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  ~ Table of Contents - Current issue
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July-December 2020
Volume 38 | Issue 3 & 4
Page Nos. 243-501

Online since Wednesday, November 4, 2020

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REVIEW ARTICLE: COVID-19 SERIES  

Steps, implementation and importance of quality management in diagnostic laboratories with special emphasis on coronavirus disease-2019 Highly accessed article p. 243
Shailesh D Pawar, Sadhana S Kode, Sachin S Keng, Deeksha S Tare, Priya Abraham
DOI:10.4103/ijmm.IJMM_20_353  
A well-established and functional quality management system is an integral part of any diagnostic laboratory. It assures the reliability and standards of the laboratory function. A pandemic situation such as that caused by the influenza H1N1 2009 virus or the recent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) increases the demands on the public health system, and the need to build, upgrade and expand the number of diagnostic laboratories. The Coronavirus disease-19 (COVID-19) pandemic caused by the SARS-CoV-2 unleashed a public health emergency of an unprecedented scale. The need has been highlighted for the accreditation of tests relating to COVID-19 by the National Accreditation Board for Testing and Calibration Laboratories (NABL) or any agencies approved by the World Health Organization (WHO) or Indian Council of Medical Research. The implementation of quality system in diagnostic laboratories would ensure accurate, reliable and efficient test results at par with the international standards. The functional aspects of a laboratory such as a well-defined organogram, standard operating procedures, good laboratory practices, quality controls, human resources, equipment management, reagents, inventory of records, proper communication need to be addressed to assure quality. Biosafety considerations should include the guidelines laid out by the WHO, the Institutional Biosafety Committee and the Department of Biotechnology, Government of India for carrying out diagnostic work in the laboratory. Currently, there are 1922 laboratories, operational for COVID-19 diagnosis in India. Considering the urgency of testing, the NABL has expedited the process of accreditation and issued accreditation to 818 laboratories. The adherence to the practicable aspects of quality described in this article would help in establishing quality in COVID-19 testing laboratories.
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Convalescent plasma – Is it useful for treating SARS Co-V2 infection? Highly accessed article p. 252
Sudha Ranganathan, Ranganathan N Iyer
DOI:10.4103/ijmm.IJMM_20_358  
The world is challenged with the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic. Although preventive measures such as social distancing, personal protective equipment and isolation would decrease the spread of the infection, a definitive treatment is still under way. Antivirals, immunisation, convalescent plasma (CP) and many more modalities are under trial, and there has been no definite answer to the management of COVID-19 infection. All patients so far have received the standard and symptomatic care. It is shown that the SARS-CoV 2 is a respiratory pathogen, and 80% of the infected patients would recover from the illness and it is the 20% of the infected patients require hospitalisation and even critical care. CP has been used to treat recent epidemic respiratory infections such as Middle East respiratory syndrome and severe acute respiratory syndrome (SARS) infections with promising results. The CP of a recovered individual contains antibodies which neutralise the virus and decrease the viral replication in the patient. It is a classic adaptive immunotherapy and has been applied in the prevention and treatment of many infectious diseases. CP is plasma taken from a person who has recovered from an infection, which contains neutralising antibodies against the said infection. Giving CP to susceptible individuals or infected patients is a form of passive antibody therapy and in the case of SARS-CoV-2, is expected to provide protection by viral neutralisation and antibody-dependent cytotoxicity and phagocytosis. The adaptive response is to a specific antigen-binding array of molecules that are foreign to the host. The human response to viruses uses both the innate and the adaptive arms in its attempt to rid the host of the invading pathogen. The humoral response is a component of the adaptive immune response that allows for antibodies to bind to foreign invading pathogens, marks the pathogens and their toxins for phagocytosis and recruits further phagocytic cells to the site via the activation of the complement system and eventually prevents the pathogen from infecting target cells. Studies from Wuhan from various institutions during the research on COVID-19 infections during December 2019 have also shown promising results. Till date, randomised controlled studies for the use of CP in SARS-CoV-2 infection are lacking, and many countries have invited institutions to participate in clinical trials. The Indian Council of Medical research and the Central Drugs Standard Control Organisation, Government of India, have allowed the use of CP as an investigational drug under a trial basis. Internationally, agencies such as the USFDA, American Association of Blood Banks, European Blood Safety and British Blood Transfusion Society have also come out with various guidelines for the use of CP in COVID-19 infection. This article will review the current guidelines for the use of CP and compare the various guidelines of different agencies.
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Paediatric COVID-19 and the GUT Highly accessed article p. 261
Rohit Gupta, Saman Beg, Alok Jain, Shrish Bhatnagar
DOI:10.4103/ijmm.IJMM_20_331  
Although children with novel coronavirus infection (COVID-19) typically present with fever and respiratory symptoms, some children have reported gastrointestinal (GI) symptoms including vomiting and diarrhoea during the course of the disease. The continuous positive detection of the viral RNA from faeces in children even after nasopharyngeal swabs turned negative suggests that the GI tract may shed virus and a tentative faecal–oral transmission. The presence of angiotensin-converting enzyme 2 receptor and transmembrane serine protease 2, which are the key proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cell entry process, in the GI tract can explain the digestive symptoms in COVID-19. COVID-19 has implications for the management of children with chronic luminal diseases. There is increasing concern regarding the risk that children with inflammatory bowel disease being infected with SARS-CoV-2.
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Effect of chloroquine and hydroxychloroquine on COVID-19 virological outcomes: An updated meta-analysis p. 265
Rashmi Ranjan Das, Bijayini Behera, Baijayantimala Mishra, Sushree Samiksha Naik
DOI:10.4103/ijmm.IJMM_20_330  
As anti-malarial drugs have been found to inhibit Corona viruses in vitro, studies have evaluated the effect of these drugs inCOVID-19 infection. We conducted an updated meta-analysis of clinical trials and observational studies published till June 2020. Patients with reverse transcription polymerase chain reaction (RT-PCR) confirmed Severe Acute Respiratory Syndrome Coronavirus 2 (COVID-19) infection were included. The drugs used in the intervention group are Chloroquine (CQ)/Hydroxychloroquine (HCQ) with or without Azithromycin. The primary outcome is time to achieve virological cure. Of 1040 citations, 11 studies provided data of 1215 patients. Compared to control, CQ/HCQ has no significant effect on the time to negative COVID-19 RT-PCR results, neither in clinical trials (mean difference [MD] 1.55; 95% confidence interval [CI] - 0.7 to 3.79; P = 0.18; n = 180), nor in observational studies (MD 1.14; 95%CI - 11.98 to 14.26; P = 0.86, n = 407). CQ/HCQ did not affect the virological cure after day 3, 7, 10, 14, 21 and 28; except after day 5, as shown by a single small non-randomised trial (odds ratio [OR] 9.33; 95% CI 1.51 to 57.65; P = 0.02, n = 30). Pooled data from 2 observational studies showed a significant effect of CQ/HCQ on virological cure by after day 10 (OR 7.86; 95% CI 4.4 to 14.04, P < 0.001, n = 373) and day 14 (OR 6.37; 95% CI 3.01 to 13.48, P < 0.001, n = 407). The GRADE evidence generated was of “very low-quality/certainty”. To conclude, CQ/HCQ does not affect the time to virological cure compared to usual/standard of care in COVID-19 infection. Recurrent infection in a smaller number of patients was noted in the CQ/HCQ group. As the evidence generated was of “very low-quality/certainty)”, large good quality studies are needed to confirm the present findings.
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REVIEW ARTICLES Top

