Bacterial translocation is the invasion of indigenous intestinal bacteria through the gut mucosa to normally sterile tissues and the internal organs. Sometimes instead of bacteria, inflammatory compounds are responsible for clinical symptoms as in systemic inflammatory response syndrome (SIRS). The difference between sepsis and SIRS is that pathogenic bacteria are isolated from patients with sepsis but not with those of SIRS. Bacterial translocation occurs more frequently in patients with intestinal obstruction and in immunocompromised patients and is the cause of subsequent sepsis. Factors that can trigger bacterial translocation from the gut are host immune deficiencies and immunosuppression, disturbances in normal ecological balance of gut, mucosal barrier permeability, obstructive jaundice, stress, etc. Bacterial translocation occurs through the transcellular and the paracellular pathways and can be measured both directly by culture of mesenteric lymph nodes and indirectly by using labeled bacteria, peripheral blood culture, detection of microbial DNA or endotoxin and urinary excretion of non-metabolisable sugars. Bacterial translocation may be a normal phenomenon occurring on frequent basis in healthy individuals without any deleterious consequences. But when the immune system is challenged extensively, it breaks down and results in septic complications at different sites away from the main focus. The factors released from the gut and carried in the mesenteric lymphatics but not in the portal blood are enough to cause multi-organ failure. Thus, bacterial translocation may be a promoter of sepsis but not the initiator. This paper reviews literature on the translocation of gut flora and its role in causing sepsis.

Purpose: To detect and identify the aetiological agent in the peripheral blood from the cases of neonatal sepsis. Materials and Methods: Four neonates from geographically different regions of South India presented with signs of neonatal sepsis and all the routine clinical and laboratory investigations were performed. Blood culture by Bac T Alert 3D was negative. To establish the aetiology, polymerase chain reaction (PCR) for eubacterial genome and subsequent amplification with Gram positive and Gram negative primers were performed followed by deoxyribonucleic acid (DNA) sequencing. Results: PCR for the detection of eubacterial genome was positive in all the four neonates and further amplification with designed Gram positive and Gram negative primers revealed the presence of Gram negative bacteria. The amplicons were identified as Orientia tsutsugamushi in three neonates and Coxiella burnetti in the other neonate. Multalin analysis was done to further characterise the strain variation among the three strains. Conclusion: PCR-based DNA sequencing is a rapid and reliable diagnostic tool to identify the aetiological agents of neonatal sepsis. This is the first case series of emerging Rickettsial neonatal sepsis in India .

Background: Hepatitis C virus (HCV) is a leading cause of chronic liver disease (CLD) that can progress to cirrhosis and hepatocellular carcinoma. Genotypes of HCV can vary in pathogenicity and can impact on treatment outcome. Objectives: To study the different genotypes among patients with HCV related CLD attending a tertiary care hospital in south India during 2002-2012. Study Design: Study subjects were those referred to clinical virology from the liver clinic. Genotyping was performed using the genotype specific core primers in nested polymerase chain reaction (PCR), 5′ non-coding regions based PCR- restriction fragment length polymorphism and NS5B sequencing methods. With the latter method, obtained sequences were compared with published GenBank sequences to determine the genotype. Results: Of the 451 samples tested, HCV genotype 3 was found to be the most predominant (63.85%). Other genotypes detected were genotype 1 (25.72%), genotype 2 (0.002%), genotype 4 (7.5%) and genotype 6 (2.7%). Genotype 3 was the common genotype in patients from Eastern India while genotype 1 and 4 were mainly seen in South Indian patients. Genotype 6 was seen exclusively in patients from North-Eastern India. Two other patients were infected with recombinants of genotype 1 and 2. Conclusions: In this study spanning a decade, HCV genotype 3 and genotype 1 were found to be the predominant genotypes in the Indian sub-continent. Genotype 4 and genotype 6 appeared to show some geographic restriction. A continued monitoring of HCV genotypes is essential for the optimum management of these chronically infected patients. In addition, knowledge of circulating genotypes could impact on future vaccine formulations.

