Nipah Virus (NiV) infection is an emerging zoonosis of public health importance in the South East Asia region. The most recent outbreak occurred in Kozhikode district, Kerala in May 2018.NiV belongs to a new genus Henipavirus under the family Paramyxoviridae. Fruit bats of the family Pteropodidae are the natural hosts of Nipah Virus. Pigs are the secondary and amplifier hosts. Infection is transmitted either directly from infected bats or pigs or indirectly through contaminated food (fruits, fruit juices). Human to human transmission has also been documented. Clinical manifestations in human beings range from asymptomatic infection to acute respiratory distress syndrome and fatal encephalitis. Case fatality rate has varied in different outbreaks from 40 –75%.In the recent Kerala outbreak a high case fatality of 91%was documented. Nipah virus is one of the most deadly viruses known to infect humans. Diagnosis is mainly by RT-PCR. There is no specific treatment or preventive vaccine for Nipah. Stringent infection control measures including standard precautions, contact and droplet precautions in health care facilities help in containing nosocomial outbreaks.

A waste autoclave is essential for treating solid waste materials before disposing to the external environment. This can be done by the hospital itself (on-site waste treatment) or by a third party. Treatment of waste materials is based on the category of the waste and their disposal policy. Fundamentally, clinical waste autoclave mechanism is slightly different from the clinical autoclave that is used in the hospital sterile supply department. The clinical waste autoclave assures that the residual air in the chamber and waste liquids will be sterile before disposal. The objective of this article is to distinguish the clinical autoclave from the clinical waste autoclave so that the functionality and advantages of the waste autoclave in reducing environmental pollution by sterilising the waste materials and the effluents (e.g. aerosols and contaminated liquid) at the same time before draining or disposal is understood.

CONTEXT: Diagnosing acute bacterial meningitis (ABM) among children presenting to tertiary health care settings is often difficult because of prior administration of antimicrobials. AIMS: The present study was an attempt to diagnose cases of ABM in children with the help of nested polymerase chain reaction (PCR). SETTINGS AND DESIGN: It is a prospective observational study, in which a total of 84 clinically suspected cases and cerbrospinal fluid (CSF) biochemical parameters suggestive of ABM were included in the study. METHODS AND MATERIAL: CSF samples were subjected to Gram staining, bacterial culture and biochemical identification tests as well as panbacterial nested PCR targeting 16S rRNA gene sequence. Subsequently, a nested multiplex PCR for detection of the three fastidious organisms, viz. Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae, was performed. STATISTICAL ANALYSIS USED: The sensitivity, specificity, PPV, NPV, LR+, and LR− of the tests were calculated. RESULTS: The sensitivity of Gram stain, bacterial culture, and nested PCR targeting 16SrRNA were observed to be 16.21%, 9.45%, and 97.29% respectively. Further, the NPV and LR− the PCR were found to be 83.33 and 0.02 respectively. Species specific nested multiplex PCR was able to detect S. pneumoniae (n = 7), N. meningitidis (n = 2) and H. influenzae (n = 1). CONCLUSIONS: The results indicates that nested PCR targeting 16S rRNA gene may be used in diagnosis of ABM. Further, nested multiplex PCR targeting the three important fastidious bacterial pathogens in ABM cases has showed their presence in our region.

CONTEXT: Rapid diagnosis and detection of Rifampicin (RIF) resistance are essential for effective disease management of tuberculosis (TB). Cartridge-based nucleic acid amplification test also known as GeneXpert Mycobacterium tuberculosis (MTB)/RIF assay is a novel integrated diagnostic system for the diagnosis of TB and rapid detection of RIF resistance in clinical specimens. AIM: In the present study, we determine the performance of the MTB/RIF assay for the rapid diagnosis of TB and detection of RIF resistance in pulmonary specimens obtained from presumptive multidrug-resistant (MDR) TB cases. SUBJECTS AND METHODS: This is a cross-sectional observational study conducted in culture and drug-susceptibility testing laboratory between January 2014 and December 2014. A total of 1994 sputum samples were obtained from presumptive MDR-TB cases of Dharwad and Belgaum districts of Karnataka. All samples were tested on GeneXpert for MTB/RIF detection. RESULTS: A total of 1994 presumptive pulmonary TB clinical samples were received of which 840 (42.1%) were MTB complex (MTBC) positive and 1154 (57.9%) were negative. The MTB/RIF assay also detected 127 (6.4%) RIF-resistant specimen and 713 (35.6%) RIF-susceptible specimens. CONCLUSIONS: The MTB/RIF test is a simple and rapid method, and staff with adequate training can perform this test with minimal laboratory setup. It helps to avoid the injudicious use of the anti-TB drug and offers high potential for the diagnosis of TB and RIF resistance due to its capacity for direct detection of MTBC, its rapidity and its simplicity.

