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  ~ Table of Contents - Current issue
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April-June 2019
Volume 37 | Issue 2
Page Nos. 133-297

Online since Tuesday, November 19, 2019

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EDITORIAL  

Metagenomic next-generation sequencing in clinical microbiology Highly accessed article p. 133
Jobin John Jacob, Balaji Veeraraghavan, Karthick Vasudevan
DOI:10.4103/ijmm.IJMM_19_401  
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SPECIAL ARTICLES Top

Pneumococcal conjugate vaccine rollout in India: Expectations and challenges p. 141
Rosemol Varghese, Balaji Veeraraghavan, Yuvraj Jeyaraman, Girish Kumar, Narendra Kumar Arora, S Balasubramanian
DOI:10.4103/ijmm.IJMM_19_320  
India is one among the four Asian countries with the greatest number of deaths due to pneumococcal infection among children under 5 years. pneumococcal conjugate vaccine (PCV) has been introduced in a phased manner in five major Indian states. Ambiguity remains in choosing the appropriate type of PCV and optimum schedule with maximum effectiveness specific for each country. Here, we discuss the evidences with respect to serotype coverage, immunogenicity, reactogenicity and dosage schedule for introduction of PCV13 in India. In addition, the expected PCV impact and the challenges are detailed. PCV13 is expected to provide >75% serotype coverage for invasive pneumococcal disease (IPD) serotypes in Indian children combined with the replacement by nonvaccine serotypes which is unpredictable due to lack of complete data. Nasopharyngeal (NP) surveillance is easy, feasible and can replace IPD surveillance in resource-poor settings. Continuous IPD as well as NP surveillance in all the regions are necessary to assess the impact of PCV in India.
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Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens p. 147
Dhiviya Prabaa Muthuirulandi Sethuvel, Naveen Kumar Devanga Ragupathi, Yamuna Devi Bakthavatchalam, Saranya Vijayakumar, Rosemol Varghese, Chaitra Shankar, Jobin John Jacob, Karthick Vasudevan, Divyaa Elangovan, Veeraraghavan Balaji
DOI:10.4103/ijmm.IJMM_19_396  
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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ORIGINAL ARTICLES Top

Experience of Indian association of medical microbiology external quality assurance scheme centre, New Delhi: Challenges and quality assessment of clinical microbiology laboratories p. 163
Chand Wattal, Jaswinder Kaur Oberoi, Neeraj Goel, Sanghamitra Datta, Reena Raveendran, KJ Prasad
DOI:10.4103/ijmm.IJMM_19_356  
Introduction: EQAS program at New Delhi under IAMM was started in January 2014 across North and North east regions of India with 217 participants, which grew up to 540 by 2018. Materials and Methods: In 2014, 4 analytes per year were sent for 3 exercises, i.e. smear culture and serology. 2018 onwards PT analytes were increased from 4 to 12 and comparative performance of techniques analysed. Results: Out of the 22 smears sent for gram staining, ZN staining, Kinyoun staining and Albert staining, completely correct results ranged between 29.55% - 79.9%, 94.3% - 99.2%, 35.5% & 93.8%, respectively. Correct results for culture isolate identification & susceptibility testing and serology exercises varied between 70 & 92.4% and 73.1 & 98.59%, respectively. In the year 2018, 470 responses were received for bacterial culture identification & antibiotic susceptibility testing out of which manual and automated systems were used by 54% & 46% and 52.5% & 47.5% participants, respectively. Techniques used in BBV assays for HBsAg, HCV & HIV found all methods like ELISA, ELFA, CLIA and Card Test performing similarly. The major challenges in running the EQA program included requirement of large amount of specimens for PT item preparation, stability in hot and humid conditions and timely delivery of PT challenges in remote parts of the country. Conclusion: A large number of the participating laboratories (77%) had an overall score of >80% for all exercises, demonstrating acceptable baseline performance of EQAS registered laboratories. However, continued EQAS participation could further improve the quality of results.
