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  ~ Table of Contents - Current issue
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January-March 2017
Volume 35 | Issue 1
Page Nos. 1-151

Online since Thursday, March 16, 2017

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EDITORIALS  

Global response to combat antimicrobial resistance Highly accessed article p. 1
Poonam Khetrapal Singh
DOI:10.4103/ijmm.IJMM_17_98  PMID:28303809
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Emerging challenges and opportunities in medical microbiology p. 4
Rajesh Bhatia
DOI:10.4103/ijmm.IJMM_17_88  PMID:28303810
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Systematic reviews of diagnostic tests: A primer p. 8
Thambu David, Prathap Tharyan
DOI:10.4103/ijmm.IJMM_17_5  PMID:28303811
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REVIEW ARTICLES Top

Global eradication of measles: Are we poised? p. 10
Raghavendra D Kulkarni, GS Ajantha, Aithal R Kiran, KR Pravinchandra
DOI:10.4103/ijmm.IJMM_16_233  PMID:28303812
Measles, a highly infectious viral disease is the next target for eradication following poliovirus. Decades of experience with highly effective vaccination has invigorated us to take on this virus. The task is not only Titanic but is laced with intricate issues. Recently, an outbreak of fever with rash occurred on a tertiary care teaching hospital campus and was confirmed serologically as measles outbreak by IgMELISA. Therefore, we searched the literature related to outbreaks, transmission of the measles virus, age groups involved, vaccination strategies, vaccination failure and epidemiological features of the disease and reviewed the possible reasons for such outbreaks and problems in the global eradication of the virus.
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Molecular typing of Chlamydia trachomatis: An overview p. 17
Jyoti Rawre, Deepak Juyal, Benu Dhawan
DOI:10.4103/ijmm.IJMM_16_341  PMID:28303813
Urogenital infection due to Chlamydia trachomatis (CT) is one of the most common bacterial sexually transmitted infections (STIs) and is a major public health problem worldwide. Molecular characterisation of CT is important for understanding the pathophysiological mechanisms of chlamydial disease and its transmission dynamics in sexual networks. Traditionally, strain typing of CT was based on serotyping methods characterising the major outer membrane protein (MOMP). With the advent of polymerase chain reaction and sequencing the era of molecular typing began. Molecular characterization of CT strains is based on sequence analysis of ompA gene encoding MOMP. However, in due course of time, improvements were made to enhance the discriminatory power of sequencing and quality of epidemiological information. New high-resolution genotyping methods using multiple loci such as multilocus sequence typing (MLST) and multiple loci variable number of tandem repeats (MLVA) were developed but were unable to differentiate mixed infections (MIs). The development of DNA-hybridisation methods emerged as a major breakthrough in detecting MIs. Although MLST and MLVA are more discriminative than other genotyping methods, they are laborious and expensive. DNA microarray technique is an affordable alternative for genotyping. Since recombination is widespread in the CT genome, ompA is not a reliable marker for phylogenetic studies; hence, whole genome sequencing may provide maximum phylogenetic resolution of CT strains. A descriptive review is provided of the various molecular CT typing methods. The vital information gained can be used for formulating screening programmes, targeted prevention and optimising therapeutic measures aiming to reduce disease transmission.
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Spoligotype defined lineages of Mycobacterium tuberculosis and drug resistance: Merely a casual correlation? p. 27
Nikita Panwalkar, Devendra S Chauhan, Prabha Desikan
DOI:10.4103/0255-0857.202327  PMID:28303814
Drug-resistant tuberculosis (TB) is a major challenge to TB control strategy worldwide. Analysis of genetic polymorphism among drug resistant Mycobacterium tuberculosis (MTB) strains may help provide some insight into the transmission dynamics of these strains. Spoligotyping is a widely used technique to identify genetic polymorphism, based on 43 known spacers interspersed between direct repeat regions. Considerable work has been done in various parts of the world using this technique to identify and analyse the polymorphic nature of MTB. Many studies have been carried out to determine the association of drug resistance with spoligotype defined lineages, and much data has been produced over the years. New information continues to be generated. This review aims to put together the findings of relevant studies in an attempt to understand the correlation of drug resistance with spoligotype defined lineages of MTB. This would help provide a perspective of the available data that can be used as a starting point to understand the molecular epidemiology of drug resistant TB.
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ORIGINAL ARTICLES Top

Prevalence and characterization of rotaviruses in children hospitalized for diarrheal disease in a tertiary care hospital, Pune p. 33
Sae Satish Pol, Ashwini Kacharu Dedwal, Sujata Sudhir Ranshing, Shobha Dattatray Chitambar, Sushma Narayan Pednekar, Renu Satish Bharadwaj
DOI:10.4103/ijmm.IJMM_16_94  PMID:28303815
Background: Diarrhoea remains the second most common cause of death among children below 5 years globally. Among various enteric pathogens, rotavirus appears to be the most important aetiological agent of acute gastroenteritis in infants and young children. Increased understanding of epidemiology of rotavirus infections is needed to improve the vaccine efficacy. Aim: This study aims to determine prevalence rotavirus infection and prevalent circulating strains of rotavirus in and around Pune. Setting and Design: Prospective hospital-based study. The study was approved by Institutional Ethical Committee. Materials and Methods: Stool samples (n = 100) were collected from children aged <5 years, hospitalised for acute diarrhoea in paediatric ward at a tertiary care hospital. Samples were subjected for rotavirus antigen capture ELISA. The viral RNA was subjected to multiplex reverse transcription polymerase chain reaction to amplify VP7 genotypes G1–G4, G8–G10 and G12 and VP4 genotypes P[4], P[6], P[8], P[9], P[10] and P[11]. Nontypable rotavirus strains were sequenced. Results: About 35% stool samples were positive for rotavirus antigen by ELISA. G9P[4] (28.6%) was found to be the most prevalent rotavirus strain. The detection of emerging strain G12P[6] (14.3%) and rare reassortant strain G9P[4] was the significant finding. Conclusion: Genotypes found in circulation are not present in the currently used vaccine. Thus, an emergence of newer genotypes over a period calls for the continued surveillance and genomic characterisation of rotaviruses to improve the vaccine efficacy.
