Diagnostic utility of in-house loop-mediated isothermal amplification and real-time PCR targeting virB gene for direct detection of Brucella melitensis from clinical specimens

AIMS

In this present study, the utility of a newly developed loop-mediated isothermal amplification (LAMP) and real-time PCR assays designed to amplify the virB gene region of Brucella melitensis was evaluated from human clinical specimens.

METHODS AND RESULTS

Fifty-four culture-confirmed cases of brucellosis and 54 culture negative but clinically suspected cases of brucellosis were included in the study. Whole blood, serum and other nonblood specimens were collected and subjected to blood culture using automatic blood culture system, serological tests, LAMP assay and real-time PCR. Overall sensitivities of LAMP and real-time PCR assays were 67·5 and 68·3% respectively. For nonblood clinical specimens, we noticed a marked increase in the sensitivities of LAMP (88·9%) and real-time PCR (100%) assays.

CONCLUSIONS

Performance of LAMP and real-time PCR was not satisfactory for whole-blood specimens because of the low abundance of bacteria or DNA. On the other hand, using nonblood specimens, both the assays showed higher sensitivity and specificity which makes them a good alternative for the rapid diagnosis of human brucellosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The developed LAMP and real-time PCR assays are a specific and rapid diagnostic tool for direct and early detection of Brucella in clinical specimens.

Variations in antibiotic use across India: multi-centre study through Global Point Prevalence survey

The aim of the study was to assess antimicrobial prescribing patterns, and variation in practice, in India. A point prevalence survey (PPS) was conducted in October to December 2017 in 16 tertiary care hospitals across India. The survey included all inpatients receiving an antimicrobial on the day of PPS and collected data were analysed using a web-based application of the University of Antwerp. In all, 1750 patients were surveyed, of whom 1005 were receiving a total of 1578 antimicrobials. Among the antimicrobials prescribed, 26.87% were for community-acquired infections; 19.20% for hospital-acquired infections; 17.24% for medical prophylaxis; 28.70% for surgical prophylaxis; and 7.99% for other or undetermined reasons. Antibiotic prescribing quality indicators, such as reason in notes and post-prescription review score, were low. This PPS showed widespread antibiotic usage, underlining the need for antibiotic stewardship to promote evidence-based practice.

Microvesicles in hepatic and peripheral vein can predict nonresponse to corticosteroid therapy in severe alcoholic hepatitis

BACKGROUND

Severe alcoholic hepatitis patients have high mortality and limited response to corticosteroids. Microvesicles reflect cellular stress and disease conditions.

AIMS

To investigate whether microvesicles are associated with severity, response to steroid therapy and inflammation in severe alcoholic hepatitis.

METHODS

Microvesicles originating from different cells were studied pre-therapy in 101 patients; (71 responder to corticosteroid therapy and 30 nonresponders) and 20 healthy controls. Microvesicles and cells were determined in peripheral and hepatic vein samples using flow cytometry and correlated with outcomes. Inflammatory signalling pathways and functional alterations of immune cells after stimulation with microvesicles were also investigated.

RESULTS

Microvesicles mean levels were higher in nonresponders for T cells (CD3⁺ CD4⁺ ; 10.1 MV/μL vs 5.4; P = 0.06), macrophages (CD68⁺ CD11b⁺ ; 136.5 vs 121.9 MV/μL; P = 0.01), haematopoietic stem-cells (CD45⁺ CD34⁺ ; 116.8 vs 13.4 MV/μL; P = 0.0001) and hepatocytes (ASGPR⁺ ; 470 vs 361 MV/μL; P = 0.01); the latter two predicting steroid nonresponse in 94% patients at baseline in peripheral plasma. Microvesicle levels correlated with histological and liver disease severity indices. Whereas, in non-responders hepatic vein CD34+ cells were lower (P = 0.02), the CD34+ microvesicles there from were higher (P = 0.04), thus suggesting impaired regeneration. Also, microvesicles of 0.2-0.4 μm size were higher in nonresponders (P < 0.03) at baseline. Microvesicles from patients trigger more (P = 0.04) ROS generation, TNF-α production (P = 0.04) and up-regulate pro-inflammatory cytokine related genes in neutrophils in vitro.

CONCLUSIONS

Pre-therapy peripheral plasma levels of CD34⁺ and ASGPR⁺ microvesicles are reliable non-invasive markers of steroid nonresponse and mortality in patients with severe alcoholic hepatitis.