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RNA-seq analysis reveals resistome genes and signalling pathway associated with vancomycin-intermediate Staphylococcus aureus p. 173
Devika Subramanian, Jeyakumar Natarajan
DOI:10.4103/ijmm.IJMM_18_311  
Context: Vancomycin-intermediate Staphylococcus aureus remains one of the most prevalent multidrug-resistant pathogens causing healthcare infections that are difficult to treat. Aims: This study uses a comprehensive computational analysis to systematically investigate various gene expression profiles of resistant and sensitive S. aureus strains on exposure to antibiotics. Settings and Design: The transcriptional changes leading to the development of multiple antibiotic resistance were examined by an integrative analysis of nine differential expression experiments under selected conditions of vancomycin-intermediate and -sensitive strains for four different antibiotics using publicly available RNA-Seq datasets. Materials and Methods: For each antibiotic, three experimental conditions for expression analysis were selected to identify those genes that are particularly involved in the development of resistance. The results were further scrutinised to generate a resistome that can be analysed for their role in the development or adaptation to antibiotic resistance. Results: The 99 genes in the resistome are then compiled to create a multiple drug resistome of 25 known and novel genes identified to play a part in antibiotic resistance. The inclusion of agr genes and associated virulence factors in the identified resistome supports the role of agr quorum sensing system in multiple drug resistance. In addition, enrichment analysis also identified the kyoto encyclopedia of genes and genomes (KEGG) pathways – quorum sensing and two-component system pathways – in the resistome gene set. Conclusion: Further studies on understanding the role of the identified molecular targets such as SAA6008_00181, SAA6008_01127, agrA, agrC and coa in adapting to the pressure of antibiotics at sub-inhibitory concentrations can help in learning the molecular mechanisms causing resistance to the pathogens as well as finding other potential therapeutics.
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Clinico-microbiological analysis of toxigenic clostridium difficile from hospitalised patients in a tertiary care hospital, Mangalore, Karnataka, India p. 186
Sherin Justin, Beena Antony
DOI:10.4103/ijmm.IJMM_17_357  
Purpose: Prevalence of Clostridium difficile, an anaerobic, Gram-positive, spore-forming bacillus, is very much underestimated in India. The present study was intended to assess the burden of toxigenic C. difficile in hospitalised patients with clinically significant diarrhoea and analysis of their clinical picture. Materials and Methods: This cross-sectional study was conducted in a tertiary care teaching hospital, South India, from January 2012 to December 2014. Stool samples were collected consecutively from 563 inpatients from various wards. The prevalence of toxigenic C. difficile was determined by toxigenic culture and a two-step algorithm. The clinical spectrum of these patients was also analysed. Associated pathogens were identified using standard procedures. Statistical analysis was done by frequency, percentage, Chi-square test and z-test. Results: Out of the 563 stool samples analysed, the prevalence of toxigenic C. difficile was 12.79% and that of non-toxigenic C. difficile was 10.83%. The prevalence of toxigenic C. difficile among oncology patients was highly significant (HS). Antibiotic treatment, prolonged hospital stay and underlying diseases/conditions were the risk factors which were HS, and fever was the significant clinical feature among the patients. Escherichia coli was the predominant associated pathogen isolated (18.47%). Conclusion: The presence of toxigenic C. difficile in our locality is a matter of concern. Constant supervision, appropriate treatment and preventive measures are crucial in controlling C. difficile infection.
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Assessment of efficacy of palm polymerase chain reaction with microscopy, rapid diagnostic test and conventional polymerase chain reaction for diagnosis of malaria p. 192
Paras Mahale, Rajas Warke, Mira Ramaiya, Deepa Balasubramanian, Suvin Shetty, Ranjit Mankeshwar, Abhay Chowdhary
DOI:10.4103/ijmm.IJMM_19_169  
Purpose: Sensitive, specific, rapid and cost-effective technique for malaria diagnosis is need of the hour. Microscopy has been the gold standard for malaria diagnosis, but its interpersonnel variability and lack of sensitivity make it subjective test. Conventional polymerase chain reaction (cPCR) has proven to be sensitive technique, but costly and time-consuming. Considering these factors, we have compared microscopy and cPCR with newly derives ultra-fast, portable PCR machine called Palm PCR. Materials and Methods: Palm PCR is arranged with three heat blocks precisely made for three stages of PCR cycles with 34 min for 1100 bp Plasmodium genus outer primer to amplify and 10 min each for Plasmodium falciparum and Plasmodium vivax inner primers of 120 bp and 205 bp, respectively. A total of 191 suspected samples were processed and evaluated using receiver operating characteristic (ROC) curve analysis. Results: The area under ROC curve analysis for Palm PCR with reference standard microscopy for P. falciparum, P. vivax and Plasmodium was 0.8969, 0.9121 and 0.9116, respectively, and with reference standard cPCR was 1.0 for all of them. ROC curve area close of suggests that Palm PCR can be as significant as cPCR in malaria diagnosis. In fact, ultra-rapid amplification with same precision makes Palm PCR better technique than cPCR. Conclusion: Palm PCR is sensitive, rapid and works on battery with simple laboratory facility requirements. Portable electrophoresis and transilluminator combined with Palm PCR could be implemented as an important diagnostic tool in resource-limited and rural areas. Similar studies with wider parameters in rural areas will help us evaluate and maybe establish Palm PCR as PCR platform of choice for such specific set-ups.