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Occurrence of enteric parasitic infections among HIV-infected individuals and its relation to CD4 T-cell counts with a special emphasis on coccidian parasites at a tertiary care centre in South India p. 37
Chinnambedu R Swathirajan, Ramachandran Vignesh, Ambrose Pradeep, Sunil S Solomon, Suniti Solomon, Pachamuthu Balakrishnan
DOI:10.4103/ijmm.IJMM_16_164  PMID:28303816
Context: Diarrhoea is one of the major complications occurring in over 90% of HIV-infected individuals in developing countries. Coccidian group of parasites, being opportunistic pathogens, have been implicated as the most common causative agents of diarrhoea among HIV-infected population. Aims: The aim was to study the magnitude of parasitic diarrhoea with special context to coccidian parasitic infections in HIV-infected individuals and their association with the patient's immunological status measured by CD4 T-cell counts. Settings and Design: This investigation was performed between January 2002 and December 2014 at a tertiary HIV care centre in Chennai, South India. Materials and Methods: Stool samples were collected and microscopically observed for parasites using direct, formal-ether-concentrated wet mounts and modified acid-fast staining for coccidian parasites. CD4 T-cell counts were done by FACScount. Statistical Analysis Used: All statistical analyses were performed using GraphPad Prism software, version 5.0, andP < 0.05 was considered statistically significant. Results: Coccidian parasitic infection accounted for about 23.4% of parasitic infections, and of these, Cystoisospora belli was observed to be the most common cause of diarrhoea (88.8%), followed by Cryptosporidium spp. (9.9%) and Cyclospora spp. (1.3%). Trend analysis of coccidian aetiology during the study period revealed a significant rise in the positivity of C. belli and Cryptosporidium spp. (P = 0.001). Among the HIV patients with CD4+ T-cell counts <200 cells/μL, Cryptosporidium infection was most common (90%), followed by infection with C. belli(61.4%). Conclusions: Coccidian parasites continue to be the most common aetiological agent of diarrhoea among patients with HIV. The increasing trend of positivity of both cystoisosporiasis and cryptosporidiosis over the study period and the high positivity of cryptosporidiosis in patients with lower CD4+ T-cell counts are issues of serious concern. The findings call for the need for the early diagnosis of coccidian parasites and appropriate intervention among HIV-infected patients.
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Screening of invasive fungal infections by a real-time panfungal (pan-ACF) polymerase chain reaction assay in patients with haematological malignancy p. 41
Malini Rajinder Capoor, Shikha Puri, Hitesh Raheja, Ritin Mohindra, Dinesh Kumar Gupta, Pradeep Kumar Verma, Ranadeep Chowdhary
DOI:10.4103/ijmm.IJMM_15_543  PMID:28303817
Background: Invasive fungal infection (IFI) is a fatal infection in haematology patients. There is an urgent need for reliable screening methods facilitating timely diagnosis and treatment. A real-time panfungal polymerase chain reaction (PCR) assay based on TaqMan technology targeting 18S ribosomal RNA gene was used to screen whole blood specimen obtained from series of Haematology malignancy patients for IFIs. Materials and Methods: The panfungal (Pan-ACF) assay was employed to investigate specimen from 133 patients in duplicate with suspected IFI. In addition twenty healthy subjects and twenty patients with bacterial infections were taken as control. The patients with suspected IFI were also diagnosed by conventional methods including direct microscopy, culture techniques and antigen detection (galactomannan antigen ELISA and latex agglutination for cryptococcal antigen). The results of molecular testing were evaluated in relation to the criteria proposed by the European Organization for Research and Treatment of Cancer and patients were classified as having proven and probable IFD. Results: Of 133 patients, 89 had proven, 18 had probable and 26 had possible IFI. One hundred four samples were reverse transcription-PCR positive. Of 89 proven cases, 84 were panfungal PCR positive. These 84 cases included 82 cases which revealed growth on fungal blood culture and two cases were negative on fungal blood culture. Of the 82 cases which revealed growth on culture: 74 grew Candida in culture, 3 grew Fusarium solani, 5 grew Aspergillus species on blood culture. The later five were also galactomannan antigen positive. The five specimen which were negative on panfungal PCR, two grew Trichosporon asahii, one grew Candida rugosa and two grew as Cryptococcus neoformans var. neoformans. Of the 18 probable cases, 18 were panfungal PCR positive. These were also galactomannan antigen positive. The sensitivity and specificity of panfungal PCR in proven cases were 94.3% and 95.2%, respectively. The positive and negative predictive values proven cases were 97.6% and 88.9%, respectively. Conclusions: The panfungal (Pan-ACF) real-time PCR assay can detect common fungal genera and it may be used as an adjunct to conventional methods for screening of IFI.