Antimicrobial susceptibility pattern in diabetic foot ulcer: a pilot study

BACKGROUND

Diabetic foot infections (DFIs) are major public health problems and knowledge of microbes that cause infections are helpful to determine proper antibiotic therapy.

AIMS

The aim was to investigate the antimicrobial susceptibility pattern of microbes in DFIs.

SUBJECTS AND METHODS

A cross-sectional study was conducted for a period of 6 months at the Department of General Surgery, KMC hospital, Manipal University, Manipal, India. During this period, 108 patients having DFIs admitted in the general surgery wards were tracked from the hospital data management system. These patients' pus samples were examined as Gram-stained smear and cultured aerobically on blood agar and MacConkey agar plates. Antimicrobial susceptibility test was performed by disc diffusion techniques according to Clinical and Laboratory Standards Institute guidelines.

RESULTS

Of the 108 specimens of the diabetic foot lesions, culture showed polymicrobial growth in 44.4% (48/108). Prevalence of Gram-negative organisms (56%, 84/150) was found to be more than Gram-positive organisms (44%, 66/150). However, Staphylococcus aureus was the most frequent pathogen (28%, 42/150). All Gram-positive aerobes were sensitive to doxycycline. All Gram-negative isolates, including extended spectrum beta lactamase producing strains of Proteus mirabilis and Klebsiella oxytoca except Acinetobacter were highly sensitive to amikacin, cefoperazone/sulbactam, and meropenem. Acinetobacter was completely resistant to all the common antibiotics tested.

CONCLUSION

Prevalence showed Gram-negative bacteria was slightly more than Gram-positive bacteria in diabetic foot ulcers. This study recommends doxycycline should be empirical treatment of choice for Gram-positive isolates and amikacin, cefoperazone/sulbactam, and meropenem should be considered for most of the Gram-negatives aerobes.

An Integrated Approach Using Liquid Culture System Can it Make an Impact for Clinical Diagnosis of Genitourinary Tuberculosis?

Tuberculosis (TB) is one of the major health problems in India. Genitourinary TB (GUTB) comprises 20% of all extrapulmonary TB, and is the most common extrapulmonary site to be affected by this disease. The spectrum of varied pathological changes occur in GUTB, hence a thorough knowledge is required to prevent complications related to GUTB. Diagnostic dilemma is a common problem faced as culture and polymerase chain reaction results vary in their sensitivity and specificity. A thorough knowledge of epidemiology, immunopathogenesis, and spectrum of the disease and importance of including liquid culture system for the diagnosis of this disease are presented in three cases.

Tuberculosis or Melioidosis? - Look Twice in Southwestern Coastal India

Melioidosis is known endemic in many Southeast Asian countries, especially Thailand, and in Northern  Australia. The disease was long considered under-recognized in India but has now gained the status  of emerging infectious disease here. Increasing isolation of the causitive agent B. pseudomallei is  encountered in the recent years from this part of western coastal India. We report one such case  of pulmonary melioidosis in an elderly patient misdiagnosed as tuberculosis ending fatally. Prompt  microbiological diagnosis prevents the unnecessary Anti-TB treatment or prophylaxis. This was also our  first of isolation of B. pseudomallei from endotracheal aspirate. SAARC Journal of Tuberculosis, Lung Diseases & HIV/AIDS; 2012; IX(2) 15-18 DOI: http://dx.doi.org/10.3126/saarctb.v9i2.7973

Recurrent pseudomonal pneumonia in a young immunocompetent adult - something fishy?

Community-acquired pneumonia due to Pseudomonas aeruginosa typically occurs in patients with pre-existing lung disease and immunocompromised individuals. We report the case of a previously healthy young adult who presented with recurrent episodes of pneumonia due to Pseudomonas aeruginosa complicated by pleural effusion. Careful and extensive evaluation ultimately revealed the unusual reason behind the patient's illness.

Native valve endocarditis and femoral embolism due to Granulicatella adiacens: a rare case report

The fastidious Gram-positive cocci Granulicatella adiacens, previously known as nutritionally variant streptococci (NVS) are unusual but significant cause of endocarditis due to increased mortality and morbidity. Difficulties in reaching correct bacteriological identification, increased resistance to beta-lactam antibiotics and macrolides and complicated clinical course have contributed to problems in management of cases of infective endocarditis caused by this bacterium. We present the first Indian case of endocarditis with arterial embolus by G. adiacens in an elderly male with no preexisting cardiac abnormality.

