Characterisation of community acquired non-typhoidal Salmonella from bacteraemia and diarrhoeal infections in children admitted to hospital in Nairobi, Kenya

BACKGROUND: In sub-Saharan Africa community-acquired non-typhoidal Salmonella (NTS) is a major cause of high morbidity and death among children under 5 years of age especially from resource poor settings. The emergence of multidrug resistance is a major challenge in treatment of life threatening invasive NTS infections in these settings. RESULTS: Overall 170 (51.2%) of children presented with bacteraemia alone, 28 (8.4%) with gastroenteritis and bacteraemia and 134 (40.4%) with gastroenteritis alone. NTS serotypes obtained from all the cases included S. Typhimurium (196; 59%), S. Enteritidis (94; 28.3%) and other serotypes in smaller numbers (42; 12.7%); distribution of these serotypes among cases with bacteremia or gastroenteritis was not significantly different. A significantly higher proportion of younger children (< 3 years of age) and those from the slums presented with invasive NTS compared to older children and those from upper socio-economic groups (p < 0.001). One hundred and forty-seven (44.3%) NTS were resistant to 3 or more antibiotics, and out of these 59% were resistant to ampicillin, chloramphenicol and tetracycline. There was no significant difference in antibiotic resistance between the two serotypes, S. Typhimurium and S. Enteritidis. Ceftriaxone and ciprofloxacin were the only antibiotics tested to which all the NTS were fully susceptible. Using Pulsed Field Gel Electrophoresis (PFGE) there were 3 main patterns of S. Typhimurium and 2 main patterns of S. Enteritidis among cases of bacteraemia and gastroenteritis. CONCLUSION: Serotype distribution, antibiotic susceptibility and PFGE patterns of NTS causing bacteraemia and gastroenteritis did not differ significantly. The high prevalence of NTS strains resistant to most of the commonly used antimicrobials is of major public health concern

Antimicrobial resistance of Campylobacter isolates from small scale and backyard chicken in Kenya

Background Thermophilic Campylobacter species are a major cause of bacterial foodborne diarrhoea in humans worldwide. Poultry and their products are the predominant source for human campylobacteriosis. Resistance of Campylobacter to antibiotics is increasing worldwide, but little is known about the antibiotic resistance in Campylobacter isolated from chicken in Kenya. In this study, 35 suspected Campylobacter strains isolated from faeces and cloacal swabs of chicken were tested for their susceptibility to seven antibiotics using a broth microdilution assay and molecular biological investigations. Results Overall, DNA of thermophilic Campylobacter was identified in 53 samples by PCR (34 C. jejuni, 18 C. coli and one mix of both species) but only 35 Campylobacter isolates (31 C. jejuni and 4 C. coli) could be re-cultivated after transportation to Germany. Isolates were tested for their susceptibility to antibiotics using a broth microdilution assay. Additionally, molecular biological detection of antibiotic resistance genes was carried out. C. jejuni isolates showed a high rate of resistance to nalidixic acid, tetracycline and ciprofloxacin of 77.4, 71.0 and 71.0 %, respectively. Low resistance (25.8 %) was detected for gentamicin and chloramphenicol. Multidrug resistance in C. jejuni could be detected in 19 (61.3 %) isolates. Resistance pattern of C. coli isolates was comparable. Resistance to ciprofloxacin was confirmed by MAMA–PCR and PCR–RFLP in all phenotypically resistant isolates. The tet(O) gene was detected only in 54.5 % of tetracycline resistant C. jejuni isolates. The tet(A) gene, which is also responsible for tetracycline resistance, was found in 90.3 % of C. jejuni and in all C. coli isolates. Thirteen phenotypically erythromycin-resistant isolates could not be characterised by using PCR–RFLP and MAMA–PCR. Conclusions To the best of our knowledge, this study is the first report about resistance to antibiotics in thermophilic Campylobacter originating from chicken in Kenya. Campylobacter spp. show a high level of resistance to ciprofloxacin, nalidixic acid and tetracycline but also a remarkable one to chloramphenicol and gentamicin and they are multidrug resistant. Resistance to antibiotics is a global public health concern. In Kenya, resistance surveillance needs further attention in the future. Efforts to establish at least a National Laboratory with facilities for performing phenotypic and genotypic characterization of thermophilic Campylobacter is highly recommended

Typhoid is over-reported in Embu and Nairobi, Kenya

The paper looks at the usefulness of the Widal agglutination test in the context of variable normal antibody titres in two different populations in Kenya, and in comparison to the blood culture method of diagnosis. It presents a prospective case-control study. We examined 846 blood cultures and an equal number of serum samples, and 782 stools from adults who presented at two study sites; Kenyatta National Hospital and one hospital and 3 clinics in Embu District, with symptoms similar to typhoid. Examined also were 360 serum samples and stools from adults who were apparently healthy (controls) who sought routine medical examination at the study sites. From blood cultures, isolation rates for typhoid for Embu (3%) and Nairobi (2.2%) were not significantly different (p>0.01). In addition the control population from the two study sites did not show any significant background O antibody titre levels characteristic of typhoid endemic areas. All the 7 commonly available Widal test kits including Murex, Europath, Biotech, Humatex, Biosystems, Microsystems and Typhex, that were evaluated for efficacy were equally specific in diagnosis of typhoid by Widal agglutination methods. However, there were minor differences in the sensitivities of the kits. The Widal test method gave a lower sensitivity (81.3%) than specificity (93%) when compared to the culture of blood for diagnosis of typhoid. Going by the reports of typhoid outbreaks in Embu and Nairobi (ca. 20-25% reported prevalence) we conclude that there has been over-reporting probably due to poor methodologies of performing the Widal test. We recommend adequate clinical examination in suspected cases of typhoid in addition to proper Widal in order to improve typhoid diagnosis. Newer improved methods that are more specific and sensitive than the Widal test need to be evaluated in improving laboratory diagnosis of typhoid.African Journal of Health Sciences Vol. 11(3-4) 2004: 103-11