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Biofilm formation capability of enterococcal strains causing urinary tract infection vis-a-vis colonisation and correlation with enterococcal surface protein gene p. 48
Shubha Garg, Balvinder Mohan, Neelam Taneja
DOI:10.4103/ijmm.IJMM_16_102  PMID:28303818
Background: Data regarding differences in biofilm formation among urinary isolates of enterococci causing nosocomial infection versus asymptomatic colonisation is lacking. Conflicting data are available for the role of enterococcal surface protein (esp) gene in the development of enterococcal biofilms. Materials and Methods: A total of 50 (25 each of asymptomatic bacteriuria and urinary tract infection (UTI) isolates were collected from admitted patients who had nosocomial acquisition of enterococci in urine culture (≥105 cfu/ml). Biofilm assay was done by the quantitative adherence assay. Screening for esp gene was carried out by polymerase chain reaction, and confocal laser scanning microscopy was used to examine biofilms. Results: Out of 25 enterococcal isolates from asymptomatic patients, 9 (36%) isolates were found to be biofilm producers (6 weak [optical densities [OD]595 < 0.2] and three medium [OD595≥0.2 to<0.5]). Twelve (48%) out of 25 enterococcal isolates from UTI cases, produced biofilms (7 weak, 4 medium, and 1 strong [OD595>0.5]). The esp gene was present in 30 (12 biofilm+, 18 biofilm−) isolates. Seventeen esp positive isolates were from asymptomatic cases whereas 13 were from UTI. However, we found that 100% of medium and strong biofilm producers were esp positive (P < 0.001). On comparing Enterococcus faecalis (n = 10) and E. faecium (n = 40) isolates, 70% of E. faecalis isolates were biofilm producers as compared to only 35% of E. faecium isolates (P > 0.05). The esp positivity was observed more in E. faecium isolates (65%) as compared to 40% in E. faecalis. Vancomycin-sensitive enterococcal and vancomycin-resistant enterococcal isolates and catheter-related and unrelated isolates showed similarity in biofilm production and esp positivity. Conclusion: The esp gene is not compulsorily required to produce biofilm but when present may enhance the biofilm formation. We did not find any correlation between biofilm formation and the ability of the strain to cause symptomatic UTI be associated with catheters or vancomycin resistance.
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Prevalence and genetic mechanisms of antimicrobial resistance in Staphylococcus species: A multicentre report of the indian council of medical research antimicrobial resistance surveillance network p. 53
Sunanda Rajkumar, Sujatha Sistla, Meerabai Manoharan, Madhan Sugumar, Niveditha Nagasundaram, Subhash Chandra Parija, Pallab Ray, Yamuna Devi Bakthavatchalam, Balaji Veeraraghavan, Arti Kapil, Kamini Walia, VC Ohri
DOI:10.4103/ijmm.IJMM_16_427  PMID:28303819
Purpose: Routine surveillance of antimicrobial resistance (AMR) is an essential component of measures aimed to tackle the growing threat of resistant microbes in public health. This study presents a 1-year multicentre report on AMR in Staphylococcus species as part of Indian Council of Medical Research-AMR surveillance network. Materials and Methods: Staphylococcus species was routinely collected in the nodal and regional centres of the network and antimicrobial susceptibility testing was performed against a panel of antimicrobials. Minimum inhibitory concentration (MIC) values of vancomycin (VAN), daptomycin, tigecycline and linezolid (LNZ) against selected methicillin-resistant Staphylococcus aureus(MRSA) isolates were determined by E-test and MIC creep, if any, was determined. Resistant genotypes were determined by polymerase chain reaction for those isolates showing phenotypic resistance. Results: The prevalence of MRSA was found to be range from moderate (21%) to high (45%) among the centres with an overall prevalence of 37.3%. High prevalence of resistance was observed with commonly used antimicrobials such as ciprofloxacin and erythromycin in all the centres. Resistance to LNZ was not encountered except for a single case. Full-blown resistance to VAN in S. aureus was not observed; however, a few VAN-intermediate S. aureus isolates were documented. The most common species of coagulase negative staphylococci (CoNS) identified was Staphylococcus haemolyticus and Staphylococcus epidermidis. Resistance among CoNS was relatively higher than S. aureus. Most phenotypically resistant organisms possessed the corresponding resistance genes. Conclusion: There were localised differences in the prevalence of resistance between the centres. The efficacy of the anti-MRSA antimicrobials was very high; however, almost all these antimicrobials showed evidence of creeping MIC.