Pulmonary melioidosis in febrile neutropenia: the rare and deadly duet

We present the first two fulminant cases of pulmonary melioidosis in febrile neutropenic patients with acute and varied presentations seen in our institution and their fatal outcome. A high index of suspicion coupled with microbiological confirmation can facilitate the administration of the appropriate therapy in cases of melioidosis that differ from other bacterial infections in terms of presentation and the response to antimicrobials.

Melioidosis in southern India: epidemiological and clinical profile

Melioidosis, which is mainly prevalent in Thailand and Australia, has shown an increasing trend in India in the last few years. We carried out a retrospective study of 25 culture-proven adult cases of melioidosis who were admitted to a tertiary care hospital in southern India during June 2001 to September 2007. There was a six-fold increase in the number of cases in 2006 and 2007 as compared to 2001. Diabetes mellitus was the predisposing factor in 68% of cases, followed by alcoholism (28%). The clinical presentations were fever (80%), pneumonia and/or pleural effusion (48%), hepatomegaly (56%), joint involvement, and/or osteomyelitis (48%), splenomegaly (40%), splenic abscess (24%) and septicemia (28%). The organism, Burkholderia pseudomallei, was sensitive to co-amoxiclav, cotrimoxazole, ceftazidime, and carbapenem. The study suggests that melioidosis is an emerging infectious disease in the southwestern coastal belt of India, and it is likely to happen at much higher incidence.

False-positive widal in melioidosis

Enteric fever is endemic in this part of the world, and Widal test is one of the time-honored laboratory tests that are being used for years to diagnose the disease. On the other hand, melioidosis is a newly emerging disease from this region, which is most often misdiagnosed or underdiagnosed by clinicians. It is well accepted that false-positive Widal reactions following certain non-typhoid Salmonella infections may occur commonly. Three cases of high titers of Widal test are described, where melioidosis was the actual diagnosis in every occasion and was never suspected until diagnosed microbiologically. All the patients had shown a partial response to ceftriaxone. Blood and pus cultures grew Burkholderia pseudomallei, whereas Salmonella typhi was not isolated from blood in any patient. With appropriate antibiotics, the patients showed clinical and microbiological improvement with lowering of Widal titers. These 3 cases show that high Widal titer in any patient may mislead the diagnosis of melioidosis, and further laboratory workup should always be done to rule out melioidosis, especially in cases with nonresponsiveness to treatment.

Emerging extra-intestinal infections with Aeromonas hydrophila in coastal region of southern Karnataka

BACKGROUND

Aeromonas species are gram-negative rods usually isolated from the gastrointestinal tract. They have been occasionally reported as a cause of extra-intestinal infections such as cellulitis, cholangitis, necrotizing fascitis, meningitis, bacteremia, or peritonitis in both immunocompetent and immunocompromised patients.

AIM

To determine the role and possible pathogenesis of Aeromonas in extra-intestinal infections.

SETTINGS AND DESIGN

Retrospective analysis carried out at Kasturba Hospital Manipal, Karnataka in the months of January and February 2007.

MATERIALS AND METHODS

Clinical manifestations and management of eight cases of extra-intestinal infections caused by A. hydrophila , from the south Karnataka coastal region were reviewed. The isolates were identified with the help of biochemical tests using standard guidelines.

RESULTS

All patients acquired Aeromonas infections in the community. Five (62.5%) had underlying illnesses, such as liver disease, diabetes mellitus or malignancy. Five (62.5%) had polymicrobial infections, and three (37.5%) were complicated with bacteremia. These included three patients with ulcers or abscess over the lower leg, two with cellulitis due to snake bite and one each with pelvic inflammatory disease, spontaneous bacterial peritonitis and pneumonia. A. hydrophila was found to be a causative agent of pelvic inflammatory disease or cellulitis following sea snake bite, and such a clinical scenario has not been previously described. Seven patients survived the illness.

CONCLUSIONS

Isolation of A. hydrophila from extra-intestinal specimens demands utmost clinical and microbiological vigilance in diagnosis, since the organism can cause serious infections among immunocompromised as well as immunocompetent individuals.

