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  ~ Table of Contents - Current issue
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October-December 2018
Volume 36 | Issue 4
Page Nos. 453-602

Online since Monday, March 18, 2019

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EDITORIAL  

IAMM recommended modification of MD microbiology curriculum to MD clinical microbiology as a speciality of medicine under consideration of MCI and Niti Ayog: Time has come to move on! Are we ready? Highly accessed article p. 453
Chand Wattal
DOI:10.4103/ijmm.IJMM_19_69  PMID:30880690
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REVIEW ARTICLES Top

Respiratory syncytial virus infections in India: Epidemiology and need for vaccine Highly accessed article p. 458
Shobha Broor, Shama Parveen, Megha Maheshwari
DOI:10.4103/ijmm.IJMM_19_5  PMID:30880691
Respiratory syncytial virus (RSV) has been identified as a leading cause of lower respiratory tract infections in young children and elderly. It is an enveloped negative-sense RNA virus belonging to Genus Orthopneumovirus. The clinical features of RSV infection range from mild upper-respiratory-tract illnesses or otitis media to severe lower-respiratory-tract illnesses. Current estimates show that about 33.1 million episodes of RSV-acute lower respiratory infection (ALRI) occurred in young children in 2015, of these majority that is, about 30 million RSV-ALRI episodes occurred in low-middle-income countries. In India, the rates of RSV detection in various hospital- and community-based studies mostly done in children vary from 5% to 54% and from 8% to 15%, respectively. Globally, RSV epidemics start in the South moving to the North. In India, RSV mainly peaks in winter in North India and some correlation with low temperature has been observed. Different genotypes of Group A (GA2, GA5, NA1 and ON1) and Group B (GB2, SAB4 and BA) have been described from India. The burden of RSV globally has kept it a high priority for vaccine development. After nearly 50 years of attempts, there is still no licensed vaccine and challenges to obtain a safe and effective vaccine is still facing the scientific community. The data in this review have been extracted from PubMed using the keywords RSV and Epidemiology and India. The data have been synthesised by the authors.
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Pneumococcal vaccines p. 465
Anand Manoharan, Ranjith Jayaraman
DOI:10.4103/ijmm.IJMM_18_442  PMID:30880692
Streptococcus pneumoniae continues to take a heavy toll on childhood mortality and morbidity across the developing world. An estimated 10.6 million invasive pneumococcal diseases (IPDs) occur every year, with nearly 1 million deaths in children under 5 years of age. Introduction of vaccines in the childhood immunisation programme in developed world has brought down the incidence of the disease considerably. However, childhood immunocompromising illnesses including HIV have increased the risk of IPD several folds. There is also a growing concern on the increasing antibiotic resistance among these invasive strains to penicillin, other beta-lactams and macrolides, making treatment difficult and expensive. It is estimated that about 62% of IPD worldwide is caused by the 10 most common serotypes. Although the ranking of individual pneumococcal serotypes causing serious disease varies among nations, the 7–13 serotypes included in pneumococcal conjugate vaccines (PCVs) may prevent 50%–80% of all paediatric pneumococcal diseases globally. The World Health Organization has recommended the use of PCV-10/13 in the national immunisation programmes (NIPs) of developing countries. Four doses of PCV-13 have been recommended by the US Association of Pediatrics and Centers for Disease Control and Prevention, at intervals of each 2 months for the first 6 months and by the 12th to 15th months after birth. This is expected to reduce the morbidity and mortality associated with IPD and simultaneously decrease colonisation with circulating antibiotic-resistant strains in immunized communities. Nevertheless, continued surveillance of antimicrobial resistance in non-vaccine serotypes is necessary to prevent the resurgence of resistance. Other virulence factors which are not serotype specific also need to be studied to overcome the drawbacks of serotype-specific pneumococcal vaccines. PCV-13 was launched during May 2017 under the NIP of five Indian states with the highest pneumococcal diseases in the country and is expected to be rolled out in the other parts of the country in the coming days.
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Prosthetic joint infection: A major threat to successful total joint arthroplasty p. 475
Sujeesh Sebastian, Rajesh Malhotra, Benu Dhawan
DOI:10.4103/ijmm.IJMM_19_11  PMID:30880693
Total joint arthroplasty (TJA) is one of the most common and reliable orthopaedic procedures that has significantly improved the quality of life of patients with degenerative joint diseases. Following the increase in the ageing population, availability of trained orthopaedic surgeons and advances in implantation procedures, demand for TJA both globally and in India is significantly increasing. Though TJA is one of the most cost-successful orthopaedic procedures, prosthetic joint infection (PJI) is one of the major complications of joint arthroplasty. Accurate diagnosis of PJI is challenging. Since total hip and knee arthroplasties comprises the majority of TJAs, this review focuses on the current understanding of incidence, risk factors, pathogenesis, causative microorganisms, diagnosis, treatment and prevention of PJI related to these two procedures.