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Characterisation of antimicrobial resistance in Salmonellae during 2014–2015 from four centres across India: An ICMR antimicrobial resistance surveillance network report p. 61
Sushila Dahiya, Priyanka Sharma, Bhavana Kumari, Sangeeta Pandey, Rooma Malik, Neelam Manral, Balaji Veeraraghavan, Agila Kumari Pragasam, Pallab Ray, Vikas Gautam, Sujata Sistla, Subhash Chandra Parija, Kamini Walia, Vinod Ohri, Bimal Kumar Das, Seema Sood, Arti Kapil
DOI:10.4103/ijmm.IJMM_16_382  PMID:28303820
Purpose: The main purpose of this study was to establish 'Antimicrobial Resistance Surveillance Network' in India and to monitor the antimicrobial susceptibility profile of clinical isolates to establish a national network across the country for monitoring antimicrobial resistance in Salmonella. Materials and Methods: This study was conducted at All India Institute of Medical Sciences, nodal centre with clinical isolates of Salmonellae collected from four centres across India, which included Christian Medical College, Vellore; Postgraduate Institute of Medical Education and Research, Chandigarh and Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry. Total 20% of the selected strains from each centre were characterised for molecular studies which included molecular mechanism of fluoroquinolones resistance and multiple locus sequence type. Results: A total of 622 Salmonellae were received from all centres during January 2014 to December 2015. Out of these 622 isolates, 380 were Salmonella Typhi, 162 were Salmonella Paratyphi A and 7 were S. Paratyphi B isolated from blood and 73 were other Salmonella serotypes. Multiple drug resistance (resistant to ampicillin, chloramphenicol and co-trimoxazole) was less than 3% in S. Typhi. In S. Paratyphi A, chloramphenicol and co-trimoxazole susceptibility was 100% and 99%, respectively, whereas ampicillin susceptibility was 86% (139/161). Ciprofloxacin and nalidixic acid susceptibility was 15% (24/162) and 1% (2/162) from all centres. S. Paratyphi B was isolated from 7 patients. All isolates were third-generation cephalosporin sensitive. The most common mutations found were at codon 83 and at codon 87. We did not find any mutation in acrR gene. Efflux pump and qnr genes were not found in any isolate tested. All 86 S. Typhi isolates clustered into two sequence types - ST1 and ST2. Out of these 86 isolates, 70 S. Typhi were ST1 and 16 were ST2. All S. Paratyphi A was clustered in ST85 and ST129 on the basis of mutation in sucA gene. Out of 27 S. Paratyphi A, 13 were grouped into ST85 and 14 were grouped into ST129. Conclusions: Enteric fever is one such infection which poses challenges in antimicrobial resistance. Hence, continuous surveillance is important to track bacterial resistance and to treat infections in a cost-effective manner.
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Detection of ofloxacin resistance by nitrate reductase assay in Mycobacterium tuberculosis isolates from extrapulmonary tuberculosis p. 69
Neeta Shrivastava, Reena Set, Sheetal Bankar, Jayanthi Shastri
DOI:10.4103/ijmm.IJMM_16_266  PMID:28303821
Context: Increased use of fluoroquinolones to treat community-acquired infections has led to the decreased susceptibility to Mycobacterium tuberculosis. There is a paucity of data on ofloxacin (OFX) resistance detection by nitrate reductase assay (NRA). Hence, the present study was carried out to find the efficacy of NRA for detection of OFX resistance in M. tuberculosis isolated from extrapulmonary tuberculosis (EPTB) cases. Aims: (1) To compare sensitivity, specificity and median time required to obtain results by NRA with economic variant proportion method (PM) for detection of OFX resistance.(2) To determine the extent of OFX resistance in clinical isolates of M. tuberculosis. Settings and Design: Seventy-three M. tuberculosis isolates from cases of EPTB were subjected to economic variant of PM for isoniazid, rifampicin and OFX. NRA was done for detection of OFX resistance. Subjects and Methods: Seventy-three isolates from clinical samples of suspected EPTB received in the Department of Microbiology were included in the study. Drug susceptibility test was performed on Lowenstein–Jensen medium with and without drugs. Statistical Analysis Used: Of turnaround time was done by Mann–Whitney test on SPSS (version 19, released in 2010, IBM Corp, Armonk NY),P < 0.05. Results: OFX resistance was seen in nine isolates. The sensitivity and specificity of OFX resistance by NRA was 100% and 96.87%, respectively. Median time required to obtain results by NRA was 10 days as compared to 28 days by PM. Conclusions: NRA is a specific and sensitive method for detection of OFX resistance in resource-restricted settings.
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Human papillomavirus and Chlamydia trachomatis infection in gyneco-obstetric outpatients from a mexican hospital p. 74
Laura Conde-Ferráez, Jorge Ramiro Carrillo Martíez, Guadalupe Ayora-Talavera, María del Refugio González Losa
DOI:10.4103/ijmm.IJMM_15_450  PMID:28303822
Context: Human papillomavirus (HPV) and Chlamydia trachomatis are the most frequent sexually transmitted infections, usually asymptomatic. Persistent infection with high-risk HPV types and other cofactors such as the concomitant infection with C. trachomatis can represent a higher risk to develop cervical lesions; therefore, screening with sensitive methods could aid to identify women at risk. Aims: The aim is to determine the prevalence and concurrence of both infections, detected with in-house molecular methods, and to identify the risk factors associated to the infections in Mexican women. Subjects and Methods: This was a cross-sectional study including gynaecological-obstetrical medical outpatients from a Social Security Hospital in Southeast Mexico. After informed consent, cervicovaginal samples were collected and tested for HPV and C. trachomatis using polymerase chain reaction (PCR). HPV positives were further tested for high-risk HPV16, 18, 58 and low-risk 11 using real-time PCR. All methods employed were in-house. Data analyses included odds ratios (OR), Chi-square and linear regressions. Results: Women included were 233, aging 15–49 (mean 30 years), 52.8% were pregnant. For HPV and C. trachomatis testing, 230 samples were adequate, resulting in 48 (20.9%) and 15 (6.5%) positives, respectively; 4 (1.7%) were positive to both. The most frequent genotype identified was HPV58 (25% of typified samples). C. trachomatis positives were 73% asymptomatic, none had pelvic inflammatory disease or infertility histories. The only variable associated to HPV infection was the history of previous sexually transmitted disease (OR = 3.69,P= 0.0019). Conclusions: More than 25% of the population was infected with either agent. We successfully used in-house molecular methodologies for diagnosis and typing, showing HPV and C. trachomatis prevalence consistent to previous reports. Concomitant infections were found, HPV high-risk types were involved in half of these cases, representing a higher risk.