Purpose: Hepatitis C virus (HCV) has emerged as a leading cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. There is a great variability in HCV's geographical presence, transmission routes, genotypic distribution etc., in studied populations. We undertook this study in a North Indian hospital on patients of chronic liver disease to observe any emerging trend in risk groups, transmission patterns, genotypic distribution of the virus in this geographical region and its correlation with viral load. Materials and Methods: There were 54 anti-HCV positive patients including 31 HCV Ribonucleic acid (RNA) positive patients were included in the study. HCV genotyping was carried out by restriction fragment length polymorphism (RFLP) followed by direct sequencing of the core region. Viral load estimation was carried out by Taqman real time polymerase chain reaction system. Results: In 45/54 (83.3%) anti-HCV positive patients, iatrogenic procedures were responsible for transmission with blood transfusion alone responsible in 36/54 (67%). Genotype 3 was observed to be the commonest type found in all risk groups followed by type 1 and 2. Subtype 3b (35.5%) was found more prevalent than subtype 3a. A higher frequency of subtype 1b (19.4%) was also seen. Genotype 1 was associated with a significantly higher viral load compared to genotypes 3 and 2. No significant difference was observed in the biochemical profile among the three genotypes except for the levels of the enzyme, aspartate aminotransferase (AST). Conclusions: Iatrogenic procedures, especially contaminated blood transfusion etc., still contributes significantly to the pool of HCV infection. Genotype 3 is the predominant genotype in North India, though the subtype distribution within genotype 3 may be changing. The association of severe liver disease is significantly more with genotype 1 as evidenced by higher viral load and deranged AST levels.

Background: It has been revealed that mutations can occur spontaneously and naturally in HBV reverse transcriptase (RT) region among untreated patients. These HBV mutants pre-exist as minor viral population in naive patients and can emerge as major viral population, conferring drug resistance and treatment failure. Objectives: The aim of this study was to investigate and identify prevalent mutations of RT region of hepatitis B virus genome in patients with chronic hepatitis B (CHB) untreated with antiviral drugs in South-West of Iran. Materials and Methods: A total of 45 cases with CHB who did not receive the treatment of lamivudine and any other antivirus drugs within the last one year were randomly chosen. After sample collection and HBV DNA extraction, RT region was amplified by polymerase chain reaction (PCR). Then PCR products were sequenced and HBV RT region mutations and amino acid changes were analyzed either manually or using web-based programs, on the basis of comparison of the obtained sequences with a set of HBV reference sequences. Results: A total of 23 (51.1%) mutations and amino acid changes were detected in studied 45 untreated patients. Of these, 3 (6.6%) patients had primary resistance mutation (rtM204I, rtA181T and rtA181S) and 20 (44.4%) patients had secondary resistance mutations. Conclusion: High prevalence of mutations was found in HBV RT region of untreated patients. Most of these mutations were associated with resistance to adefovir and one patient had primary resistance mutation to lamivudine. Awareness of these resistance patterns might help in the antiviral therapy and for predicting clinical outcomes.

Background: Early diagnosis of tuberculosis is critical for its effective management and prevention. Several gene amplification methods are used in the detection of tubercle bacilli from clinical specimens. MPB64 gene and IS6110 region have been identified as potential gene targets for the specific detection of Mycobacterium tuberculosis from direct clinical specimens. Objective: The present study was conducted to evaluate the diagnostic utility of simultaneous application of two nested polymerase chain reaction (nPCRs) targeting MPB64 and IS6110 region for the detection of M. tuberculosis genome. Materials and Methods: A total of 100 and 354 clinical specimens from the control group and clinically suspected tuberculosis patients, respectively, were included in the study. nPCRs targeting MPB64 and IS6110 region were performed. Results and Conclusion: All of the 100 clinical specimens from the control group were negative for both nPCRs. Out of the 354 clinical specimens, 339 were positive for both culture and nPCRs, 10 and 5 were positive for culture, and nPCR targeting IS6110 and MPB64 regions, respectively. To conclude, nPCRs targeting MPB64 and IS6110 region are reliable and specific targets when applied simultaneously on clinical specimens to attain 100% sensitivity for the detection of M. tuberculosis genome.

Purpose: To evaluate multiplex Polymerase Chain Reaction (MPCR) utilising multiple targets (IS6110, Protein b [Pab] and MPB64 genes) in Mycobacterium tuberculosis Direct Test (MTD) negative but culture positive cases and comparison of MPCR with Real-Time polymerase chain reaction (RT-PCR) for diagnosis of tuberculosis. Materials and Methods: MPCR was carried out on 28 culture positive sputum samples. Out of 28 culture positive samples, 17 were originally reported, as MTD test negative and 11 were MTD test positive, respectively. The results of MPCR were compared with RT-PCR. To check the specificity of the tests, MPCR and RT-PCR were also evaluated with 16 non-tuberculous mycobacterial (NTM) isolates. Results: Out of 28 culture positive sputum samples, MPCR was positive in all 28/28 samples, whereas RT-PCR was positive in 27/28 samples and MTD test was originally tested positive in six sputum samples and on repeating MTD testing, five more sputum samples were positive and thus total number of MTD positive were 11/28 sputum samples, respectively. All the tests were negative on evaluation with all the 16 NTMs, thus giving specificity of 100% to all the tests; sensitivity of MPCR, RT-PCR and MTD tests were 100%, 96.42% and 39.28%, respectively, in these specifically selected samples. Conclusions: MPCR may be an important tool in the rapid diagnosis of tuberculosis especially in disease endemic, resource limited countries.