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ORIGINAL ARTICLES Top

Multidrug-resistant Enterobacteriaceae colonising the gut of adult rural population in South India p. 488
Sherly Antony, Kandasamy Ravichandran, Reba Kanungo
DOI:10.4103/ijmm.IJMM_18_388  PMID:30880694
Background: Multidrug-resistant (MDR) colonisers act as a reservoir for transmission of antibiotic resistance and are a source of infection. Exposure to antibiotics by the commensal flora renders them resistant. Antibiotic consumption and hospitalisation are two major factors influencing this. We studied, antibiotic-resistant bacteria colonising rural adult population who had restricted access to health care and presumably had low consumption of antibiotics. Aim: Detection of multidrug resistance genes of extended spectrum β-lactamase (ESBL-CTX-M), AmpC β-Lactamase (CIT), Klebsiella pneumoniae carbapenemase (KPC) and New Delhi Metallo β-lactamase (NDM) in Enterobacteriaceae colonising the gut of adult population in a South Indian rural community. Methodology: Faecal samples of 154 healthy volunteers were screened for Enterobacteriaceae resistant to commonly used antibiotics by standard methods, followed by phenotypic detection of ESBL by double disk synergy method, AmpC by spot inoculation and carbapenemases by imipenem and ethylenediaminetetraacetic acid + imipenem combined E-test strips and modified Hodge test. Polymerase chain reaction was done to detect blaCTX-M,blaCIT,blaKPC-1 and blaNDM-1 genes coding for ESBL, AmpC, KPC and NDM, respectively. Results: Colonisation rate of enteric bacteria with MDR genes in the community was 30.1%. However, phenotypically, only ESBL (3.2%) and NDM (0.65%) were detected. While the genes coding for ESBL, AmpC and NDM were detected in 35.6%, 17.8% and 4.4% of the MDR isolates, respectively. Conclusions: Carriage of MDR strains with a potential to express multidrug resistance poses a threat of dissemination in the community. Awareness for restricted use of antibiotics and proper sanitation can contain the spread of resistant bacteria.
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Characterization of In vitro inhibitory effects of consensus short interference RNAs against non-structural 5B gene of hepatitis C virus 1a genotype p. 494
Imran Shahid, Waleed Hassan Almalki, Munjed M Ibrahim, Sultan Ahmad Alghamdi, Mohammed H Mukhtar, Shaia Saleh R. Almalki, Saad Ahmed Alkahtani, Mohammad S Alhaidari
DOI:10.4103/ijmm.IJMM_17_146  PMID:30880695
Purpose: Chronic hepatitis C has infected approximately 170 million people worldwide. The novel direct-acting antivirals have proven their clinical efficacy to treat hepatitis C infection but still very expensive and beyond the financial range of most infected patients in low income and even resource replete nations. This study was conducted to establish an in vitro stable human hepatoma 7 (Huh-7) cell culture system with consistent expression of the non-structural 5B (NS5B) protein of hepatitis C virus (HCV) 1a genotype and to explore inhibitory effects of sequence-specific short interference RNA (siRNA) targeting NS5B in stable cell clones, and against viral replication in serum-inoculated Huh-7 cells. Materials and Methods: In vitro stable Huh-7 cells with persistent expression of NS5B protein was produced under gentamycin (G418) selection. siRNAs inhibitory effects were determined by analysing NS5B expression at mRNA and protein level through reverse transcription-polymerase chain reaction (PCR), quantitative real-time PCR, and Western blot, respectively. Statistical significance of data (NS5B gene suppression) was performed using SPSS software (version 16.0, SPSS Inc.). Results: siRNAs directed against NS5B gene significantly decreased NS5B expression at mRNA and protein levels in stable Huh-7 cells, and a vivid decrease in viral replication was also exhibited in serum-infected Huh-7 cells. Conclusions: Stable Huh-7 cells persistently expressing NS5B protein should be helpful for molecular pathogenesis of HCV infection and development of anti-HCV drug screening assays. The siRNA was effective against NS5B and could be considered as an adjuvant therapy along with other promising anti-HCV regimens.
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Validation of pneumococcal iron acquisition (piaA) gene for accurate identification of Streptococcus pneumoniae p. 504
Sreeram Chandra Murthy Peela, Sujatha Sistla, Kadhiravan Tamilarasu, Sriram Krishnamurthy, B Adhishivam
DOI:10.4103/ijmm.IJMM_18_274  PMID:30880696
Purpose: The pneumococcal iron acquisition (piaA) gene is found to be highly specific and hence proposed as a diagnostic marker for identification of pneumococci. The objective of the present study was to evaluate the piaA gene as a genetic marker for the identification of pneumococci. Methods: Twenty isolates were initially sequenced for lytA gene using published primers. PiaA-PCR (piaA polymerase chain reaction) was performed using in-house primers and protocol. Based on the sensitivity and specificity results, a final sample of 30 pneumococcal isolates and 11 non-pneumococcal isolates confirmed with lytA- sequencing were selected. Statistical analyses were performed using OpenEpi v3.01 and GraphPad Quickcalc at P < 0.05 as the level of statistical significance. Results: Of the initial 20 samples tested, piaA PCR was positive in only 71.43% (10/14) of the pneumococcal isolates but was 100% specific (0/6 non-pneumococcal isolates) P = 0.011. When the PCR was performed on 41 samples, the sensitivity increased to 73.33% (95% of confidence interval [CI] = 55.55–85.82) and specificity remained the same P < 0.001. The level of agreement between the PCR and lytA-sequencing was found to be moderate (κ = 0.694; 95% CI = 0.432–0.955). Conclusions: PiaA-PCR can be used as a specific marker for the identification of pneumococcus, though it is less sensitive. As the level of agreement was moderate, further analyses on a large number of samples can give conclusive evidence for its use as a diagnostic marker for pneumococcus.