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Bacterial and fungal biofilm formation on contact lenses and their susceptibility to lens care solutions p. 80
Siddharth Kackar, Ethel Suman, M Shashidhar Kotian
DOI:10.4103/ijmm.IJMM_16_273  PMID:28303823
Background: Microbial biofilm formation on contact lenses and lens storage cases may be a risk factor for contact lens-associated corneal infections. Various types of contact lens care solutions are used to reduce microbial growths on lenses. Objectives: The present study aimed at comparing the growths of biofilms on the different contact lenses and lens cases. The study also aimed at determining the effect of lens care solutions and bacteriophage on these biofilms. Materials and Methods: One type of hard lens and two types of soft lenses were used for the study. The organisms used were Staphylococcus aureus ATCC 25923, Pseudomonas aeruginosa ATCC 27853, Candida albicans ATCC 60193 and Escherichia coli ATCC 25922. Biofilm production was performed by modified O'Toole and Kolter method and effect of lens cleaning solutions and a crude coliphage on biofilms was also studied. Results were visualised using scanning electron microscopy and quantitated by colony counting method and spectrophotometric measurement of optical density (OD). Statistical analysis was done by SPSS 11.5, Kruskal–Wallis test and Chi-square test. Results: Soft lens cleaning solutions had a significant inhibitory effect (P = 0.020) on biofilm formation on soft lenses and also lens cases (P < 0.001). Soft lens cleaning solution 2 was more efficient than solution 1. However, no such inhibitory effect was observed with regard to hard lens cleaning solution, but for a significant reduction in the OD values (P < 0.001). There was no significant inhibitory effect by bacteriophages. Conclusion: This study showed the importance of selecting the appropriate lens cleaning solution to prevent biofilm production on contact lenses.
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Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry rapid detection of carbapenamase activity in Acinetobacter baumannii isolates p. 85
Noha Abouseada, May Raouf, Eman El-Attar, Pacinte Moez
DOI:10.4103/0255-0857.202335  PMID:28303824
Introduction: Carbapenamase-producing Acinetobacter baumannii are an increasing threat in hospitals and Intensive Care Units. Accurate and rapid detection of carbapenamase producers has a great impact on patient improvement and aids in implementation of infection control measures. Aim: In this study, we describe the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF MS) to identify carbapenamase-producing A. baumannii isolates in up to 3 h. Isolates and Methods: A total of 50 A. baumannii isolates (of which 39 were carabapenamase producers) were tested using MALDI TOF MS. Isolates were incubated for 3 h with 0.25 mg/ml up to 2 mg/ml of imipenem (IMP) at 37°C. Supernatants were analysed by MALDI TOF to analyse peaks corresponding to IMP (300 Da) and an IMP metabolite (254 Da) using UltrafleXtreme (Bruker Daltonics, Bremen, Germany). Results: All carbapenamase-producing isolates were evidenced by the disappearance or reduction in intensity of the 300 Da peak of IPM and the appearance of a 254 Da peak of the IPM metabolite. In isolates that did not produce carbapenamase, the IPM 300 Da peak remained intact. Conclusion: MALDI TOF is a promising tool in the field of diagnostic microbiology that has the ability to transfer identification and antimicrobial susceptibility testing time from days to hours.
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Evaluation of loop-mediated isothermal amplification assay for rapid diagnosis of Acanthamoeba keratitis p. 90
Abhishek Mewara, Sumeeta Khurana, Shakila Yoonus, Kirti Megha, Parveen Tanwar, Amit Gupta, Rakesh Sehgal
DOI:10.4103/ijmm.IJMM_16_227  PMID:28303825
Background: The clinical features of Acanthamoeba keratitis (AK) are non-specific and closely resemble bacterial, viral and fungal keratitis. Materials and Methods: We compared loop-mediated isothermal amplification (LAMP) with microscopy, non-nutrient agar (NNA) culture and polymerase chain reaction (PCR) in clinical suspects of AK. Results: Of 52 clinical samples (42 AK suspects and 10 proven bacterial, viral or fungal keratitis), 3 were positive by direct microscopy (sensitivity 60%, confidence interval [CI]: 17%–92.7%), and 5 by NNA culture, 18S rDNA PCR and LAMP (sensitivity 100%, CI: 46.3%–100%). The limit of detection of Acanthamoeba DNA was 1 pg/μl by both LAMP and PCR. Conclusion: PCR and LAMP assays targeting 18S rDNA gene were found particularly suitable for a rapid and accurate diagnosis of AK. LAMP assay takes 2–3 h lesser than PCR, and thus offers a rapid, highly sensitive and specific, simple and affordable diagnostic modality for patients suspected of AK, especially in resource limited settings
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Prevalence of pneumococcal serotypes in adults ≥50 years of age p. 95
Chand Wattal, Neeraj Goel, SP Byotra
DOI:10.4103/ijmm.IJMM_16_132  PMID:28303826
Context: Currently, majority of studies on antibiotic resistance and serotype prevalence in Streptococcus pneumoniae are in paediatric population and there is limited epidemiologic data pertaining to elderly Indian population. Aims: This study was undertaken to assess antibiotic resistance pattern and the coverage of the polysaccharide vaccine 23 (PPV23) in the elderly population. Settings and Design: This was a prospective 2-year pneumococcal surveillance study in patients with community-acquired pneumococcal infections of ≥50 years' age group on fifty isolates of S. pneumoniae. Materials and Methods: Antibiotic susceptibility by Kirby-Bauer disc diffusion method and minimum inhibitory concentration susceptibility testing by E-test method were performed for various antibiotics. All isolates were serotyped by the capsular Quellung method with commercial antisera. Results: All S. pneumoniae isolates were sensitive to penicillin and ceftriaxone. Non-susceptibility to levofloxacin, co-trimoxazole, erythromycin and clindamycin was noted as 16%, 74%, 10% and 6%, respectively. Prevalence of multidrug resistance in S. pneumoniae was observed as 6%. The most common serotypes observed in our study were 19A (14%), 8 (10%), 19F (8%), 3 (6%) and 9N (6%). PCV7, PCV10, PCV13 and PCV23 coverage was observed as 16%, 24%, 48% and 66%, respectively. The non-vaccine serotypes (NVTs) comprised 30% (n = 15) of the isolates. Conclusions: Our study shows different antibiotic susceptibility patterns of S. pneumoniae as compared to other neighbouring regions in Asia. The modest coverage of S. pneumoniae serotypes by PPV23 vaccine and prevalence of diverse NVTs in adult population make it a challenging task to recommend further changes in the future vaccine.