Role of surveillance cultures in infection control p. 277
Manisha Biswal, Archana Angrup, Rimjhim Kanaujia
DOI:10.4103/ijmm.IJMM_20_129  
Hospital-acquired infections are a known menace to the primary disease, for which a patient is admitted. These infections are twenty times more common in developing countries than in the developed ones. Surveillance for colonised patients can be passive or active process. In many hospitals, active surveillance culture for certain sentinel organisms followed by contact precautions for the same is an important part of infection control policy. Specific measures can be taken on early detection of multidrug-resistant organism, allowing prevention of widespread transmission in hospitals. Cultures are the most conventional and economical microbiological method of detection. The cost of active surveillance is a major challenge, especially for developing nations. These nations lack basic infrastructure and have logistic issues. The guidelines regarding this are not very clearly delineated for developing countries. Each hospital has its own challenges and the process is to be tailor-made accordingly. The following review delineates the various aspects of active surveillance for the colonisation of various organisms and the advantages and disadvantages of the same.
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Can quantitative RT-PCR for SARS-CoV-2 help in better management of patients and control of coronavirus disease 2019 pandemic p. 284
Ashok Rattan, Hafiz Ahmad
DOI:10.4103/ijmm.IJMM_20_380  
The emergence of SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), represents a public health emergency of unprecedented proportion. The global containment efforts have been focused on testing, tracing of contacts and treatment (isolation) of those found COVID-19 positive. Since the whole genome sequences of a number of strains of this novel RNA virus were available in the public domain by early January 2020, a number of real-time polymerase chain reaction (RT-PCR) protocols were designed and used for diagnosis of this infection. Most RT-PCRs are designed for qualitative COVID-19 reporting (SARS-CoV-2 detected or not detected), but have been used for semi-quantitative estimation of viral load based on cycle threshold value. Our manuscript discusses the utility of quantitative PCR testing for COVID-19 and its patient management benefits.
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ORIGINAL ARTICLES Top