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A road less travelled: Clinical comparison of HIV seropositive and seronegative patients with cystoisosporiasis – An 11-year experience from a tertiary care centre in Northern India p. 508
Ujjala Ghoshal, Vidhi Jain, Nidhi Tejan, Sonali Khanduja Kalra, Prabhat Ranjan, Richa Sinha, Dinesh Gangwar, Uday C Ghoshal
DOI:10.4103/ijmm.IJMM_18_99  PMID:30880697
Background: Cystoisospora is a well-known opportunistic enteric parasite among human immunodeficiency virus (HIV) seropositive patients but there is a paucity of data among HIV negative patients. This study investigated Cystosporiasis on both HIV positive and negative patients, with or without diarrhea, presenting to a tertiary care and super specialty center of northern India. Methodology: Oocysts of Cystoisospora were detected on light microscopy, by modified Kinyoun staining of stool specimens, over an 11-year study period. Results: Of the 10,233 stool specimens evaluated, Cystoisospora was detected in 64 patients, 37 (57.81%) of whom were HIV positive. Year-wise analysis showed an overall declining trend of cystoisosporiasis. Maximum cases were detected in May and June in HIV positive patients and February and September among HIV negative patients. Among HIV positive patients, the mean CD4 count was 152.04 ± 81.12cells/μL, mean absolute eosinophil count (AEC) was 229.16 ± 175.62 cells/μL and 12.5% patients had mild eosinophilia. Tuberculosis was the most common co-morbidity. Dual infections of Cystoisospora with Cryptosporidium and Giardia were also seen. Among HIV negative patients, eight had primary autoimmune disorders, seven were solid organ transplant recipients and the rest had chronic bowel diseases. The mean AEC was 485.47 ± 414.88 cells/μL, with 14.81% patients showing mild and 11.11% showing marked eosinophilia. Dual infection with Giardia was seen. Recurrent cystoisosporiasis was noted, despite cotrimoxazole treatment in a single case. Conclusion: The epidemiology of cystoisosporiasis differs between HIV seropositive and seronegative patients in terms of year-wise and month-wise trends, co-infections and most importantly, AECs.
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Dual therapy with lopinavir/ritonavir plus lamivudine could be a viable alternative for antiretroviral-therapy-naive adults with HIV-1 infection regardless of HIV viral load or subgenotype in resource-limited settings: A randomised, open-label and non-inferiority study from China p. 513
Linghua Li, Haolan He, Yun Lan, Jinfeng Chen, Huolin Zhong, Jingmin Nie, Xiejie Chen, Fengyu Hu, Xiaoping Tang, Weiping Cai
DOI:10.4103/ijmm.IJMM_18_172  PMID:30880698
Backgrounds: This randomised controlled, open-label, non-inferiority trial was conducted in antiretroviral-naïve HIV-1-infected patients to assess the efficacy and safety of 48-week dual therapy of LPV/r plus 3TC (DT group) compared with Chinese first-line triple-therapy regimen (TT group). Methods: 198 were randomised to DT (n = 100) or TT (n = 98). Results: Ninety-two DT patients (92%) and 88 TT patients (89.8%) achieved HIV-1 RNA <50 copies/ml at week 48 (P = 0.629). Moreover, the safety profile was similar between two groups, and no secondary HIV resistance was observed. Conclusion: The results suggest that dual therapy of LPV/r plus 3TC is non-inferior to the first-line triple-therapy regimen in China.
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Human papillomavirus prevalence and genotype distribution among Turkish women with or without cervical lesion p. 517
Mehmet Demirci, Aylin Dag Guzel, Aynur Adeviye Ersahin, Eda Yorulmaz, Suat Suphan Ersahin, Baris Ata Borsa
DOI:10.4103/ijmm.IJMM_18_232  PMID:30880699
Context: Human papillomavirus (HPV) infection is the main cause of cervical cancer, but the risk is associated with the various HPV genotypes which may be found in women with or without clinical findings. Aims: We aimed to identify HPV prevalence and genotype distribution in women with or without cervical lesions admitted to Gynaecology and Obstetrics Clinics of one of the largest private hospitals in Istanbul between 2013 and 2017. Subjects and Methods: In the present study, cervical cytobrush samples collected from 2464 women with different cytological conditions, and investigated for the presence of HPV, and the different genotypes. Results were evaluated based on the HPV positivity in different cytological findings, and ages. Furthermore, distribution of high-risk (HR) and low-risk (LR) genotypes in different groups was investigated. Results: Among all participants, 1925 (78.1%) was with the normal cytological condition, 354 (14.4%) with ASC-US; 151 (6.1%) with low-grade squamous intraepithelial lesion (LSIL), and 34 (1.4%) with high-grade squamous intraepithelial lesion (HSIL). Our results showed that 649 out of 2464 patients (26.3%) were positive, and 1815 (73.7%) were negative for the presence of HPV. Among 649 positive patients, 223 (34.3%) were found positive for more than one genotype. HPV 16 was found the most common HR-HPV type in ASC-US and LSIL whereas HPV 18 was the most common in HSIL. HPV 6 was found the most common LR-HPV type in ASC-US and LSIL whereas HPV 11 was the most common in HSIL. 26.9% of women <50 years old, and 22.3% of women ≥50 years old was positive for HPV. The most common HR-HPV genotype was 16 in both groups with (19%) or without (17%) abnormal cytology. Conclusions: We concluded that HPV prevalence and genotype distribution in women with or without clinical findings is an important predictor of cervical cancer.
