Inconclusive SARS CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) reports for the detection of infection in symptomatic patients or during screening of asymptomatic contacts can cause clinical, diagnostic and infection control uncertainty. It has been noted that up to 5% of COVID RT-PCR reports may be inconclusive. The reasons for these inconclusive reports are varied and may be classified into virological causes, sample collection and sample quality-related issues and finally technical issues related primarily due to problems in RNA extraction. The objective of this article is to discuss these causes and suggest corrective measures.

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BACKGROUND: Non-tuberculous mycobacteria (NTM) may cause pulmonary disease that resembles tuberculosis (TB) and it may also coexist with Mycobacterium tuberculosis. Here, we aimed to study the occurrence and diversity of NTM among suspected and confirmed cases of TB. METHODS: During 2017–2018, we received 11,094 sputum samples, of which 4288 samples were from equal number of presumptive TB patients. The rest of 6866 samples were from known multidrug-resistant TB patients and at different months of treatment follow-up. All samples were subjected to liquid culture and recovered isolates were identified as M. tuberculosis complex (MTBC) or NTM based on microscopy and immunochromatograhic (MPT-64Ag) tests. NTM isolates were further speciated using commercial GenoType^® Mycobacterium CM assay. RESULTS: A total of 2782 culture isolates were recovered, of which 2722 were MTBC and the rest 60 were considered as NTM. NTM was isolated both from presumptive and confirmed TB cases. NTM speciation could be achieved for 42 isolates; Mycobacterium intracellulare (50%) was identified as the most prevalent species, followed by Mycobacterium abscessus (23.8%), Mycobacterium fortuitum (16.7%) and others (9.5%). CONCLUSION: The proportion of NTM isolation among suspected/confirmed cases of pulmonary TB is low; however, if isolated, patients should be carefully evaluated for possible NTM disease. Molecular speciation of NTM is useful to provide rapid and precise diagnosis.

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BACKGROUND: Coliforms and other bacterial indicators are known to be present in Community water samples causing faecal pollution of water. There is also a growing body of evidence demonstrating that the aquatic environmental microbes are drug resistant. OBJECTIVE: The objective of this study was to evaluate the microbial quality of the water from tap, well and pond in urban households of Kochi, Kerala state. MATERIALS AND METHODS: A total of 100 water samples (46 from well water, 45 from tap water and 9 from lakes and ponds) were analysed by the multiple fermentation tube method to determine the presumptive coliform count or the most probable number (MPN) of coliforms, and the isolates were identified using standard procedures, followed by susceptibility testing. RESULTS: Eighty samples were positive for growth (76 grew coliforms, four samples grew non-pathogens). A total of 105 coliform isolates were grown in culture. The MPN numbers were noted to be >100 for over 50% of all the samples (n = 56), thus making the water unsatisfactory for drinking purposes. The highest number of organism isolated was Klebsiella pneumonia (n = 55), followed by Enterobacter spp (n = 34) and Escherichia coli (n = 16). Well water had the highest proportion of all three of these organisms. Up to 26%–40% resistance was seen to amoxicillin–clavulanic acid and 5.4%–5.8% of resistance was noted to third-generation cephalosporins, while two isolates were extended-spectrum beta-lactamase-producing Enterobacteriaceae (CTX-M and TEM types). CONCLUSION: The city municipal water authorities need to adopt more aggressive treatment/disinfection practices to combat high coliform contamination. The bacteriological quality of well water at the source needs to be monitored. Meanwhile, continued adequate home purification is suggested for drinking water. The city water does not pose a threat of antibiotic resistance for now. Environmental sampling should be given equal priority as clinical sampling in the coming days.

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CONTEXT: Viral hepatitis has become the most common viral infections encountered in dialysis patients. Patients undergoing haemodialysis (HD) have a significantly increased risk of exposure to hepatitis B, hepatitis C, HIV and other blood-borne viruses. Hepatitis B virus (HBV) and hepatitis C virus (HCV) infections are the most important causes of morbidity and mortality among HD patients. Patients on routine maintenance HD fail to maintain protective titres against HBV that further poses the risk of developing viral hepatitis. In this study, we are studying the prevalence of HBV and HCV infection among patients undergoing maintenance HD. SETTING AND DESIGN: This was a cross-sectional study. METHODS: This study aims to detect and compare the seroprevalence of HBV and HCV infection among chronic HD patients. This study was conducted from July 2015 to January 2017. All patients (n = 150) of various age groups admitted during the study period for maintenance HD at our tertiary care hospital were included. Viral markers were detected using third-generation enzyme-linked immunosorbent assay kits available commercially. STATISTICAL ANALYSIS USED: Statistical analysis was done with the help of statistical package for SPSS. RESULTS: Out of 150 patients recruited into the study, 7 (4%) were positive for hepatitis B surface antigen and 29 (19.33%) were positive for HCV. One (0.67%) patient was found positive for both HBV and HCV infections. In this study, the duration of dialysis was significantly correlated with seropositivity for both HCV and HBV (P ≤ 0.0001). The number of blood units transfused was also found to be significantly associated with seropositivity (P ≤ 0.0001). CONCLUSIONS: The prevalence of HCV is more common compared to HBV infection in HD patients. Seropositivity significantly correlates with duration of dialysis. The number of blood units transfused is also significantly associated with seropositivity.