Purpose: There are increasing reports on failure of clinical response to ciprofloxacin in typhoid fever despite the strain being sensitive to drug in in-vitro using standard guidelines and showing mutations in DNA gyrase. But this increased MIC and clinical failures with ciprofloxacin are not always co-related with mutations presently identified in gyrA and parC genes. This shows that there may be other mechanisms such as an active drug efflux pump responsible as has been shown in other Enterobacteriaceae. This study was carried out to determine the role of efflux pump in Salmonella Typhi isolates. Materials and Methods : Total 25 already characterized nalidixic acid sensitive and nalidixic acid resistant S. Typhi strains with different range of ciprofloxacin MIC were included to study the role of efflux pump in the presence of CCCP (efflux pump inhibitor). For genotypic characterization, the entire acrR gene was sequenced to confirm the presence of any mutation in the gene. Results: The MIC of ciprofloxacin remained same in the presence and absence of CCCP in the studied strains and no significant mutations were found in the acrR gene in any of the isolates studied. Conclusions: No role of efflux pump in ciprofloxacin resistance was found in strains studied. There is a need to explore further mechanism of ciprofloxacin resistance in Salmonella Typhi.

Purpose: The frequency of mycotic infections of the nose and paranasal sinuses has been increasing over the past three decades. Apart from the common causes of fungal rhinosinusitis such as Aspergillus species and Penicillium species, there have been reports of rare and unusual fungi isolated from India and other countries. Objective: The objective of this study is to find out the prevalence of fungal infections of the nose and paranasal sinuses caused by unusual fungal isolates at a tertiary care teaching hospital in South India. Materials and Methods: Duration of the study period was from April 2009 to March 2010. Specimens were collected from the nose and paranasal sinuses of all clinically and radiologically diagnosed cases of rhinosinusitis. All the clinical specimens were processed by standard methods for fungal culture. This included initial screening by 10% potassium hydroxide, inoculation of the specimen onto Sabouraud dextrose agar and incubation at 25°C and 37°C, followed by slide culture and other special techniques wherever necessary. Histopathological examination was also performed for the specimens. Results: A total of 60 specimens were received for fungal culture from cases of rhinosinusitis during the period, out of which 45 showed no growth. There were nine cases of Aspergillus flavus, 1 each of Aspergillus fumigatus and Penicillium species. The rest four specimens grew rare fungal isolates, i.e. Acremonium sp., Scedosporium apiospermun, Cladosporium cladosporioides and Lasiodiplodia theobromae. Histopathological findings were also positive for these four cases. Conclusion: Apart from the common causes, unusual fungal pathogens were isolated from cases of rhinosinusitis during the study period, which is in accordance with similar reports from other parts of India and some other countries.

Objectives: The objective of this study is to determine the prevalence of antibiotic resistance factors, including the production of extended-spectrum beta-lactamases (ESBLs) and the presence of class 1 integrons among Escherichia coli isolated from clinical specimens. Materials and Methods: Bacterial species identification was performed using a VITEK-2 system (VITEK2 GN-card; bioMérieux, France). Antimicrobial susceptibility testing was determined using the disk diffusion method according to the 2010 Clinical and Laboratory Standards Institute guidelines. Polymerase chain reaction (PCR) was used to detect integrons and amplify variable regions of the bla _TEM, bla _SHV and bla _CTX-M genes. Gene cassettes were detected by deoxyribonucleic acid sequencing. Results: In this study, 58% (100/172) of clinical E. coli isolates were identified as ESBL producers. We found that 90% of the ESBL-producing E. coli isolates harbored the bla_CTX-M gene, whereas only 59% and 32% possessed the bla_TEM and bla_SHV genes respectively. The presence of class 1 integrons was based on the detection of the integrase gene by PCR. A total of 69% of the ESBL-producing isolates were integron-positive. Resistance to 10 antibiotics, including quinolones, sulfonamides and β-lactam/enzyme inhibitors, was significantly higher in the class 1 integron-positive isolates (P < 0.05). The occurrence of class 1 integrons in bla_TEM , bla_SHV and bla_CTX-M gene carriers was 72.9%, 84.4% and 68.9%, respectively. Class 1 integrons were detected in 61.5% of the isolates with only one ESBL genotype, but in 69.0% and 92.3% of the isolates with two or three different ESBL genotypes, respectively. Conclusions: Our findings indicate that clinical strains of bacteria with multiple ESBL genotypes may have greater opportunities to carry class 1 integrons.