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An emerging threat of ceftriaxone-resistant non-typhoidal salmonella in South India: Incidence and molecular profile p. 198
Agila Kumari Pragasam, Shalini Anandan, James John, Ayyanraj Neeravi, Vignesh Narasimman, Dhiviya Prabaa Muthuirulandi Sethuvel, Divyaa Elangovan, Balaji Veeraraghavan
DOI:10.4103/ijmm.IJMM_19_300  
Background: Non-typhoidal Salmonella (NTS) infection is a serious public health problem globally. Although NTS infections are self-limited, antimicrobial therapy is recommended for severe infections and immunocompromised patients. Antimicrobial resistance (AMR) in these pathogens further limits its therapeutic options. Here, we report an incidence of ceftriaxone resistance in NTS over the past 9 years in a southern Indian region. Materials and Methods: Molecular mechanisms of resistance in ceftriaxone-resistant NTS have been tested by both phenotypic and molecular methods. Minimum inhibitory concentration was determined by the E-test and broth microdilution method. AMR gene markers of β-lactamases such as AmpCs (blaMOX, blaCMY, blaDHA, blaFOX, blaACC and blaACT) and extended-spectrum β-lactamases (ESBLs) (blaSHV, blaTEM, blaVEB, blaPER, blaCTXM-1like,blaCTXM-2like, blaCTXM-8like, blaCTXM-9like and blaCTXM-25like) were screened. The presence of IncH12 and IncI1 plasmid was also analysed. Results: The study reports a 5% prevalence of ceftriaxone resistance in NTS. The most common serogroup was Salmonella Group B followed by Salmonella Group E and Salmonella group C1/C2. The occurrence of blaCTX-M-1, blaTEM, blaCMY and blaSHV genes was observed in 54%, 54%, 48% and 3% of the isolates, respectively. Interestingly, few isolates carried dual resistance genes (ESBLs and AmpCs). IncH12 and IncI1 plasmid was identified in isolates carrying ESBL and AmpC genes, respectively. Conclusion: This study shows that ceftriaxone resistance is mainly mediated by β-lactamases such as ESBL and AmpC. As the incidence of ceftriaxone resistance is rising gradually over the years, it is imperative to monitor the AMR in this species.
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Review of a 7-year record of the bacteriological profile of airway secretions of children with cystic fibrosis in North India p. 203
Vikas Gautam, Parinitha Kaza, Joseph L Mathew, Varpreet Kaur, Megha Sharma, Pallab Ray
DOI:10.4103/ijmm.IJMM_18_424  
Background: Cystic fibrosis (CF) is now a recognised entity in India, with prevalence rates between 1/10,000 and 1/50,000. However, no data were available with regard to the profile of respiratory pathogens in the Indian setting. Materials and Methods: The records of respiratory secretion bacterial cultures of children with CF in a tertiary care hospital in North India from January 2010 to December 2016 were reviewed. Culture data were evaluated; the organisms were noted and their antimicrobial susceptibilities were analysed. The microbiological profile and antimicrobial susceptibility pattern of CF patients were evaluated. Results: A total of 445 samples from 146 children were processed, of which 246 (55%) samples showed bacterial growth. Mixed infections 48 (19.5%) were common in older children. Children aged 3–6 months (62.5%) showed the highest culture positivity. The most commonly isolated organisms were Pseudomonas aeruginosa (52.6%) and Staphylococcus aureus. Children with initial cultures positive for P. aeruginosa had 55% of their subsequent cultures showing polymicrobial infections. P. aeruginosa was most susceptible to ciprofloxacin (89%) and piperacillin-tazobactum (88%). Among the staphylococcal isolates, 38% were methicillin-resistant S. aureus (MRSA). The percentage of MRSA increased from 66% in 2010 to 75% in 2012, followed by a decline to 24% in 2016. Conclusions: The pattern of airway colonisation in the Indian setting is different from the Caucasian population, and P. aeruginosa and Burkholderia cepacia complex appear early. Colonisation with P. aeruginosa benefits from therapy. In case of infection, care must be taken while initiating empiric therapy. It should be based on local antibiograms to prevent the emergence of resistant microbes.