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Occurrence of II and V staphylococcal cassette chromosome mec types among coagulase-negative staphylococci from Northeastern part of India p. 522
Deepshikha Bhowmik, Pinki Chakraborty, Rituparna Bhowmick, Rakesh Sarkar, Shiela Chetri, Amitabha Bhattacharjee
DOI:10.4103/ijmm.IJMM_18_285  PMID:30880700
Introduction: Coagulase Negative Staphylococci, the most commonly isolated pathogen are becoming emerging threats to the community as well as to the nosocomial environment. The present study underscores the distribution of Staphylococcal cassette chromosome mec (SCCmec) types among Methicillin resistant Coagulase Negative Staphylococci from the environmental origin. Methods and Materials: Environmental and food sample (n = 460) from different location of northeastern region of India were collected for a period of one year and were phenotypically and genotypically screened using cefoxitin disc and PCR techniques for mecA and mecC gene detection. All the MR-CoNS isolates possessing mecA gene were subjected to 16srDNA sequencing for species identification. SCCmec typing was determined by evaluating using primer sets from type I to type V. Antibiotic susceptibility testing was performed for all the isolates. Statistical analysis with chi-square test using SPSS-21 statistical software. Results: Methicillin resistance shown by one hundred forty three isolates were carried out for molecular analysis, among them 53.84% serves as mecA carrier. Distribution of Staphylococcus haemolyticus was more frequent and was found that SCCmec types II and V were predominant among the study isolates. Linezolid was the drug of choice for the CoNS isolates. Statistical analysis showed an insignificant result for the tested antibiotics and SCCmec types. Conclusion: This study therefore interprets the relative importance of SCCmec types among MR-CoNS isolates.
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A study of influenza 2017–2018 outbreak in Andhra Pradesh, India p. 526
Nagaraja Mudhigeti, Rishi Gowtham Racherla, Padmalatha Anjaneyulu Mahalakshmi, Madhavi Latha Pamireddy, Umapathi Nallapireddy, Meenakshi Kante, Usha Kalawat
DOI:10.4103/ijmm.IJMM_18_272  PMID:30880701
Background and Objectives: Influenza virus is a typical human pathogen causing serious respiratory illness resulting in significant mortality throughout the globe. Andhra Pradesh witnessed the first case of influenza A H1N1 in India from Hyderabad (now in Telangana) on May 16, 2009. In the recent past, Andhra Pradesh witnessed exponential increase in the number of confirmed cases of influenza infection. In this study, we present the salient features of the recent outbreak of influenza during 2017–2018 in the state of Andhra Pradesh, first of its kind after the division of the state. Materials and Methods: Clinically, suspected cases of influenza-like illness received in the Virus Research and Diagnostic Laboratory, Department of Microbiology, Sri Venkateswara Institute of Medical Sciences (SVIMS), Tirupati, from January 2017 to May 2018 were included in the study. The samples were tested for influenza A, influenza A (H1N1) pdm09, influenza A (H3N2), influenza B, influenza B/Yamagata and influenza B/Victoria. Results: A total of 1286 samples were received for testing. The positive samples were influenza A unsubtypable (109), influenza A (H1N1) pdm09 (356), influenza A (H3N2) (38) and influenza B (19; Victoria - 2, Yamagata - 17). There was no significant difference in positivity between genders with 260 (49.81%) females and 262 (50.19%) males being positive. Conclusion: The outbreak started in the late monsoon (January) of 2017 and had two peaks; one in summer months and another in winter months. Influenza B virus was reported from December 2017 to May 2018. Age groups ≤5 years and 6–18 years had higher positivity as compared to other age groups. Regular surveillance programmes are required for assessing the trends of influenza infections due to various subtypes and to plan timely and adequate steps for preventing the spread to larger vulnerable population.
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A study on the circulating genotypes of hepatitis C virus in a tertiary care hospital in Central Kerala p. 532
Maria John, Seema Oommen, Ozhiparambhil Anilkumar Jagan, Sincy George, Sivan Pillai
DOI:10.4103/ijmm.IJMM_18_239  PMID:30880702
Background: Hepatitis C is an emerging infection in India, which is known to progresses to liver cirrhosis and hepatocellular carcinoma. The persistence of chronic HCV infection is due to the existence of various genotypes and its various subtypes. There are seven different genotypes of HCV. These genotypes vary in their severity to cause infections as well as their response to treatment. Aim: This study aims at identifying the predominant genotypes of HCV in a population of patients presenting in a tertiary care center in Central Kerala. Settings and Design: This study was conducted at a tertiary care hospital and medical college, located in Central Kerala in the Department of Microbiology from January 2014 to June 2015.The sample size was 600 and a high risk group of patients attending the gastroenterology department, deaddiction centre and health care workers were screened. Materials and Methods: Serum samples were subjected to EIA, either rapid card or ELISA. Serum samples that were positive for HCV antibodies were confirmed by PCR. Twenty seven samples were positive for HCV antibodies by ELISA/rapid card, out of which 16 were confirmed by PCR. These 16 samples were subjected to gene sequencing to identify the genotype. Results: The prevalent genotypes isolated in this study was genotype 1, 3 and 4. Genotype 1 and 3 was predominantly seen transmitted by blood transfusions and multiple hemodialysis. The variability in laboratory parameters like SGOT and SGPT and its ratio with each genotype was also evaluated. Conclusion: To conclude, the occurrence of genotype 4 at a similar level to genotype 1 shows diffusion of new genotype in Kerala.