Trauma contributes to a significant proportion of mortality and morbidity in the economically productive age group of 15-45 years. Infections are the second most important cause of death in trauma patients after head injury. Despite advances in trauma care, deaths due to septicemia are increasing. An epidemiological study of septicemia-related deaths were conducted at a level 1 Trauma Centre from January 2011 to December 2011. A total of 201 patients died due to suspected septicemia. The average age of the deceased trauma victims was 35.9 years and the median length of stay in hospital before death was 27 days. In our study, a high proportion of patients had grown pathogens in significant counts from respiratory specimens (36%) and blood (23%) during ante-mortem period, which may have contributed to their fatal outcome. Infections are one of the most common and fatal complications following trauma and complicate the recovery of a significant number of injured patients.

Anaerobes are important causes of pleural space infections. The aim of the study is to evaluate the role of the anaerobic bacteria in pleural infections. The study involved 278 consecutive clinical samples sent to the Clinical Microbiology Laboratory of Tertiary Chest Hospital. Anaerobes were isolated in 39 community acquired and five nosocomial cases out of 278 anaerobic cultivations (15.8%). Total of 56 anaerobe strains were identified and 21 aerobes were accompanied to anaerobic isolates. Aerobe isolates were associated with anaerobic microorganisms in 19 cases (43.2%). Bacteroides species (21.4%) and Pseudomonas aeruginosa (33.3%) were the most common anaerobic and aerobic isolates.

The aim of this study was to explore baseline data, laboratory and molecular analyses to determine if any could serve as potential prognostic marker(s) for treatment response to second line tuberculosis regimens. Of a total number of 50 multi-drug resistant tuberculosis (MDR-TB) patients starting second-line drug MDR-TB treatment in Iraq, only 21 showed treatment adherence and thus, included in this study. Response to treatment was monitored for 11 months by sputum microscopy and culture. We explored baseline data, laboratory and molecular analyses to determine if any could serve as potential prognostic marker(s) for treatment response. Highly significant association (P = 0.019) was detected between mutations in katG315 codon and good response to second-line anti-TB drugs. Spoligotyping and mycobacterial interspersed repetitive unit variable number tandem repeat confirmed that katG315-mutatnt isolates were genotypically unrelated. The katG315 mutation is a potential prognostic marker for treatment response to second-line anti-tuberculosis drugs. One possible explanation of our results is that the katG315-mutants are sensitive to bacterial killing by "oxidative killing."

Entomophthoromycosis is chronic granulomatous fungal infection with varied presentation as subcutaneous,mucocutaneous and visceral infections. The majority of the subcutaneous infection caused by entomophthoralean fungi involves Basidiobolus spp, C. coronatus, or C. incongruous. A case of rhinoentomophthoromycosis in an immunocompetent male involving maxillary sinus and nose is presented. The patient was clinically diagnosed as malignancy of nose but microscopy and histopathology of the aspirate clinched the diagnosis. The patient responded to antifungal therepy.

Subcutaneous Human Dirofilariasis is an uncommon zoonotic infection caused by Dirofilariarepens. The reports of this infection in humans in India are limited, although increasingly being reported worldwide. We report a case of Dirofilariasis with subcutaneous presentation from the state of Meghalaya and to emphasize the importance of considering this entity in the differential diagnosis of patients presenting with subcutaneous nodules.

Ralstonia paucula (formerly classified as CDC (Centre for Disease Control) group IVc-2, Wautersia paucula; recently renamed as Cupriavidus pauculus) is an environmental Gram-negative bacillus isolated from water sources and can cause serious human infections. Patients recover bacteriologically indicating low virulence. A total of 32 cases have been reported world-wide, but no isolation has ever been reported from cerebrospinal fluid or in India. The first case of R. paucula meningitis and septicemia is being reported here along with the brief summary of cases reported world-wide.

Nontyphoidal Salmonella (NTS) are established foodborne pathogens, most commonly reported in cases of gastroenteritis. These pathogens are however, increasingly being implicated in cases of bacteraemia and other extraintestinal manifestations. We report a case of a scalp abscess due to Salmonella enterica serotype Enteritidis, which is a serotype of NTS, in a child suffering from a haematologic malignancy. The child was on steroid and anticancer chemotherapy and developed the abscess secondary to bacteraemia with Salmonella Enteritidis. The abscess was drained and resolved following a course of intravenous antibiotic treatment.

Primary intramuscular hydatid cyst should be considered for the differential diagnosis of cystic soft tissue masses especially in the endemic areas though primary muscular hydatidosis is a rare clinical entity. We aimed to report the case of a 30-year-old female patient with infected primary intramuscular hydatid cyst located in the sartorius muscle.