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Characterisation of virulence genes associated with pathogenicity in Klebsiella pneumoniae p. 210
PA Remya, M Shanthi, Uma Sekar
DOI:10.4103/ijmm.IJMM_19_157  
Purpose: This study was undertaken to characterise the virulence factors in clinical strains of Klebsiella pneumoniae and analyse their association with various infections caused and also to determine the association between virulence factors and antimicrobial resistance profile. Materials and Methods: A total number of 370 clinically significant, non-duplicate isolates of K. pneumoniae isolated from both hospitalised patients and patients attending clinics were included in this study. Polymerase chain reaction (PCR) was carried out for the detection of various virulence genes such as mucoviscosity-associated gene A (magA), gene associated with allantoin metabolism (allS), Klebsiella ferric iron uptake(Kfu), capsule-associated gene A (K2A), regulator of mucoid phenotype A (rmpA), enterobactin (entB), yersiniabactin (YbtS), aerobactin, Fimbrial adhesin (FimH) and uridine-diphosphate galacturonate 4-epimerase (uge). Antimicrobial susceptibility testing and PCR-based detection of beta-lactamase-encoding genes such as extended-spectrum beta-lactamases, AmpCs and carbapenemases were performed. Univariate analysis was done to find the association between virulence genes and mortality. Results: The siderophore, entB, was present in most (90.5%) of the isolates. Of the 370 isolates, 345 carried multiple virulence genes; 15 harboured single virulence genes and 10 did not harbour any of the studied virulence genes. The most common combination of occurrence was entB and FimH. A mortality rate of 12.75% (38/298) was observed among hospitalised patients. None of the virulence genes had any significant association with mortality. Conclusion: Pathogenic K. pneumoniae can harbour single to multiple virulence genes. Invasive infection with even a single virulence gene-harbouring K. pneumoniae can lead to poor outcomes. Both multidrug-resistant (MDR) and non-MDR K. pneumoniae can harbour a variety of virulence genes. None of the virulence genes have a significant association with mortality.
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Characteristics of treatment-naïve HBV-infected individuals with HIV-1 coinfection: A cross-sectional study from South India p. 219
John Paul Demosthenes, Jaiprasath Sachithanandham, Gnanadurai John Fletcher, Uday George Zachariah, George Mathew Varghese, Hubert Darius John Daniel, Lakshmanan Jeyaseelan, Priya Abraham, Rajesh Kannangai
DOI:10.4103/ijmm.IJMM_19_16  
Purpose: Human immunodeficiency virus-1 (HIV-1) and hepatitis B virus (HBV) coinfection has become a major health problem across the globe. The increased life expectancy of HIV-1 patients due to antiretroviral therapy has led to the emergence of liver disease as a major mortality factor among them. The purpose of the study was to examine the baseline characteristics of HBV in treatment-naïve HBV/HIV coinfection from southern India compared to monoinfected individuals. Materials and Methods: The study was cross sectional in design, and samples were examined from 80 HIV-1, 70 HBV and 35 HBV/HIV-coinfected individuals using chemiluminescent microparticle immunoassay, real-time polymerase chain reaction and flow cytometry assays. Results: There was a significant increase in HBV DNA (P = 0.0001), higher hepatitis B e antigen percentage difference (P = 0.027) and lower CD4 counts (P = 0.01) among the HBV/HIV-coinfected individuals, but no difference in the HIV-1 viral load compared to HIV-1-monoinfected individuals. Also, the aspartate aminotransferase levels, prothrombin time and the international normalised ratio were significantly high among coinfected individuals. Conclusion: These findings conclude that HIV-1 coinfection can have serious implications on the outcome of HBV-related liver disease. To the contrary, HBV infection had no consequence on the progression of HIV-1 disease but distinctly lowered CD4+ T-cells.
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The prevalence of anti-hepatitis C antibody among acute febrile illness cases in Idar Taluk, Gujarat, West India p. 225
Shekara Nikitha, Sasidharanpillai Sabeena, Sudandiradas Robin, Dodia Hiren, Varamballi Prasad, Sushama Aswathyraj, Santhosha Devadiga, Jayaram Anup, Govindakarnavar Arunkumar
DOI:10.4103/ijmm.IJMM_19_17  
Purpose: The major cause of chronic hepatitis is infections with hepatitis B virus and hepatitis C virus (HCV) globally. However, there exists sparse epidemiological data regarding the prevalence of HCV infection from India. Methodology: We carried out a cross-sectional study to estimate the prevalence of anti-HCV antibody among acute febrile illness cases aged between 1 and 65 years in Idar Taluk, Sabarkantha district, Gujarat state located in West India. A total of 702 serum samples collected from the study area during the year 2017, were screened for anti-hepatitis C IgG by enzyme-linked immunosorbent assay. The serum samples screened positive were then subjected to molecular testing for confirmation. Results: Among the 702 study participants screened, 16 cases were reported to be anti-HCV IgG positive with an estimated seroprevalence rate of 2.3% (95% confidence interval: 1.4%–3.7%). Out of the 16 cases, two samples were confirmed positive by molecular testing indicating active infection. When analysed phylogenetically, one strain was genotyped as HCV1b genotype, and the other one was clustered along with HCV3a genotype. Both the patients with hepatitis C infection were observed to be having a probable 1-year survival rate of 100% and a 2-year survival rate of 85% when the Child-Turcotte-Pugh classification was applied. Conclusion: The estimated seroprevalence of hepatitis C in Idar Taluk, Sabarkantha district, west India was 2.3%. HCV genotypes 1b and 3a were observed to be circulating in the study area.