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Transcriptional response of AcrEF-TolC against fluoroquinolone and carbapenem in Escherichia coli of clinical origin p. 537
Shiela Chetri, Anutee Dolley, Deepshikha Bhowmik, Debadatta Dhar Chanda, Atanu Chakravarty, Amitabha Bhattacharjee
DOI:10.4103/ijmm.IJMM_18_308  PMID:30880703
Introduction: Efflux pump systems constitute a major means of intrinsic resistance in Escherichia coli. AcrEF-TolC pump is known to exhibit higher expression level in quinolone resistant isolates. However, the transcriptional response of this pump is yet to be known when exposed to quinolone and other group of antibiotics. Objective: The present study analyses the transcriptional response of AcrEF-TolC in the presence of quinolones and carbapenems. Methodology: A total of 167 non-duplicate clinical isolates from Silchar medical college and Hospital, Silchar, India were included in this study. Of which 27 were devoid of any carbapenemase activity and among them 13 isolates showed overexpression of AcrE and AcrF gene. Transcriptional response of AcrE was directly proportional to increasing concentration of levofloxacin and ofloxacin. However, the response of AcrE and AcrF was inconsistent with carbapenems. Result: The study isolates showed susceptibility towards amikacin (68.4%), gentamicin (59.6%), cefepime (52.7%) and pipercillin/tazobactam (48.3%). The present investigation highlights that apart from qnr genes and mutational changes in gyr region, AcrEF-TolC plays a major role in fluoroquinolone resistance in this part of the world. Conclusion: Upregulation of AcrE in the presence of levofloxacin and ofloxacin warrants further investigation to establish their active role in efflux of this drug.
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High-sensitivity detection of human malaria parasites by the use of rapid diagnostic tests and nested polymerase chain reaction in burdened communities of North East India p. 541
Ramzan Ahmed, Kuldip Devnath, Deep Bhowmik, Indu Sharma
DOI:10.4103/ijmm.IJMM_18_394  PMID:30880704
Background and Objectives: The study aimed to evaluate the diagnostic performance of malaria through microscopy and rapid diagnostic test (RDT) analysis performed locally and the accuracy evaluated by nested polymerase chain reaction (PCR) for diagnosis of Plasmodium falciparum from hotspot regions of North East (NE) India. Materials and Methods: One thousand one hundred and seventy-three blood samples were collected for identification of P. falciparum infection using microscopy and RDT analysis. DNA was extracted from whole blood using QIAamp DNA blood mini kit, and nested PCR was performed to confirm P. falciparum for evaluating sensitivity and specificity from various epidemiological surveys and geographical areas of NE India. Results: Of 1173 symptomatic malaria suspected patients, 15.6% (183/1173) patients were diagnosed as malaria positive by RDT and 67.94% cases (53/78) with microscopy. Of 183 malaria-positive patients, 42.62% (78/183) were diagnosed with P. falciparum and 84.61% (66/78) further confirmed to be P. falciparum positive by nested PCR. High sensitivity (97.9%) and low specificity (2.03%) of the RDT and high sensitivity (99.1%) and low specificity (0.9%) in microscopy against nested PCR results was statistically significant (P < 0.05). Epidemiological comparisons expressed highest incidences in Manipur (51.11%) followed by Meghalaya (48.93%) and Assam (35.16%). Overall incidence rate among the genders was observed to be higher in males than in females. Conclusions: Our findings suggest that PCR, RDT and microscopy can potentially determine hotspots at moderate transmission intensities, but PCR testing has a diagnostic advantage as transmission intensity falls. Therefore, malaria control programs should consider PCR testing when the prevalence of infection is low.
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Real-time multiplex polymerase chain reaction with high-resolution melting-curve analysis for the diagnosis of enteric infections associated with diarrheagenic Escherichia coli p. 547
Thingujam Surbala Devi, Elantamilan Durairaj, Wihiwot Valarie Lyngdoh, Sourabh Gohain Duwarah, Annie Bakorlin Khyriem, Clarissa Jane Lyngdoh
DOI:10.4103/ijmm.IJMM_18_277  PMID:30880705
Introduction: Although diarrheagenic Escherichia coli (DEC) strains are important bacterial causative agents of diarrhoea, they are not routinely sought as stool pathogens in clinical laboratories as conventional microbiological testing are unable to distinguish between normal flora and pathogenic strains of E. coli. This study was undertaken to determine the prevalence of DEC pathotypes amongst children with and without diarrhoea and to detect specific virulent genes present in different DEC pathotypes, using real-time multiplex polymerase chain reaction (PCR) with high-resolution melting (HRM) technology. Materials and Methods: Stool samples were obtained from cases and controls. Using a set of conventional biochemical tests, E. coli strains were identified. Further, these isolates were subjected to multiplex PCR system for the detection of virulence genes of different pathotypes of DEC. Real-time multiplex PCR was performed for the detection of specific virulent genes of DEC pathotypes, using Rotor-Gene Q instrument (Qiagen) having High-resolution Melt analyser using Type-it HRM PCR kit (Qiagen) containing EvaGreen fluorescent intercalating dye. Results: In this study, we had successfully standardised two multiplex PCR assays which were found to be effective for direct detection of enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC). A total of 42 DEC strains were detected at an overall rate of 19.3% (n = 42), from the total 217 E. coli isolates recovered from the cases (n = 39, 17.9%) and control (n = 3, 3.8%) groups. Amongst the 42 DEC pathotypes (39 from cases and 3 from controls), EPEC (10%), EAEC (8.82%), ETEC (2.94%) and EIEC (1.18%) were found in children with diarrhoea (cases) and in children without diarrhoea (control) only EAEC (2.13%) and EPEC (4.26%) were detected. Age distribution, gender variation, seasonal variation and clinical features were also analysed Conclusion: This study helped evaluate the prevalence of DEC amongst children (<18 years of age) with and without diarrhoea using multiplex real-time PCR with HRM analysis.
