amplicor PCR. The infection was associated with the nonuse or inconsistent use of condoms in women (P = 0.026) and a previous sexually transmitted infection in men (P = 0.023). The most frequent genotypes determined by sequencing the omp1 genes of 25 clinical isolates were E (44%) and F (20%), and some strains harbored mutations, but E genotype strains did not.