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Infectious hepatitis: A 3-year retrospective study at a tertiary care hospital in India p. 230
Arghadip Samaddar, Shripad Taklikar, Pradnya Kale, Chaya A Kumar, Sujata Baveja
DOI:10.4103/ijmm.IJMM_19_197  
Context: Acute viral hepatitis (AVH) is predominantly caused by hepatitis A virus (HAV) and hepatitis E virus (HEV), the prevalence of which varies in different geographical regions. Aims: This study aimed to determine the prevalence of HAV and HEV infections in patients with AVH, the rate of HAV-HEV co-infection and the prevalence of HEV infection among pregnant women with hepatitis. Settings and Design: It was a retrospective observational study conducted over 3 years from January 2015 to December 2017, after obtaining clearance from the institutional ethics committee. Subjects and Methods: A total of 675 serum samples were collected from patients with a clinical diagnosis of AVH, between January 2015 and December 2017. The study population included outdoor and hospitalised patients between 3 and 70 years of age who presented with signs and symptoms of hepatitis. The presence of IgM anti-HAV and IgM anti-HEV antibodies in serum were assessed by enzyme-linked immunosorbent assay. Statistical Analysis Used: Chi-square test. Results: The prevalence of HAV, HEV and HAV-HEV co-infection was found to be 6.96%, 9.63% and 2.07%, respectively. Among males, this was 7.3%, 8.8% and 2.6%, respectively and in females 6.7%, 10.2% and 1.7%, respectively. However, these differences in the prevalence rates were of no statistical significance. The prevalence of HEV infection in pregnant women with hepatitis was 9.4%. HAV and HEV infections showed a seasonal trend with predominance during summer and rainy seasons (May to September). Conclusions: A higher seroprevalence of HEV as compared to HAV together with a co-infection rate of 2.07% mandates screening for HEV in all suspected cases of acute hepatitis, particularly pregnant women in whom the outcomes of HEV infection are poor. Health and civic authorities should make necessary efforts to counter epidemic or outbreak situations, thus reducing morbidity, mortality and economic burden.
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A descriptive study on prevalence pattern of Japanese encephalitis in State of Manipur p. 235
Leimapokpam Shivadutta Singh, Huidrom Lokhendro Singh, Natasha Thokchom, RK Manojkumar Singh
DOI:10.4103/ijmm.IJMM_18_180  
Background and Objective: Japanese encephalitis (JE) surveillance is not well established in many countries, and laboratory confirmation is challenging, the true extent and prevalence of the virus and burden of disease are not well understood. It is estimated that 67,900 clinical cases of JE occur annually despite the widespread availability of vaccine, with approximately 13,600–20,400 deaths and an overall incidence rate of 1.8/100,000 in the 24 countries with JE risk. The present study aimed at determining the prevalence rate (PR) and distribution (time, place and person) of JE cases in Manipur. This descriptive study was conducted over 24-month period (2016–2017). Materials and Methods: A total of 1770 cases of acute encephalitis syndrome tested for JE including 251 confirmed JE were diagnosed by IgM antibody-capture enzyme-linked immunosorbent assay. Results: The JE cases were most commonly reported in the age group of >15 years. Most of JE prevalence was seen in rural distribution in our study. There is a strong seasonal pattern of JE occurrence in Manipur which peaked in July–August and declined by October each year, which corresponds to the monsoon season. The JE cases were reported in all the districts of the state expanding in the plains and hill regions. Conclusions: The changing pattern of JE cases among different age groups was also observed in our study. The present study reveals the changing pattern of the prevalence of JE in the State of Manipur and initiated a systematic approach of JE surveillance also highlights the need for further expanding of surveillance across the state.