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Evaluation of biomarkers: Galactomannan and 1,3-beta-D-glucan assay for the diagnosis of invasive fungal infections in immunocompromised patients from a tertiary care centre p. 557
Shreya Singh, Harsimran Kaur, Hansraj Choudhary, Shveta Sethi, Pankaj Malhotra, Krishan Lal Gupta, Shivaprakash M Rudramurthy, Arunaloke Chakrabarti
DOI:10.4103/ijmm.IJMM_18_366  PMID:30880706
Purpose: Due to limitations of traditional microbiological techniques, standardised fungal biomarker tests such as Galactomannan Index (GMI) and 1,3-beta-D-glucan (BDG) are being preferred for diagnosis of invasive fungal infections (IFIs). These tests have been extensively used in developed countries but seldom in developing countries. The present study was performed to evaluate these tests for the diagnosis of IFIs in immunocompromised patients at an Indian tertiary care centre. Materials and Methods: A retrospective hospital-based study was done in immunocompromised patients with clinical suspicion of IFI. The demographic, clinical, radiological and mycological details of the patients were recorded. The patients were categorised into proven, probable and no IFI (as per European Organization for Research and Treatment of Cancer/Mycoses Study Group criteria). The sensitivity and specificity of BDG Fungitell and Platelia Aspergillus antigen assays was estimated. Results: A total of 70 consecutive patients were included, of which 41 had IFI (10 proven and 31 probable) while 29 had no IFI. A significant association was found between IFI and the presence of a central venous line (P = 0.035) and history of intake of T-cell immunosuppressants (P = 0.001). Median BDG values (pg/ml) in patients with proven IFI, probable IFI and no IFI were 300 (range: 70–500), 165 (range: 53–500) and 45 (range: 31–500), respectively. The receiver operating characteristic (ROC) curve analysis for BDG revealed an area under the curve of 0.995, sensitivity: 97.4% and specificity: 96.6% for IFI diagnosis. The ROC curve analysis of GMI revealed an AUC of 0.75 and 90% patients with invasive aspergillosis (IA) had positive GMI. Conclusion: BDG has good sensitivity and specificity for distinguishing IFI from no IFIs and GMI may be used for diagnosing IA.
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Exserohilum keratitis: Clinical profile of nine patients and comparison of morphology versus ITS-Based DNA sequencing for species identification of the fungal isolates p. 564
Rajagopalaboopathi Jayasudha, Savitri Sharma, Paavan Kalra, Dilip Kumar Mishra
DOI:10.4103/ijmm.IJMM_19_51  PMID:30880707
Purpose: The objective of this study was to describe the microbiological and clinical features of nine cases of Exserohilum keratitis. Patients and Methods: Fungal isolates from corneal scrapings were identified based on macroscopic and microscopic characteristics of the colonies and DNA sequencing of ITS1-5.8S-ITS2 region in the rRNA gene. All patients were treated with topical and if required systemic antifungals. Therapeutic penetrating keratoplasty (TPK) was done in case of failed medical therapy. Results: Morphologically, all fungal isolates were Exserohilum rostratum except one Exserohilum mcginnisii. Based on the BLAST analysis, 6 isolates showed 100% similarity to Setosphaeria rostrata (CBS 112815) and E. mcginnisii (CBS 20308). The other three isolates were Setosphaeria holmii (CBS 128053), not reported earlier in fungal keratitis. Three patients were lost to follow-up and response to medical therapy was good (Healed scar – 4 patients). Two out of nine patients were advised TPK. Conclusions: Diagnosis and clinical features of Exserohilum keratitis are akin to other dematiaceous keratitis. The two morphological species of E. mcginnisii and E. rostratum are indistinguishable from Setosphaeria rostratum at DNA sequence level, which justifies the retention of the latter nomenclature.