Increasing prevalence of multidrug-resistant non-typhoidal salmonellae, Kenya, 1994–2003

Over the last decade there has been a steady increase in the proportion of multidrug resistance among non-typhoidal salmonellae (NTS) isolated from adult patients with bacteraemia in Kenya. The prevalence of NTS multiply resistant to all commonly available drugs including ampicillin, streptomycin, co-trimoxazole, chloramphenicol and tetracycline rose from 31% in 1994 to 42% at present, with concomitantly higher MICs of each drug. Resistance is encoded on large self-transferable 100–110 kb plasmids. Pulsed field gel electrophoresis of XbaI and SpeI digested chromosomal DNA revealed three main digest patterns for Salmonella enterica serotype Typhimurium and two main patterns for Salmonella enterica serotype Enteritidis. Although the genotypes of NTS remained fairly stable over the last decade, the large increase in MICs of all commonly used drugs and increased MICs of ciprofloxacin, poses a major challenge for treatment of invasive NTS infection. © 2004 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved

Typhoid in Kenya Is Associated with a Dominant Multidrug-Resistant Salmonella enterica Serovar Typhi Haplotype That Is Also Widespread in Southeast Asia▿ †

In sub-Saharan Africa, the burden of typhoid fever, caused by Salmonella enterica serovar Typhi, remains largely unknown, in part because of a lack of blood or bone marrow culture facilities. We characterized a total of 323 S. Typhi isolates from outbreaks in Kenya over the period 1988 to 2008 for antimicrobial susceptibilities and phylogenetic relationships using single-nucleotide polymorphism (SNP) analysis. There was a dramatic increase in the number and percentage of multidrug-resistant (MDR) S. Typhi isolates over the study period. Overall, only 54 (16.7%) S. Typhi isolates were fully sensitive, while the majority, 195 (60.4%), were multiply resistant to most commonly available drugs—ampicillin, chloramphenicol, tetracycline, and cotrimoxazole; 74 (22.9%) isolates were resistant to a single antimicrobial, usually ampicillin, cotrimoxazole, or tetracycline. Resistance to these antibiotics was encoded on self-transferrable IncHI1 plasmids of the ST6 sequence type. Of the 94 representative S. Typhi isolates selected for genome-wide haplotype analysis, sensitive isolates fell into several phylogenetically different groups, whereas MDR isolates all belonged to a single haplotype, H58, associated with MDR and decreased ciprofloxacin susceptibility, which is also dominant in many parts of Southeast Asia. Derivatives of the same S. Typhi lineage, H58, are responsible for multidrug resistance in Kenya and parts of Southeast Asia, suggesting intercontinental spread of a single MDR clone. Given the emergence of this aggressive MDR haplotype, careful selection and monitoring of antibiotic usage will be required in Kenya, and potentially other regions of sub-Saharan Africa

Projector augmented-wave approach to density-functional perturbation theory

The density-functional theory total energy within the projector-augmented wave formalism is expressed in a form suitable for application of the variation-perturbation formalism. We derive the corresponding expressions up to the third order. The much deeper complexity of the projector-augmented wave formalism, compared to the norm-conserving pseudopotential case, implies the introduction of several new notations. However, the structure of the resulting formalism is quite similar, and should be as useful, accurate, and widely applicable

Phylogeny of Kenyan strains showing the two subclades.

<p>Phylogeny of Kenyan strains showing the two subclades.</p

Global and seventh pandemic phylogeny.

<p>1a, a maximum likelihood phylogenetic tree of <i>V</i>. <i>cholerae</i> based on the SNP differences within the core genome. The 6 major O1 clinical groups are shown in this tree with the 7^th pandemic El Tor in blue, classical lineage in green and other colours are match the colours of strains in Table S2. In red are the environmental non O1/O139 strains from Kenya. The date range on the wave 3 node is the BEAST estimated time when the seventh pandemic wave 3 cholera entered Kenya. 1b, a maximum likelihood phylogenetic tree of the 7th pandemic lineage of <i>V</i>. <i>cholerae</i> based on the SNP differences across the whole core genome, excluding likely recombination events. The pre-7th pandemic isolate M66 was used as an outgroup to root the tree. Blue, green and red branches and the clade cartoon represent wave 1, 2, 3 and Kenyan clade respectively. 1c, a maximum likelihood phylogenetic sub-tree showing the position of Kenyan sporadic or travel linked clustering with south Asian strains. All the scales are given as the number of substitutions per variable site.</p