INTRODUCTION: Urinary tract infections (UTIs) are among the most common bacterial infections. Escherichia coli remains the most frequent cause of UTIs. More important is the increase in resistance to some antimicrobial agents. Furthermore, bacterial species are capable of living in a biofilm. There is increasing evidence for the role of bacterial biofilm in causing recurrent UTIs. AIM: The present study aimed to evaluate the ability of E. coli, isolated from UTIs to form a biofilm, and its association with catheterisation and to correlate the role of biofilms with their antimicrobial resistance. MATERIALS AND METHODS: A total of 403 urine samples were processed. All the isolated E. coli strains (226) were grown in Luria broth and were incubated overnight in high-glucose Dulbecco's modified Eagle's medium using a microtitre plate. The plate was stained with crystal violet, and the biofilm was quantified using an enzyme-linked immunosorbent assay plate reader at 570 nm. An optical density value more than that of the mean negative control plus three standard deviations is taken as positive for biofilm production. The antibiogram was done using the Kirby–Bauer disk diffusion method. RESULTS AND DISCUSSION: Of 226 strains, 54.4% were found to produce biofilms. Of them, 81.3% of patients were catheterised. Most of them were found to be resistant to commonly used antibiotics such as Cephalosporins, Quinolones and Aminoglycosides. Imipenem and Nitrofurantoin are the most effective antibacterial agents, showing 77.3% and 73.2% sensitivity, respectively. CONCLUSION: The biofilm assay using a microtitre plate is convenient and useful in screening the biofilm producers. Catheterisation is a risk factor for biofilm production, and catheter care is of paramount importance to prevent catheter-associated UTI.

CONTEXT: Rapid detection of pathogens in infected body fluids will help in establishing an aetiological diagnosis, thereby facilitating specific therapy. Molecular methods have an advantage over conventional bacteriological techniques in particularly identifying slow-growing, fastidious or non-cultivable organisms. AIM: The aim of this study is to evaluate the use of 16S rRNA polymerase chain reaction (PCR) for detecting bacterial pathogens in body fluids and compare with conventional culture methods. SETTINGS AND DESIGN: This study was done at the Clinical Laboratory of the Department of Microbiology. This was a cross-sectional study design. MATERIALS AND METHODS: A total of 100 consecutive samples which included synovial fluid, cerebrospinal fluid, ascitic fluid and pleural fluid received in the laboratory during the study period were subjected to PCR for 16S rRNA using specific primers and conventional culture by standard protocol. Samples which were positive for 16S rRNA were sequenced to identify the organism. Results of sequenced products were compared in terms of number of organisms, with culture isolates. RESULTS: The detection rate of 16S rRNA PCR was at 13% as compared to culture at 3% (P = 0.0009). The diagnostic sensitivity and specificity of the PCR were 100% and 89.7%, respectively. The concordance of PCR and culture for both identical positive and negative samples was 90%. CONCLUSIONS: The 16S rRNA PCR proved to be rapid method for detection of bacterial pathogens in body fluids. It may be a valuable tool in the diagnostic armamentarium for differentiating bacterial infection from others and starting empiric treatment.

This case series proposes to describe the clinical features and laboratory findings associated with fungal infective endocarditis (FIE) encountered in this tertiary care referral centre for cardiology. All cases of FIE, proved by culture of blood or tissue samples for a period of 10 years from June 2007 to June 2017 were included. Retrospective data on patients, whose blood culture grew fungi, mould or yeast, were collected from the medical records section and analysed. A total of 276 cases of IE occurred, in this period and 14 cases (5.07%) of culture-positive FIE occurred. Prosthetic valves (11 cases) were more common than native valves (3). There were eight Candida parapsilosis and all except two were from prosthetic valve which included both metallic (5) and bio-prosthetic valve (1). Other candida spp. included one Candida albicans isolated from bio-prosthetic valve, one Candida haemolunii isolated from bio-prosthetic valve and one Candida pelliculosa isolated from a native aortic valve, detected during surgery for ventricular septal defect closure. There were two mould fungi, namely Wangiella dermatitidis and Aspergillus niger. Out of 14 cases, 10 vegetations were more than 10 mm in size. In 9/14 patients, C-reactive protein (CRP) was greater than100 units when done at admission. One C.parapsilosis was resistant to fluconazole and voriconazole, while another was resistant to fluconazole and amphotericin B. Embolisation to brain and peripheral areas was the most common complication. Surgical excision was successful in three cases, while medical treatment was successful only in one case. Though culture negativity was achieved with drugs, embolisation was the most common cause of death even after culture became negative. In conclusion, FIE is a rare cause of endocarditis. It occurs more commonly in prosthetic valves. Most common aetiological agent in this series was C.parapsilosis. Among prognostic factors, CRP showed a very consistent increase. Surgical excision was curative and embolisation to the brain was the most common cause of death. A multicentre study will be needed to study prognostic factors and risk factors for mortality and to find the best combination of antifungals for treatment.