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BRIEF COMMUNICATIONS Top

Sub-inhibitory concentration of ertapenem induces overexpression of regulator of antibiotic resistance A in Escherichia coli p. 569
Shiela Chetri, Kabita Singha, Deepshikha Bhowmik, Debadatta Dhar Chanda, Atanu Chakravarty, Amitabha Bhattacharjee
DOI:10.4103/ijmm.IJMM_18_436  PMID:30880708
AcrAB-TolC is a tripartite efflux pump system constitutively expressed which functions as an intrinsic-resistant mechanism found to be responsible for conferring resistance towards dyes, detergents and different compounds including various classes of antibiotics. One global regulator belonging to AraC-type regulator family, regulator of antibiotic resistance A (RarA) up-regulates the expression of AcrAB-TolC encoded in Klebsiella pneumoniae, Enterobacter sp. 638, Serratia proteamaculans 568 and Enterobacter cloacae resulting in multidrug-resistant phenotypes. The present work was initiated to find out the transcriptional response of RarA in clinical isolates of Escherichia coli against concentration gradient carbapenem stress. A total of 22 clinical isolates of E. coli and expression level of regulators were analysed via quantitative real-time polymerase chain reaction with and without carbapenem stress. As a result, a strong correlation between the expressional levels of RarA in AcrAB overexpressed isolates of E. coli and elevated expression was observed when exposed under concentration gradient ertapenem stress. The clones containing pRar showed reduction in the zone of inhibition towards carbapenem, indicating the active participation of RarA in AcrAB overexpressed isolates of E. coli conferring resistance towards carbapenems.
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Carbapenem-resistant enterobacteriaceae screening: A core infection control measure for critical care unit in India? p. 572
Yamunadevi V Ramanathan, Ramasubramanian Venkatasubramanian, P Senthur Nambi, Madhumitha Ramabathiran, Ramesh Venkataraman, MA Thirunarayan, P Samundeeswari, Nagarajan Ramakrishnan
DOI:10.4103/ijmm.IJMM_18_437  PMID:30880709
Background: Infection/colonization due to carbapenem-resistant enterobacteriaceae (CRE) are emerging as an important challenge, particularly in high risk patients due to widespread use of Carbapenems. Therefore, preventing both CRE infections and their transmission has become an important infection control objective. Aims and Objective: Determine the proportion of asymptomatic carriers of CRE among patients admitted to our critical care unit (CCU) from the community and other health care facilities. Enumerate risk factors and guide implementation of infection control interventions. Methods: This prospective surveillance study was done in a 24 bed CCU of a tertiary care hospital, at Chennai, India between August2017 through December 2017. Patients were screened based on a composed questionnaire framed from Centers for Diseases Control and Prevention CRE tool-kit. Two rectal swabs were collected from each patient. They were processed in microbiology laboratory. Results: A total of 102 patients were included. CRE colonization were identified in 8 (7.8%) of the total samples. Among 8 CRE colonized patients 3 (37.5%) patients developed systemic infection. Patients who were exposed to high end antibiotic and past history of surgery had significant association with CRE colonization of (P = 0.0029) and (P = 0.0167) respectively. Conclusion: Overall CRE colonization rates among our CCU patients were found to be low. Risk factors associated with CRE colonization were high end antibiotic exposure and surgery in past 90 days. Hence rectal screening should be a risk factor–based active surveillance. Association of systemic infection among CRE colonizers was more significant. This study led us to modify our infection control practices in CCU.
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National survey of infection control programmes in South Asian association for Regional Cooperation countries in the era of patient safety p. 577
Shakti Kumar Gupta, Vijaydeep Siddharth, Mahesh R Belagere, Andrew James Stewardson, Sunil Kant, Sanjeev Singh, Nalini Singh
DOI:10.4103/ijmm.IJMM_18_82  PMID:30880710
Background: The implementation of hospital infection prevention and control (IPC) in south Asia is not well described. We aimed to assess IPC programmes in hospitals in this region and explore opportunities for improvement. Methods: Attendees from hospitals in the South Asian Association for Regional Cooperation (SAARC) region who were at one of four National Initiative for Patient Safety workshops organised by All India Institute of Medical Sciences (New Delhi) from 2009 to 2012 were invited to complete a semi-structured questionnaire. The survey addressed six main components of IPC programmes. Results: We received responses from 306 participants from 82 hospitals. Five key opportunities for improvement emerged: (1) lack of healthcare epidemiologists, (2) relative infrequency of antibiotic guidelines (53%) and prescribing audits (33%) (3) lack of awareness of needle stick injury rates (84%) (4) only 47% of hospitals were prepared for surge capacity for patients with infectious diseases, and (5) limited coordination of hospital infection control personnel with other support services (55%-66%). Conclusion: These results outline IPC challenges in the SAARC region and may be useful to guide future quality improvement initiatives.
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Clinical relevance of cagA and vacA and association with mucosal findings in Helicobacter pylori-infected individuals from Chennai, South India p. 582
Anand Vadivel, C P. Girish Kumar, K Muthukumaran, G Ramkumar, R Balamurali, Rang Lal Meena, S Venkatasubramanian, T Rajkumar Solomon, P Ganesh, S Jeevan Kumar
DOI:10.4103/ijmm.IJMM_18_406  PMID:30880711
Helicobacter pylori is associated with a spectrum of severe gastrointestinal conditions. In this study, an attempt was made to correlate endoscopic mucosal patterns with H. pylori infection and examine the pathogenic potential of the strains. Among the 147 dyspeptic individuals studied, 42.2% were H. pylori infected. Association of H. pylori with type 3 and 4 mucosal patterns (P = 0.001) and intestinal metaplasia (P = 0.012) was seen. vacA was associated with histological (P = 0.014) and endoscopy findings (P = 0.009). Association of mucosal patterns with H. pylori infection could be useful for clinicians to decide on the need for eradication therapy.