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Characterisation of the human oral microbiome in patients with coronary artery disease using next-generation sequencing of 16SrRNA amplicons p. 101
Thangam Menon, Sathya Narayanan Gopalakrishnan, Rayvathy Balasubramanian, Stalin Roy Justin
DOI:10.4103/ijmm.IJMM_16_370  PMID:28303827
Introduction: Oral health is suspected to be linked to heart disease since species of bacteria that cause periodontitis and dental caries have been found in the atherosclerotic plaque in arteries in the heart. Objectives: The aim of this study was to characterize the oral microbiome in patients with coronary artery disease (CAD) and in a patient with dental caries (DC) without any clinical symptoms of CAD. Methods: DNA was extracted from the oral swabs collected from the patients and sequencing was performed by next generation sequencing method using Illumina (MiSeq) platform. The resulting sequencing data set was analysed using QIIME. Results: A total of 31 phyla were found in all the samples. The predominant phylum found in both CAD and DC was Firmicutes (46.09% & 38.98%), Proteobacteria (17.73% & 9.79%), Fusobacteria (13.44% & 17.95%), Bacteroidetes (11.82% & 22.73%), Actinobacteria (8.33% & 7.71%) and TM7 (2.25% & 2.71%). We found a similarity in the bacterial diversity in the two groups of patients. Conclusion: A comparison of the oral microbiome in patients with CAD and DC shows a similarity in the composition of the oral microbiota with variations in the proportion of a few genera.
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High prevalence of cryptococcal antigenaemia amongst asymptomatic advanced HIV patients in Pune, India p. 105
Dileep Kadam, Ajay Chandanwale, Renu Bharadwaj, Neetal Nevrekar, Samir Joshi, Sandesh Patil, Nikhil Gupte, Shashi Sangle, Kavita Chopade, Vandana Kulkarni, Usha Balasubramanian, Nishi Suryavanshi, Divyashri Jain, Savita Kanade, Sujata Dharmashale, Anju Kagal, Amita Gupta, Vidya Mave
DOI:10.4103/ijmm.IJMM_15_596  PMID:28303828
Background: The World Health Organization recommends routine cryptococcal antigen (CrAg) screening in advanced AIDS patients initiating antiretroviral treatment (ART). India has yet to adopt this strategy as the burden of cryptococcal antigenaemia is unknown. Methods: A prospective study was conducted in a large public sector ART centre and the inpatient wards of Sassoon Hospital, Pune, India. All consenting patients >18 years of age with CD4 count <100 cells/mm3 were screened for CrAg by latex agglutination assay. Those with positive CrAg underwent cerebrospinal fluid analysis, chest radiograph and abdominal ultrasound to rule out cryptococcal disease. The impact of CrAg positivity on all-cause mortality was assessed by logistic regression analysis. Results: Amongst 208 AIDS patients with CD4 cells <100 cells/mm3 who underwent CrAg testing, median age was 40 (interquartile range [IQR], 35–49) years, 134 (64%) were male and median CD4 count was 64.5 cells/mm3 (IQR, 37–82). Overall, 16 (8%, 95% confidence interval [CI], 4–12) patients were positive for CrAg, of which 8 (50%) had CD4 cells <50 cells/mm3 and 3 (19%) CrAg-positive patients had incidental cryptococcal meningitis. At 6-month follow-up, the case fatality rate was higher amongst CrAg-positive patients (38%) compared with CrAg-negative patients (18%) (P = 0.06). After adjusting for age, sex, CD4 count and ART, there was a trend towards increased all-cause mortality (adjusted OR, 3.18, 95% CI, 0.60–16.88,P= 0.17). Conclusions: We found an 8% prevalence of cryptococcaemia amongst adult AIDS patients with CD4 cells <100 cells/mm3. Given the high fatality rates observed, routine screening for CrAg should be considered for all Indian persons with advanced HIV disease.