Diarrhoeal illness is manifested as watery diarrhoea or loose stool and mucus with or without blood. Campylobacter spp. act as one of the important bacterial causes of diarrhoea in children. Awareness about the presence of these organisms is scant in Thrissur region of Kerala, India. Hence, we herein present a case of campylobacter diarrhoea in an infant that was preliminarily identified by Gram stain examination of stool sample and further confirmed by culture and multiplex polymerase chain reaction.

Vancomycin-resistant Enterococci have become one of the most challenging nosocomial pathogens with limited therapeutic options. We report three cases of Vancomycin-resistant Enterococcus faecium isolated from urine, perinephric collection and blood of paediatric patients over a period of one year from June 2015–2016 in a tertiary care centre in South Kerala.

Low-temperature sterilisation basically depends on four types of sterilisation systems, i.e. gamma irradiation, Ethylene oxide sterilisation, Hydrogen peroxide (H₂O₂) and steam Formaldehyde sterilisation. The article has been described on the basis of these low-temperature sterilisation systems with their infrastructural ease, regulatory requirements, cycle time, sterilisation efficacy, safety features and cost. In our experience, the H₂O₂-based sterilisation system is superior over the other methods due to its easy installation and cycle time that helps to perform more procedure in a day and reduces infection by providing terminal sterilisation (ready-to-use) processes. Besides due to the short cycle time of the H₂O₂ steriliser, it requires fewer inventories and saves cost to the management in the long run.

Achromobacter xylosoxidans is a rare pathogen in clinical settings. Infections are reported infrequently in immunocompromised neonates. We report a case of late-onset sepsis in a 28-day-old neonate whose cerebrospinal fluid and blood culture grew A. xylosoxidans

Shewanella are Gram-negative non-fermentative oxidase-positive saprophytic bacteria producing H2S. Although rarely associated with infection, they are seldom associated with skin and soft-tissue infections, abscesses, wound infection, osteomyelitis, intracranial infections, peritonitis, neonatal infections and outbreak infections. A 24-year-old male presented with open wound over the dorsum of the right foot with exposed muscles and tendons five days following a road traffic accident (RTA) with pus discharge. X-ray of the right foot showed fracture third metatarsal. Wound swab culture showed the growth of Shewanella algae and Escherichia coli. S. algae was susceptible to Amikacin, Cefotaxime, Ceftazidime and Imipenem and resistant to Ciprofloxacin. The patient was treated with injection Amikacin, regular dressings, limb elevation and analgesics for 10 days. Tissue specimen from the wound was sent for culture after 10 days and was negative for bacterial growth. Open reduction and internal fixation with axial K-wire with plates and screw and split skin rafting was done. The patient responded well to the treatment, and follow-up was uneventful. In the present case, there was no history of contact with marine environment, and infection developed following RTA wound. Although S. algae is rarely isolated, clinicians must be aware of rare pathogens. The present case highlights the importance of Shewanella spp. as a potential emerging infectious agent.

CONTEXT: Because of limited exposure to the vast field of microbiology in the undergraduate time, a notion is generated among young doctors that microbiology only deals with laboratory diagnosis and teaching. When a young medical graduate enrols him/herself to microbiology and see the vastness of the subject and shrinkage of known job prospects, a sense of uncertainty and scepticism about the future creeps into the students mind. It has become a role of a postgraduate teacher to act as a mentor in such moment of crisis. AIM: The present article is aimed to explore the job prospect of a medical microbiologist in various fields, namely hospital setup, laboratory practice, research, corporate world, further studies and also to discuss the job profile, the challenges and future prospectus in each field. CONCLUSIONS: Now, microbiology has evolved beyond a subject encaged in laboratory and teaching or research; in its current form, it has an immense role in patient care and treatment and it has a great market value in the corporate field.