Citrobacter freundii infection in glutaric aciduria type 1: adding insult to injury

Glutaric aciduria type 1 (GA1) is an inborn error of organic acid metabolism, where the brain is the principal organ affected with exposure to toxic metabolic product, 3-hydroxyglutaric acid (3-OHGA). A 2-year-old boy with GA1 and delayed developmental milestones had an acute neurological crisis leading to massive brain abscess with Citrobacter freundi infection, a rare cause of neonatal meningitis and often associated with brain abscess. Both 3-OHGA and C. freundii can damage the blood-brain barrier and can cause significant trauma which demands immediate and appropriate management. Encephalopathic manifestations of GA1 may consequently increase the risk of meningeal infection and it has not been previously documented.

Aetiology and management of chronic granulomatous osteomyelitis: look before you leap

We report a rare difficult-to-manage case of chronic granulomatous osteomyelitis due to Burkholderia pseudomallei, the category two organism with atypical sensitivity pattern. The patient was a 29-year-old who presented with a history of dull aching pain in the left thigh region for one year. Local examination revealed a diffuse swelling and tenderness. Any similar presentation should therefore always be supported by microbiological opinion to prevent prolonged morbidity, especially in immunocompromised patients.

Intestinal protozoal infestation profile in persistent diarrhea in children below age 5 years in western Nepal

Unlike acute diarrhea, the role of pathogens in persistent diarrhea in children in Nepal is unclear. Protozoal parasites are suspected to be a major cause. The study was carried out to find the association between protozoal agents and persistent diarrhea in children below age 5 years from western Nepal. Stool samples were collected from 253 children with persistent diarrhea, from 155 children with acute diarrhea (disease controls) and from 100 healthy children from the community (normal controls). Of 253 children with persistent diarrhea, 90 (35.5%) had protozoal infections, 63 (24.9%) helminthic infections, 32 (12.6%) had bacterial infections and 16 had mixed infections. Giardia lamblia was the most prevalent (67.7%), followed by Entamaeba histolytica (27.7%). HIV infection and severe malnutrition were associated with Cyclospora cayetanensis and Cryptosporidium spp causing persistent diarrhea. We conclude that stool microscopy should be routinely performed in children with persistent diarrhea since protozoal infections can be cured with effective treatment and control can be achieved by proper health education.

Ciprofloxacin-resistant Salmonella enterica serotype typhi in a patient with osteomyelitis of the rib

Salmonella osteomyelitis of the rib is a rare clinical entity. In our case, a muhidrug resistant Salmonella enterica serotype Typhi was isolated from an immuno-competent patient with osteomyclitis of the ribs, who was treated earlier with ciprotloxacin for typhoid fever. The patient was successfully treated for osteomyclitis with intravenous ceftriaxone.

Persistence of parvovirus B19 IgM antibodies and DNA in pure red cell aplasia resulting in myelodysplasia--a case report

Human erythrovirus B19 (B19), previously known as parvovirus B19, is a small spherical, non-enveloped single stranded DNA virus. It has been shown to cause a wide spectrum of clinical conditons including various hematological disorders. We report here for the first time from Inida a case of pure red cell aplasia in a 45-year-old female for last 7 years due to chronic persistent B19 infection leading to myelodysplasia after 4 years. Her sera were positive for two times 4 months apart for B19 IgM and B19 DNA at the initial stage. Presently the patient is on repeated blood transfusion on every 15-20 days.

Ralstonia mannitolilytica infection in renal transplant recipient: first report

Ralstonia mannitolilytica is being increasingly identified as an opportunist pathogen in immunocompromised patients. We report the first case of post renal transplant infection by R. mannitolilytica, in a 14-year-old recipient. The graft and the patient were saved with prompt microbiological identification, sensitivity testing and subsequent administration of appropriate antibiotic.