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BRIEF COMMUNICATIONS Top

Mutation pattern in the genome of Neisseria gonorrhoeae and its association with multidrug-resistant isolates from Delhi, India p. 109
Divya Sachdev, Indu Kumari, Manju Bala, Vineet Kumar, Daman Saluja
DOI:10.4103/ijmm.IJMM_16_46  PMID:28303829
Mutations in PenA, PorB, MtrE and MtrR genes responsible for antimicrobial resistance were checked in 27 drug-resistant clinical isolates of Neisseria gonorrhoeae (NG). Phenotype PIB (88.88%) and mutation at G120 and A121 positions of porB were recurrent. N122K, a novel mutation, was observed in PorB in three resistant isolates. Substitution H105Y in MtrR was widespread (37% of clinical isolates). The presence of a novel mutation (L33V), along with G45D mutation in MtrR, was associated with less-resistant isolates, in contrast to isolates with G45D mutation alone. African-type penicillinase-producing NG plasmid was observed most frequently (17/27) in penicillin-resistant isolates.
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Multiplex polymerase chain reaction for the detection of high-risk-human papillomavirus types in formalin-fixed paraffin-embedded cervical tissues p. 113
Mini P Singh, Nalini Gupta, T Deepak, Archit Kumar, Radha Kanta Ratho
DOI:10.4103/ijmm.IJMM_15_277  PMID:28303830
Detecting high-risk-human papillomavirus (HPV) types has become an integral part of the cervical cancer screening programmes. This study aimed to develop a multiplex polymerase chain reaction (PCR) for identification of HPV types 16 and 18 along with the beta globin gene in formalin-fixed and paraffin-embedded cervical biopsy specimens. A total of 59 samples from patients with cervical abnormalities were tested. HPV 16 positivity was 50% in cervical cancers and 52.9% in cervical intraepithelial neoplasia. Our multiplex PCR protocol can be used as a simple and cost-effective tool for high-risk-HPV detection in cervical cancer screening programmes.
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Strengths and limitations of various screening methods for carbapenem-resistant Enterobacteriaceae including new method recommended by clinical and laboratory standards institute, 2017: A tertiary care experience p. 116
Agila Kumari Pragasam, Balaji Veeraraghavan, Yamuna Devi Bakthavatchalam, Radha Gopi, Raziya Fathima Aslam
DOI:10.4103/ijmm.IJMM_17_10  PMID:28303831
Carbapenemase-mediated carbapenem resistance is a major concern across the world. Rapid detection of carbapenemase-producing organisms is of great importance in clinical settings. However, it is essential to have a test with good sensitivity and specificity. The aim of the study was to compare the performance of RAPIDEC® CARBA NP and modified carbapenem inactivation method (mCIM) recommended by Clinical and Laboratory Standards Institute guideline 2017. A total of ninety carbapenem resistant Escherichia coli and Klebsiella pneumoniae have been tested. The presence of various carbapenemases was screened by conventional multiplex polymerase chain reaction. RAPIDEC® CARBA NP detected 90%, whereas mCIM detected 99% of the study isolates tested. Although RAPIDEC® CARBA NP is a rapid test, the sensitivity is reduced for blaOxa-48Likedetection; while mCIM could pick up blaOxa-48Likeenzymes with excellent sensitivity. Further, organisms producing low carbapenemase activity enzymes, thickness of the inoculum and the disc potency are likely to influence the test results of mCIM with an overnight delay.
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Coagulase-negative staphylococci: Emerging pathogen in central nervous system shunt infection p. 120
Preeti Lata Bhatia, Sunil Lilani, Ritesh Shirpurkar, Chhaya Chande, Shrikant Joshi, Abhay Chowdhary
DOI:10.4103/ijmm.IJMM_16_157  PMID:28303832
Central nervous system (CNS) shunts are commonly used to treat patients with hydrocephalus. Its placement is associated with increased risk of infection. The study was intended to evaluate infection rate associated with CNS shunt surgeries and identify risk factors for shunt infection. The frequency and characterisation of aetiological agents along with their antibiotic resistance pattern were also studied. A prospective study of 86 patients who underwent 97 surgeries over a period of 18 months was conducted. One hundred seventy-six cerebrospinal fluid samples and 44 shunt tips obtained were processed using standard microbiological techniques. Of 86 patients, 39 (45.35%) operated for shunt revision were infected while 47 patients operated for shunt insertion were not found to be infected. Methicillin-resistant Staphylococcus epidermidis was the predominant isolate. 57.58% isolates of Staphylococci were found to be biofilm producers. Mortality of 15% was observed among infected patients. Shunt infection remains a serious issue in the patients undergoing shunt surgery. Accurate diagnosis, treatment and prevention of infection are essential in such patients.
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Antimicrobial susceptibility of Leptospira spp. isolated from environmental, human and animal sources in Malaysia p. 124
Douadi Benacer, Siti Nursheena Mohd Zain, Peck Toung Ooi, Kwai Lin Thong
DOI:10.4103/ijmm.IJMM_15_458  PMID:28303833
Leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes of the genus Leptospira. The aim of this study was to evaluate the susceptibility of isolates obtained from different hosts. A total of 65 Leptospira isolates from humans (n = 1), zoonoses (rat, n = 60; dog, n = 1; swine, n = 1) and environment (n = 2) were tested against six antibiotics. All the isolates were resistant to trimethoprim and sulphamethoxazole and had high MIC toward chloramphenicol (MIC90: 6.25 μg/ml). All except one environment isolate were sensitive to ampicillin, doxycycline and penicillin G.