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Non-typhoidal Salmonella are important food-borne pathogens that are associated with gastroenteritis, bacteraemia and focal infections. Salmonella enterica subspecies enterica serovar bareilly has been implicated in gastroenteritis and nosocomial infections. There are not much literature available on the hepatobiliary involvement by S. bareilly. We report a case of acute pancreatitis with pseudocyst. S. bareilly was isolated from blood and pseudocyst aspirate.

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Chromobacterium violaceum is a Gram-negative, facultative anaerobe. It is a common inhabitant of soil and water. It causes localised skin infection or localised lymphadenitis following contact with stagnant water or soil and then progresses to fulminant septicaemia with necrotising metastatic lesions. A three day-old girl presented with fever and multiple abscesses all over her body. On blood culture, C. violaceum was isolated. She had a history of consumption of holy water three days after birth. She was treated with Piperacillin-Tazobactam, Amikacin and Ciprofloxacin.

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INTRODUCTION: Clostridioides difficile infection (CDI) is one of the hospital-acquired infections and the most common cause for antibiotic-associated diarrhoea. Documentation of CDI is difficult, and interpretation of diagnostic results often requires consultation with clinical microbiologists. The purpose of this study was to compare the results of the combination of glutamate dehydrogenase enzyme (GDH) and toxin assay with the polymerase chain reaction (PCR) results, in order to find if the combination could substitute for the expensive molecular tests. MATERIALS AND METHODS: The sample size was statistically calculated to be 30, using an SPSS software. Both GDH and toxin assay were simultaneously tested in all the randomly selected stool samples, by simple random sampling, and irrespective of the results, they were also tested for tcdB gene by PCR in the present study. All the samples were also plated onto Brazier's C. difficile agar and incubated anaerobically. RESULTS: The sensitivity and specificity of GDH (using PCR as gold standard) were found to be 100% and 76.47%, respectively, and the sensitivity and specificity of toxin enzyme immunoassay (EIA) assay (using PCR as gold standard) were found to be 66.67% and 92.86%, respectively. However, when the toxin-equivocal results were also considered as positive, the sensitivity of toxin EIA was found to be 100%. The overall agreeability, using Cohen's Kappa statistic between GDH and toxin detection by enzyme-linked fluorescence assay, showed that they had moderate and substantial agreement, respectively, when compared to PCR. CONCLUSIONS: In this study, each of the toxin negatives and positives was also PCR negative and positive, respectively. All the toxin-equivocal samples tested positive on PCR, so it is our conclusion that in the settings where they cannot be taken for further molecular testing, those samples be considered as harbouring toxigenic C. difficile.

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Scrub typhus, a potentially fatal rickettsial infection, is common in India. As the clinical features include fever, vomiting, headache, respiratory infection and rashes the differential diagnosis includes Enteric fever, Dengue, Leptospirosis and Malaria. Though many methods are available for diagnosis, IgM ELISA is the most sensitive method. A prospective study was carried out at the Sree Gokulam Medical College Thiruvananthapuram from January 2019 to December 31 2019. A total of 178 samples were screened for scrub typhus. Commercially available IgM ELISA was used. Out of 178 samples 28 samples were positive for scrub typhus(15.7%). 20-40 years age groups showed maximum number of cases and cases were more from June to September. Males were more commonly affected (57%). Scrub typhus is considered one of the important differential diagnoses of pyrexia of unknown origin in this area.

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Surgical site infection is the second most common nosocomial infection in healthcare facilities. Open-heart surgery is a clean surgery, and sternal wound infection after open-heart surgery has a great impact on the patient both psychologically and financially. Sternal wound infections are preventable infections if stringent infection control practices are followed. Sternal wound infection after cardiac surgery due to Nocardia is very rare. Nocardia species are aerobic actinomycetes ubiquitously found in soil and aquatic habitats. Nocardia are beaded Gram-positive, branching rods that are partially acid fast. We report two cases of post-operative sternal wound infection caused by Nocardia.

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Arcanobacterium haemolyticum is a well-recognised cause of pharyngitis and skin and soft-tissue infections. It is often under-reported in microbiology laboratories probably because diphtheroids are commonly considered as colonizers or contaminants in bacterial cultures. A. haemolyticum usually cause infections in immunocompromised patients. Here, we present a case of septic arthritis in an immunocompetent individual. The purpose of this case report is to create increased awareness of the pathogenic potential of this organism in bone and joint infections.

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OBJECTIVE: The objective was to study anti-tubercular drug susceptibility level among 'newly diagnosed' pulmonary tuberculosis (TB) cases by two methods of drug sensitivity testing i.e., standard proportion method (SPM) and BACTEC radiometric method. MATERIALS AND METHODS: Sputum samples from fifty new cases of pulmonary TB were cultured and subjected to antitubercular drug susceptibility testing by using conventional SPM and radiometric method (BACTEC 460 TB system) and compared. RESULTS: Monoresistance was found to be 2%, 8%, 0% and 2% for Streptomycin (S), Isoniazid (H), Rifampicin® and Ethambutol (E), respectively. Any resistance (with or without resistance to other drugs) was 4%, 28%, 10% and 16% for S, H, R and E, respectively. Primary multidrug resistance was 10% (5/50) namely H + R, 6% (3/50); H + R + E, 2% (1/50); H + R + S, 0% (0/50) and H + R + E + S, 2% (1/50). H + E resistance was found in 10% (5/50) of isolates. CONCLUSION: Comparing with other studies, the levels of H, R and multi drug resistance (MDR) were within the expected levels in our study. However, more number of similar studies on drug resistance need to be undertaken regularly to assess the changing trends.

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