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Evaluation of loop-mediated isothermal amplification assay for detection and typing of human papilloma virus 16 and 18 from endocervical samples p. 241
Nagaraja Mudhigeti, Usha Kalawat, Narendra Hulikal, Meenakshi Kante
DOI:10.4103/ijmm.IJMM_19_58  
Background: Many human papillomavirus (HPV) types are associated with cervical cancer (CC). Therefore, HPV genotyping has both clinical and epidemiological importance. HPV 16 and 18 are two principal high-risk types responsible for more than 70% of all CC cases. Although several commercial and non-commercial genotyping assays are available, there is a need for a cost-effective and sensitive genotyping method for low- and middle-income countries. Methods: The study was aimed at evaluation of loop-mediated isothermal amplification (LAMP) assay for HPV genotyping in cervical samples. A total of six primer sets for each HPV type were selected for the assay. The LAMP assay was standardised and validated with HPV control panel. Cervical biopsies were subjected to nested multiplex polymerase chain reaction (NM-PCR; as a part of routine diagnostic workup) and LAMP (HPV 16 and 18) simultaneously. Results: A total of 225 clinical samples were processed during the study period. The sensitivity of the assay was determined using the 10-fold dilutions of positive controls. Both the HPV 16-LAMP and HPV 18-LAMP assays were shown to detect as low as 10 viral copies per reaction, which is similar to that of NM-PCR. The LAMP assay had a good agreement (new cases; 92%, post-chemoradiotherapy [post-CRT]; 89.1%) with NM-PCR for the detection of both HPV 16 and 18. As compared to histology (new cases; 79.8%, post-CRT; 51.3%), LAMP had better agreement with NM-PCR for detection of HPV from post-CRT cases. Conclusions: We evaluated the LAMP assay for simultaneous detection and typing of HPV 16 and 18. The assay had good agreement with NM-PCR for detection of both HPV 16 and 18. The LAMP assay is a promising tool for HPV genotyping along with routine cervical cytology, especially in resource-constrained settings.
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Genetic diversity of human respiratory syncytial virus in children with acute respiratory infections in Chennai, South India p. 248
Anusha Hindupur, Thangam Menon, Prabu Dhandapani
DOI:10.4103/ijmm.IJMM_19_193  
Introduction: Human respiratory syncytial virus (HRSV) an RNA virus belonging to Pneumoviridae family, is an important cause of acute respiratory infections (ARIs) in young children. HRSV circulates as two subgroups A and B, which are further categorised into several genotypes. New genotypes may replace existing ones over successive epidemic seasons and multiple genotypes may cocirculate in the same community rendering it important to monitor them at the molecular level. The present study assessed the circulating genotypes of HRSV in Chennai. Materials and Methods: Two hundred and sixty-seven children with ARI were recruited during the study from April 2016 to March 2018 for detecting HRSV A and B by real-time reverse transcription-polymerase chain reaction. Phylogeny and selection pressure analysis were done. Results: Fifty-seven of the 267 samples (21.3%) were positive for HRSV, of which 7.1% and 14.2% were HRSV A and B, respectively, indicating that HRSV B was the major subgroup circulating in Chennai. Peak activity of HRSV was observed during the monsoon and winter months. Phylogenetic analysis of 2nd hypervariable region (HVR) of attachment glycoprotein gene (G gene) revealed that the HRSV A strains belonged to ON1 and HRSV B strains belonged to BA9 genotypes. Several unique amino acid substitutions were observed among the study strains. The Shannon entropy plot revealed that the HRSV A strains from our study have a high potential for amino acid substitutions in the 2nd HVR of G gene. Conclusion: This study underlines the genetic diversity of HRSV and emphasises the need for continued molecular surveillance for infection management and prevention strategies.
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Predominance of high-risk human papillomavirus genotype 16 and 39 in women with premalignant and malignant cervical pathology from Raipur, Chhattisgarh: Clinical evaluation of tagging oligonucleotide cleavage and extension mediated genotyping assay p. 255
Sanjay Singh Negi, Anudita Bhargava, Priyanka Singh, Sarita Aggarwal, Nighat Hussain, Padma Das
DOI:10.4103/ijmm.IJMM_19_162  
Background: Identification of 14 high-risk human papillomavirus (HR-HPV) is immensely important in elucidating molecular epidemiology, patient monitoring and evidence-based treatment. There is paucity of such data from Chhattisgarh state of Central India. The present study has evaluated tagging oligonucleotide cleavage and extension-mediated Anyplex HR-HPV genotyping assay in identification of 14 HR-HPV genotypes attributable to premalignant and malignant cervical lesion in comparison to GP5+/6+ assay, cytology and colposcopy. Materials and Methods: A total of 185 clinically suspected cases of premalignant and malignant cervical lesion were investigated by HR-HPV genotyping, GP5+/6+, cytology and colposcopy. Results: Genotyping assay showed clinical sensitivity and specificity of 86.5% (confidence interval [CI]: 80.7–91.0) and 100% (CI: 86.3–100) respectively and found noninferior to GP5+/6+ assay (P > 0.05). HR-HPV prevalence was 76.3%, 88.4%, 94.8%, 100% and 100% among cervical intraepithelial neoplasia (CIN) Grade I–III, squamous cell carcinoma and adenocarcinoma cases, respectively. The four most common genotypes detected in CIN I–III were HPV 16 (63.9%), HPV 39 (15.0%), HPV 18 (6.0%) and HPV 33 (5.3%). In cervical cancer (CC) cases, HPV 16 (44.4%), HPV 39 (11.1%), dual infection of HPV 16, 18 (11.1%) and triple infection of HPV 16, 18, 33 (11.1%) were the four most identified genotypic aetiologies. A novel coinfection of HR-HPV 35, 39 were found in two and one cases of CIN I and II. Finding of HPV 39 as the second most prevalent genotype was unusual and underscores the importance of genotyping screening. Conclusion: Anyplex HR-HPV assay is arguably the useful assay for better patient management and can be useful for HR-HPV screening by its unique individual genotype identification of all HR-HPV. Finding of HPV 16, 39, 18, 33 and coinfection of 16,18 and 16, 18, 33 in CIN and CC would help vaccine manufacturer to design specific future HPV polyvalent vaccine preparation to curb down the CC-associated mortality.
