Baseline titres of O, H and AH agglutinins to Salmonella Typhi and Paratyphi A in blood donors in Sri Lanka.

Background: Sri Lanka is considered as an endemic country for enteric fever. Due to difficulties in performing blood cultures, the Widal test is still commonly carried out for the diagnosis of enteric fever. However, there are no published data on current baseline Widal titres in the country. This study was carried out to determine the baseline titres of O, H and AH agglutinins among the Sri Lankan population.Method: Five hundred and one (501) serum samples of blood donors from 31 blood banks in Sri Lanka were collected during 2012 and 2013 and were screened for Salmonella O, H and AH agglutinins using the Widal tube test. A titre of 20 and above was considered positive. Age and gender of the study participants were recorded.Results: Of the 501 sera tested, 58% were positive for at least one of the O, H and AH agglutinins. Salmonella O, H and AH agglutinins were positive in 46.1%, 26.5% and 8.4% of the study population respectively. Of the study population, 97.5% had O, H and AH agglutinin titres less than or equal to 80, 160 and 80 respectively. A significantly higher percentage of females (H-36.7%, p=0.019; AH-15.3%, p=0.15) were positive for H and AH agglutinins than males (H-24.9%; AH-7.4%). The baseline titre of AH agglutinins was higher in females (160) than males or the total population (80). Highest test positivity (40%) was seen among the 31-40 year age group. A significant number of donors below 20 were negative for Salmonella O agglutinins (p=0.024).Conclusion: We recommend baseline titres of 80, 160 and 80 for Salmonella O, H and AH agglutinins respectively to be used in Sri Lankan settings. As there is a variation in baseline titre with age and gender it is necessary to consider both when interpreting Widal test results.</p

Phenotypic and genotypic distribution of ESBL, AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae in community-acquired and hospital-acquired urinary tract infections in Sri Lanka

Objectives: Although Sri Lanka belongs to a region with a high prevalence of extended-spectrum β-lactamase (ESBL), AmpC β-lactamase and carbapenemase-producing Enterobacteriaceae, data regarding antimicrobial resistance (AMR) is limited. We studied the prevalence and diversity of β-lactamases produced by Enterobacteriaceae urinary pathogens from two hospitals in the Western Province of Sri Lanka. Methods: ESBL, AmpC β-lactamase and carbapenemase production was detected by phenotypic testing followed by genotyping. Results: The species responsible for urinary tract infections (UTI) were Escherichia coli (69%), Klebsiella pneumoniae (16%) and Enterobacter sp (6%). The prevalence of ESBL (50%), AmpC β-lactamase (19%) and carbapenemase (11%) phenotypes was high, and greater in hospital-acquired (HA-UTI) (75%) than in community-acquired UTI (CA-UTI) (42%). Identification of CA-UTI caused by carbapenemase-producing Enterobacteriaceae (5%) is alarming. Only one ESBL gene, blaCTX- M-15, was detected. AmpC β-lactamase genes found in E. coli and K. pneumoniae were blaCMY-2, blaCMY-42 and blaDHA-1, while Enterobacter sp. carried blaACT-1. Carbapenemase genes were blaNDM-1, blaNDM-4, blaOXA-181 and blaOXA-232, while blaKPC, blaIMP and blaVIM were absent. Co-occurrence of multiple bla genes, with some isolates harbouring six different bla genes, was common. Carbapenem-resistant isolates without carbapenemase genes displayed mutations in the outer membrane porin genes, ompF of E. coli and ompK36 of K. pneumoniae. Factors associated with UTI with β-lactamase-producing Enterobacteriaceae were age ≥50 years, previous hospitalization, presence of an indwelling urinary catheter, history of diabetes mellitus or other chronic illness and recurrent urinary tract infections. Conclusion: This study adds to the currently scarce data on AMR in Sri Lanka

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research

Levofloxacin and moxifloxacin resistant Haemophilus influenzae in a patient with common variable immunodeficiency (CVID): a case report

Fluoroquinolones are important in the treatment of respiratory infections and resistance to them amongst Haemophilus influenzae is rare. We report a case of persistent respiratory tract colonization with an H. influenzae strain resistant to ciprofloxacin, levofloxacin and moxifloxacin.Two sputum cultures obtained 4.5 months apart, from a patient with common variable immunodeficiency (CVID), yielded H. influenzae in colony counts exceeding 107 CFU/ml. Antibiotic susceptibility testing using disk diffusion and E-tests revealed both isolates to be resistant to ciprofloxacin, levofloxacin and moxifloxacin.Although quinolone resistant H. influenzae remains extremely rare, its emergence in Sri Lanka heralds microbiological and clinical challenges with important implications for the treatment of community acquired respiratory infection.</p

Transverse myelitis secondary to Melioidosis; A case report

<p>Abstract</p> <p>Background</p> <p>Melioidosis has become an emerging infection in Sri Lanka; a country which is considered non endemic for it. Paraplegia due to <it>Burkholderia pseudomallei</it> is a very rare entity encountered even in countries where the disease is endemic. There are no reported cases of transverse myelitis due to melioidosis in Sri Lankan population thus we report the first case.</p> <p>Case presentation</p> <p>A 21 year old farmer presented with sudden onset bi lateral lower limb weakness, numbness and urine retention. Examination revealed flaccid areflexic lower limbs with a sensory loss of all modalities and a sensory level at T₁₀ together with sphincter involvement. MRI of the thoracolumbar spine showed extensive myelitis of the thoracic spine complicating left psoas abscess without definite extension to the spinal cord or cord compression. <it>Burkholderia pseudomallei</it> was isolated from the psoas abscess pus cultures and the diagnosis of melioidosis was confirmed with high titers of <it>Burkholderia pseudomallei</it> antibodies and positive PCR. He was treated with high doses of IV ceftazidime and oral cotrimoxazole for one month with a plan to continue cotrimoxazole and doxycycline till one year. Patient’s general condition improved but the residual neurological problems persisted.</p> <p>Conclusion</p> <p>The exact pathogenesis of spinal cord melioidosis is not quite certain except in the cases where there is direct microbial invasion, which does not appear to be the case in our patient. We postulate our patient’s presentation could be due to ischemia of the spinal cord following septic embolisation or thrombosis of spinal artery due to the abscess nearby. A neurotrophic exotoxin causing myelitis or post infectious immunological demyelination is yet another possibility. This emphasizes the necessity of further studies to elucidate the exact pathogenesis in this type of presentations.</p> <p>Health care professionals in Sri Lanka, where this is an emerging infection, need to improve their knowledge regarding this disease and should have high degree of suspicion to make a correct and a timely diagnosis to reduce the morbidity and mortality due to <it>Burkholderia pseudomallei</it> infection. It is highly likely that this infection is under diagnosed in developing countries where diagnostic facilities are minimal. Therefore strategies to improve the awareness and upgrade the diagnostic facilities need to be implemented in near future.</p