Effect of glycosylation on structure and dynamics of MHC class I glycoprotein: a molecular dynamics study

Complex carbohydrates linked to glycoproteins are recently being implicated to play a variety of biological roles. The lack of well-resolved crystallographic coordinates of the carbohydrates makes it difficult to assess the contributions of the glycan chain on protein structure and dynamics. We have modeled two different oligosaccharides NeuNAc2Gal3Man3GlcNAc5Fuc and Man3GlcNAc4 to generate two glycosylation variants of major histocompatibility complex (MHC) class I glycoprotein. Molecular dynamics simulations of the isolated fourteen- and seven-residue oligosaccharides have been done in vacuo and in solution. The dynamics of the two glycoforms of MHC class I protein have been simulated in solution in the free as well as in the peptide-bound form. Good agreement between the calculated solution conformations of the oligosaccharides in isolated and conjugated forms and the average conformations obtained from x-ray or NMR data was observed for most of the glycosidic linkages. These molecular dynamics simulations of the isolated glycan chains and the glycoconjugates reveal the details of the conformational flexibility of the glycan chains; they also provide atomic level details of protein-carbohydrate interactions and the effect of the ligand binding on the carbohydrate structure and dynamics. It was found that though there is some flexibility in some of the glycosidic linkages in the isolated oligosaccharides, in the protein-conjugated form the linkages adopt more restricted conformations. The glycan chains protrude out into the solvent and might hinder the lateral association of the proteins. The presence of the bulky glycan chains does not affect the average backbone fold of the protein but induces local changes in protein structure and dynamics. It has been noted that the extent of the changes depends upon the nature of the attached glycan chain. The glycan chains do not appear to influence the peptide binding property of the protein directly, but may stabilize the protein residues that are involved in ligand binding.

Prevalence of HIV among low and high risk population of eastern part of northern India

A total of 7,904 persons visiting University Hospital of Banaras Hindu University (BHU), Varanasi, were screened for HIV antibody by ELISA and/or rapid test. The overall seroprevalence of HIV (3.17%) in this area was higher than that of Uttar Pradesh and India as a whole. The seroprevalence of HIV/AIDS among the high risk group (HRG) (6.42%) being significantly higher than low risk group (LRG) (0.37%). In the LRG, the prevalence among medical and surgical patients; and ANC (antenatal cases) was 1.17% and 0.14%, respectively. However, HIV infection was not detected in HCWs (healthcare workers), BHU students and foreigners. Among HRG, CSWs (commercial sex workers) had the highest prevalence (14.0%) and STD (sexually transmitted diseases) patients, the lowest prevalence (1.99%). The STD patients had significantly lower prevalence rate as compared to others in HRG. Majority of the HIV positive were found to be within the age group 15-44 years, with heterosexual mode as the main route of transmission. Seven HIV positive children were of 2-5 yr old age group. Majority of seropositive women (62.52%) were working in a low income jobs and were mainly infected by their spouses who was mostly migrating labourers of lower socioeconomic group and with less than primary level of education. Married females, being mainly the spouses of HIV positive males had the highest seropositivity (60.25%). These population people were directly transmitting the infection from the metropolitan cities to the rural areas of this region. Prevalence of HIV-2 was negligible as compared to HIV-1, the actual reason is yet to be explored.

Molecular modelling of MHC class I carbohydrates

In this article we present the results of molecular modelling of four complex carbohydrates which have been found in the MHC class I proteins. Though these proteins show diversity in their sequences, the glycosylation sites are highly conserved indicating a possible structural/functional role of the glycan chain. Similar glycan chains have been found linked with other proteins of completely different function, such as IgG, and erythropoeitin. Thus, the molecular modelling of these carbohydrates will not only provide structural/dynamic information of these complex molecules but will also provide conformational information which can be utilised to build the glycoprotein models. The results presented here indicate that although several linkages show less conformational flexibility, terminal linkages can be quite flexible.

GD1a in phospholipid bilayer: a molecular dynamics simulation

Molecular dynamics simulation of ganglioside GD1a attached to the upper layer of a fully hydrated lipid bilayer of dimyristoyl phosphatidyl choline (DMPC) at room temperature under periodic boundary conditions was performed. The time average conformation of GD1a reveals that the terminal sialic acid is more exposed into the solvent than the internal branched one. Many interresidual contacts between N-acetyl galactosamine-internal branched sialic acid; external Gal-external sialic acid; N-acetyl galactosamine-internal gal are also observed. The conformation of the GD1-hexasaccharide is stabilized by a number of intra molecular hydrogen bonds that were previously observed experimentally. The simulation results indicate that the presence of a single GD1a molecule has local effects on the bilayer. A local disorder in the arrangement of the acyl chains as well as the head groups is evident in the upper layer due to the presence of GD1a.