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Ultrasound gel as a source of hospital outbreaks: Indian experience and literature review p. 263
Dhanalakshmi Solaimalai, Naveen Kumar Devanga Ragupathi, Kala Ranjini, Hema Paul, Valsan P Verghese, Joy Sarojini Michael, Balaji Veeraraghavan, Ebor Jacob James
DOI:10.4103/ijmm.IJMM_19_249  
Purpose: Hospital outbreaks are observed increasingly worldwide with various organisms from different sources such as contaminated ultrasound gel, intravenous (IV) fluids and IV medications. Among these, ultrasound gel is one of the most commonly reported sources for Burkholderia cepacia complex (Bcc) outbreaks. In this study, we describe our experience on investigation and the management of Bcc bacteraemia outbreak due to contaminated ultrasound gel from a tertiary care centre, South India. Materials and Methods: Over a 10-day period in October 2016, seven children in our Paediatric intensive care unit (ICU) were found to have bacteraemia with Bcc isolated from their blood culture. Repeated isolation of the same organism with similar antimicrobial susceptibility pattern over a short incubation period from the same location, confirmed the outbreak. An active outbreak investigation, including environmental surveillance, was carried out to find the source and control the outbreak. Isolates were subjected to multi-locus sequence typing (MLST) and global eBURST (goeBURST) analysis. Results: Environmental surveillance revealed contaminated ultrasound gel as the source of infection. MLST and goeBURST analysis confirmed that the outbreak was caused by a novel sequence type 1362 with the same clonal complex CC517. The outbreak was controlled by stringent infection control measures, withdrawal of contaminated ultrasound gel from regular usage and implementing the practice of using ultrasonogram (USG) probe cover for USG screening and guided procedures. Conclusion: This report highlights the importance of early identification of an outbreak, prompt response of the ICU and infection control teams, sound environmental and epidemiological surveillance methods to identify the source and stringent infection control measures to control the outbreak. Contaminated ultrasound gel can be a potential source for healthcare-associated infection, which cannot be overlooked.
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REVIEW ARTICLE Top

Gut microbiota and its mysteries Highly accessed article p. 268
Premalatha Pushpanathan, Gifty Sara Mathew, Sribal Selvarajan, Krishna G Seshadri, Padma Srikanth
DOI:10.4103/ijmm.IJMM_19_373  
Gut microbiota are microorganisms that inhabit the gut; they coexist peacefully with the host, thereby contributing to the health and well-being of individuals. Bacteroidetes and Firmicutes largely dominate the gut microbial flora. The intestinal flora promotes intestinal mucosal integrity, provides essential nutrients such as vitamins and enzymes, protects the body against pathogens and produces antimicrobial peptides such as defensins, C-type lectins, cathelicidins, they also play an active role in the innate and adaptive immune system. Gut microbial flora plays an active role in the synthesis of short-chain fatty acids such as butyrate, propionate and acetate. Gut microbiota also plays a significant role in the cognitive and behavioural functions of the host. A balanced gut microbiota shifts to dysbiosis, due to intake of high fat or sugar or other factors like sedentary lifestyle. The dysbiosis of the gut results in increased permeability, endotoxaemic, insulin resistant, systemic inflammation, adiposity and metabolic disorders such as type 2 diabetes mellitus, non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, irritable bowel disorder, colorectal cancer, etc. A prudent lifestyle modification, added on with use of probiotics and prebiotic restore the normal flora of the gut, especially in patients with Clostridium difficle-associated diarrhoea, inflammatory bowel syndrome, liver disease and colon cancer. Faecal microbial transplant is an important therapeutic tool in many illness related with the gut. Thereby, understanding the gut microbial signatures in various diseases yields various novel therapeutic targets. Human gut microbiota has a prognostic, diagnostic and therapeutic potential which is recognised worldwide.