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Trends in spoligotype patterns of Mycobacterium tuberculosis strains in central India p. 129
Prabha Desikan, Devendra S Chauhan, Nikita Panwalkar, Pragya Sharma, Priyanka Yadav
DOI:10.4103/ijmm.IJMM_16_12  PMID:28303834
This study aims to understand trends in spoligotype patterns of Mycobacterium tuberculosis (MTB) in Central India. Elucidation of these trends may provide baseline information to understand the transmission dynamics of strains of MTB in the region. Spoligotyping was carried out on 340 MTB strains isolated from clinical samples received from 2007 to 2011. The prevalence of ST26/CAS1_Del, ST11/EAI3_IND, ST288/CAS2, ST25/CAS1_Del and Beijing lineages showed waxing and waning trends. ST26/CAS1_Del and ST11/EAI3_IND lineages were consistently present and were predominant. Well-established lineages showed a consistent presence in the community. New orphan lineages appeared to be less capable of establishing themselves.
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Trends of respiratory syncytial virus sub-types in children hospitalised at a tertiary care centre in Jaipur during 2012–2014 p. 134
M Anjaneya Swamy, Bharti Malhotra, P V. Janardhan Reddy, Jitendra Kumar Tiwari, Neeraj Kumar, Manohar Lal Gupta
DOI:10.4103/ijmm.IJMM_15_306  PMID:28303835
Respiratory syncytial virus (RSV) causes high mortality and morbidity in infants. The study was planned to determine the trends of RSV sub-types in hospitalised children. Nasopharyngeal aspirate and throat swabs were collected from the hospitalised children up to 5 years of age. Viral nucleic acid was extracted using easyMAG automated extraction system, and real-time reverse transcription polymerase chain reaction was performed. Total positivity for RSV was found to be 25.40%, predominantly for RSV B (20.03%), followed by RSV A (2.90%) and RSV AB mixed infections (2.47%). Palivizumab prophylaxis can be planned to be given to infants from post-monsoon to end of winter.
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Carbapenem nonsusceptibility with modified OprD in clinical isolates of Pseudomonas aeruginosa from India p. 137
Debarati Choudhury, Anupam Das Talukdar, Manabendra Dutta Choudhury, Anand Prakash Maurya, Debadatta Dhar Chanda, Atanu Chakravorty, Amitabha Bhattacharjee
DOI:10.4103/ijmm.IJMM_15_220  PMID:28303836
This study was undertaken to investigate OprD porin-mediated carbapenem nonsusceptibility in clinical isolates of Pseudomonas aeruginosa from a tertiary referral hospital of Northeast India. A total of 267 nonduplicate, consecutive clinical isolates of P. aeruginosa were obtained. Mutation and expression levels of OprD gene were determined in carbapenem-nonsusceptible carbapenemase-nonproducing isolates. Among 19 carbapenem-nonsusceptible carbapenemase-nonproducing isolates, 11 of them demonstrated variable band pattern while performing denaturing gradient gel electrophoresis with amplified products of OprD gene. Sequencing of variable band products revealed three mutation patterns in three isolates. Relevant decrease in expression of OprD gene could also be observed in them. All the three isolates exhibited a higher minimum inhibitory concentration for imipenem (64–128 μg/mL) compared to meropenem (16–64 μg/mL). Inactivating mutation and decreased expression of OprD contribute mainly to imipenem resistance as well as to meropenem.
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Prevalence of multiple drug-resistant Plasmodium falciparum malaria cases in Northeast India p. 140
Jitendra Sharma, Siraj Ahmed Khan, Monika Soni, Prafulla Dutta
DOI:10.4103/ijmm.IJMM_15_470  PMID:28303837
Two numbers of Plasmodium falciparum field isolates from Gossingpara, Runikhata area in Chirang district of Assam had shown multiple mutations in Pfcrt-dhfr-dhps gene (up to seven mutations: One mutation in Pfcrt gene, three mutations in Pfdhfr gene and three mutations in Pfdhps gene). Similarly, two cases in Bat camp, Miao area under Changlang district of Arunachal Pradesh had shown a total of eight mutations, of which one mutation in Pfcrt gene, three mutations in Pfdhfr gene, three mutations in Pfdhps gene and one mutation in PfATPase6 gene. One case in 3 Miles, Miao area of Changlang district has shown mutations in Pfcrt(one mutation), Pfdhfr(four mutations) and Pfdhps(three mutations) gene. These results indicated that there is an existence of multiple mutant P. falciparum malaria cases in northeastern region of India.
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CORRESPONDENCE Top

Introducing rubella vaccine into the national immunisation schedule p. 143
Valsan Philip Verghese
DOI:10.4103/ijmm.IJMM_17_40  PMID:28303838
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Emergence of ST39 and ST656 extensively drug-resistant Klebsiella pneumoniae isolates in Wenzhou, China p. 145
Haiyang Liu, Jonathan Wilksch, Bin Li, Jia Du, Jianming Cao, Xiaoxiao Zhang, Tieli Zhou
DOI:10.4103/ijmm.IJMM_16_381  PMID:28303839
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Prevalence of bi-component pore-forming toxin genotypes of Staphylococcus aureus causing skin and soft tissue infections p. 146
Nagaraj Perumal, Betsy Sowndarya Dass, Stalin Mani, Padma Krishnan
DOI:10.4103/ijmm.IJMM_16_424  PMID:28303840
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Clinico-epidemiological profile of dengue cases prevalent in lakhimpur district of Assam p. 148
Jitendra Sharma
DOI:10.4103/ijmm.IJMM_16_38  PMID:28303841
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REVIEWERS Top

Reviewers,2016 p. 150

DOI:10.4103/0255-0857.202354  
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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