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Deciphering polymyxin B minimum inhibitory concentration from colistin minimum inhibitory concentration and vice versa: An analysis on 156 carbapenem-resistant Enterobacteriaceae isolates p. 587
Bijayini Behera, Jayanti Jena, Punyatoya Kar, Srujana Mohanty, Ashoka Mahapatra
DOI:10.4103/ijmm.IJMM_18_293  PMID:30880712
The susceptibility determination to polymyxins (colistin and polymyxin B) remains a challenge for clinical microbiology laboratories. We evaluated the minimum inhibitory concentration (MIC) of both antimicrobials by the broth microdilution method in a selected subset of 156 carbapenem-resistant Enterobacteriaceae (CRE) isolates. Good concordance between polymyxin B and colistin MIC values was obtained, and there was 98% categorical agreement in CRE isolates. Future large-scale multicentre study is needed to draw conclusion if the MIC of colistin can be used to extrapolate the MIC of polymyxin B and vice versa.
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Improved case detection using Xpert Mycobacterium tuberculosis/rifampicin assay in skeletal tuberculosis p. 590
Swapna Rajesh Kanade, Gita Nataraj, Preeti Rajiv Mehta
DOI:10.4103/ijmm.IJMM_19_10  PMID:30880713
Background: In India, musculoskeletal tuberculosis (TB) accounts for 10%–25% of extrapulmonary TB. Data on drug-resistant skeletal TB are lacking. At present, the diagnosis is based mainly on radiological techniques. Laboratory confirmation of skeletal TB is delayed as 6–8 weeks are required for culture results. Xpert Mycobacterium tuberculosis/rifampicin (MTB/RIF) assay is a fully automated test which simultaneously detects MTB and RIF resistance within 3 h. Hence, this study was done to compare the yield of case detection using Xpert assay in comparison with culture in specimens received from clinically suspected skeletal TB cases. Methods: Retrospective analysis of microscopy, culture and Xpert assay results was carried out on specimens received in laboratory from skeletal TB cases from January 2016 to December 2017. Results: Of the 201 patients analysed, majority of the specimens were obtained from the spine (55.72%). MTB was detected in 48.68% of tissue and 24% of pus specimens. Xpert assay was detected MTB in 67 (33.33%) specimens of which 53 (47.32%) were from the spine. Culture was detected MTB in 66 (32.83%) specimens. Xpert assay was detected two specimens more than culture. One specimen was positive by only culture. RIF-resistant MTB was detected in 10 (14.92%) specimens by Xpert assay. Conclusion: The spine is the most common site involved. Tissue specimen is better for early diagnosis. High RIF resistance in skeletal TB is an alarming situation. Ability of Xpert MTB/RIF assay for rapid and simultaneous detection of MTB and RIF resistance in comparison with culture makes it a useful diagnostic tool in skeletal TB.
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CASE REPORTS Top

Fungal keratitis caused by Podospora austroamericana: A first case report p. 594
Gunasekaran Rameshkumar, Mariappan Ponlakshmi, Appavu Selvapandiyan, Ravindran Ramsudharsan, Raja Subramanian Krishnan, Prajna Lalitha
DOI:10.4103/ijmm.IJMM_19_1  PMID:30880714
We report a case of keratitis caused by a rare fungus Podospora austroamericana. Clinical and microbiological evaluation of the corneal ulcer was done and the treatment outcome was studied. The fungus was grown from the corneal scraping, and it was identified as P. austroamericana based on DNA sequence and analysis of the internal transcribed spacer region. The patient was treated with topical azithromycin, natamycin and voriconazole. Despite maximum medical therapy, the ulcer progressed very rapidly and the patient developed panophthalmitis and evisceration of the eye had to be done. This is the first reported case of keratitis caused by P. austroamericana.
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A case of septicaemic melioidosis: Utility of therapeutic drug monitoring and high-dose meropenem in successful management p. 597
Karthik Gunasekaran, Anushree Amladi, Sumith K Mathew, T Angel Miraclin, Ramya Iyyadurai
DOI:10.4103/ijmm.IJMM_18_433  PMID:30880715
Melioidosis is an emerging infectious disease of major public health importance. We describe a patient who presented with septicaemic melioidosis with multi-organ dysfunction. He had only marginal response on standard doses of meropenem. Therapeutic drug monitoring (TDM) revealed suboptimal concentration of meropenem following which drug dose was increased, with which he showed rapid clinical improvement and microbiological clearance. Melioidosis presents with multisystem involvement with disseminated abscess, standard dosing of meropenem may not be sufficient in achieving therapeutic levels and TDM with increased dosing in these critically ill patients will improve outcome.
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An unusual case of unresolving tunnel infection in a patient on continuous ambulatory peritoneal dialysis p. 600
S Mohamed Marzuk, Anusha Rohit, P Nagarajan, Victorine Nzana, Verus Mboneko Katuraga, Rajeevalochana Parthasarathy, Milly Mathew, Georgi Abraham
DOI:10.4103/ijmm.IJMM_18_425  PMID:30880716
Atypical mycobacteria remain a rare cause of peritoneal dialysis catheter-related tunnel infection (TI) and poses serious risk because of the resistant nature to most antibiotic therapy. Non-tubercular mycobacterial infections lead to chronicity requiring peritoneal dialysis catheter removal. We report an 82-year-old male, with diabetic nephropathy who had a coinfection with Staphylococcus hominis and Mycobacterium abscessus who presented with pus discharge at exit site and TI. He was treated with relocation of the extraperitoneal part of the catheter with a new exit site without catheter removal and multidrug mycobacterial therapy.
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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