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BRIEF COMMUNICATIONS Top

Clinico-epidemiological analysis of scrub typhus in hospitalised patients presenting with acute undifferentiated febrile illness: A hospital-based study from Eastern India p. 278
Bijayini Behera, Manisha Biswal, Rashmi Ranjan Das, Anupam Dey, Jayanti Jena, Sagarika Dhal, Srujana Mohanty, Baijayantimala Mishra, Ashok Kumar Praharaj
DOI:10.4103/ijmm.IJMM_19_147  
Acute undifferentiated febrile illness (AUFI) constitutes the predominant cause of healthcare seeking in Odisha. This prospective study was conducted to analyse the clinical, epidemiological and laboratory profile of scrub typhus patients presenting with AUFI from January to December 2017. Four hundred and thirty-two samples were tested for dengue, malaria, scrub typhus and enteric fever. Scrub typhus was overall the most common cause of AUFI (26.3%, 114/432) followed by dengue (19.2%, 83/432). Eschar was seen in 6.1% of cases. Aetiologies of 38.6% of AUFI remained unidentified. In the present study, there was no mortality attributed to scrub typhus.
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Detection of cytomegalovirus disease by real-time quantitative PCR targeting immediate early gene (ppUL83) in different samples among post-renal-transplant recipients p. 281
Ramya Barani, Vigna Seshan, Yazhini Ravi, Periasamy Soundararajan, Gunasekaran Palani, Padma Srikanth
DOI:10.4103/ijmm.IJMM_19_364  
Renal transplantation is a treatment option for end-stage renal disease (ESRD). Cytomegalovirus (CMV) infection was analysed among symptomatic and asymptomatic post-renal-transplant recipients (PRTRs). A total of 30 PRTRs were enrolled. DNA was extracted and quantitative real-time PCR for CMV (CMV R-Gene, France) targeting ppUL83 gene was performed on whole blood, urine and saliva. The detection rate of CMV was found to be 27% (n = 8) in different samples, including whole blood, urine and saliva. Among 30 PRTRs, 53% (n = 16) of the PRTRs did not shed virus in saliva. About 7% of CMV was detected only in saliva among PRTRs who were symptomatic.
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CORRESPONDENCE Top

Increase in Chlamydia trachomatis genital and extra-genital infections in Indian males p. 285
Sonu Kumari Agrawal, Jyoti Rawre, Neena Khanna, Benu Dhawan
DOI:10.4103/ijmm.IJMM_19_7  
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A typical Escherichia coli: A Dilemma of a Clinical Diagnostic Laboratory p. 287
Tonushyam Sonowal, Malini Shariff
DOI:10.4103/ijmm.IJMM_19_60  
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CASE REPORTS Top

Ocular infection by a psychrophile: Pseudomonas fluorescens p. 289
Sanchita Mitra, Suryasnata Rath, Sujata Das, Soumyava Basu
DOI:10.4103/ijmm.IJMM_18_263  
Accurate identification of infectious pathogens is essential for appropriate management of ocular infections. Routine laboratory protocols typically support bacterial growth at 37°C. We report a case, wherein we serendipitously isolated Pseudomonas fluorescens – an organism that prefers lower temperatures for optimal growth (psychrophilic) in the environment – from eviscerated contents of an eye with total corneal melt. This case highlights the need for being vigilant for organisms with different temperature sensitivities in culture media than that found in routine protocols.
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Multifocal hepatic abscesses in immunocompetent patient due to Bartonella henselae: Case report with review of literature p. 292
Sonu Kumari Agrawal, Prasenjit Das, Shalimar , Gupta Swatantra, Rama Chaudhry
DOI:10.4103/ijmm.IJMM_19_4  
To the best of our knowledge, this is the first case of multifocal hepatic abscesses in a young immunocompetent adult from India, which was successfully treated with hepatectomy and short course of oral antibiotic regimen. Publishing further such case reports will provide more clarity regarding the clinical significance of the disease, including associated risk factors and appropriate treatment.
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Combined treatment modality for phthiriasis palpebrarum p. 296
Chitaranjan Mishra, Usha Kim, Mulasthanam Sai Dheera
DOI:10.4103/ijmm.IJMM_19_251  
Phthiriasis palpebrarum (PP) is the infestation of eyelids caused by the ectoparasite Phthirus pubis, frequently misdiagnosed as allergic conjunctivitis, blepharitis or dermatitis. There is no standard treatment of choice although various treatment modalities have been described. A 6-year-old male child with PP was successfully treated with local application of 20% fluorescein solution over the eyelashes and eyebrows of both the eyes, followed by the mechanical removal of all parasites and trimming of the eyelashes from the base and application of ophthalmic ointment.
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2004 - Indian Journal of Medical Microbiology
Published by Wolters Kluwer - Medknow

Online since April 2001, new site since 1st August '04