Utility of a multiplex real-time polymerase chain reaction for combined detection and serotyping of dengue virus in paediatric patients hospitalised with severe dengue: A report from Chennai p. 288
S Balasubramanian, Sara Chandy, Robinson Peter, Gothai S Nachiyar, Amullya Sudhakar, A Sumanth, Anand Manoharan
DOI:10.4103/ijmm.IJMM_20_249  
Objective: Molecular detection and serotyping are rapid, sensitive and accurate techniques for early diagnosis of paediatric dengue. The present study evaluates multiplex real-time polymerase chain reaction (PCR) for diagnosis of dengue virus in children hospitalised with severe dengue (SD) and attempts to establish an association of clinical severity with specific serotypes. Methods: Four hundred and eighty-five samples were received from hospitalised paediatric patients with suspected dengue from March 2019 to February 2020. Multiplex real time PCR was employed for diagnosis. An in-house real-time PCR that combined diagnosis and serotyping was established. Non-structural protein 1 (NS1) assay and real-time PCR were assessed for their accuracy in diagnosing severe paediatric dengue. Results: Three hundred and twenty-five (67%) patients were positive for dengue RNA by real-time PCR. All four serotypes were identified throughout the year; dengue serotype 2 (DEN-2) was predominant (61%) followed by DEN-3, 20%. Compared to the commonly used NS1 testing, multiplex real-time PCR showed greater sensitivity in diagnosing SD. Conclusions: Compared to NS1, multiplex real-time PCR is a rapid and accurate diagnostic test for children hospitalised with SD. DEN-2 was the predominant serotype in severe cases. Continued surveillance of serotypes should be carried out year-round in endemic areas.
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Evaluation of matrix assisted laser desorption ionisation-time of flight mass spectrometry in direct identification of bacteriuria from urine samples p. 293
Balvinder Mohan, Neha Gautam, Nandini Sethuraman, Harsimran Kaur, Neelam Taneja
DOI:10.4103/ijmm.IJMM_20_206  
Objective: The use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI) directly on urine can significantly improve turnaround time for diagnosing urinary tract infection (UTI). The present study was planned to compare the performance of MALDI directly on urine samples with conventional urine culture and evaluate an algorithm using a combination of significant pyuria and MALDI directly on urine samples as a screening method for diagnosing UTI. Materials and Methods: A total of 1000 urine samples from patients with symptoms suggestive of UTIs were analysed. Urine microscopy, urine culture and MALDI were performed simultaneously on all the samples. Results: MALDI correctly identified the microorganisms in 73.83% monomicrobial samples. In culture showing a mixed growth of two and more than three organisms, MALDI was able to identify one microorganism in 27.58% and 15.78% of samples, respectively. There were no peaks by MALDI in 93.53% of 464 sterile samples. The sequential algorithm using urine microscopy and MALDI could correctly identify UTI in 66.23% cases. Conclusion: MALDI can be utilised to rule out bacteriuria in >93% of sterile urine samples. The combination of significant pyuria and direct MALDI as screening method to diagnose UTI (whether monomicrobial or polymicrobial) was not found to be superior than using direct MALDI on urine samples alone.
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A systematic review and meta-analysis of different diagnostic procedures to detect gonococcus infection in resource-limited scenario p. 299
Aromita Mallik, Nibedita Das, Swati Mukherjee, Shibani Datta
DOI:10.4103/ijmm.IJMM_20_312  
Context: Neisseria gonorrhoeae is a Gram-negative diplococcus, an obligate human pathogen, and the etiologic agent of the sexually transmitted infection (STI), gonorrhoea. culture is the standard procedure for diagnosis, which may be supported by nucleic acid tests and microscopy. Aims: To determine the best possible method of diagnosis for Gonococcus infection in resource-limited settings. Settings and Design: The meta-analyses were designed to determine the difference in diagnosis between Culture and nucleic acid amplification tests (NAATs) and also between the different Amplification Tests and widely available Roche COBAS AMPLICOR test. Subjects and Methods: Databases searched were Pubmed, Medline, Google Scholar and Cochrane reviews. Risk ratio (RR) with 95% confidence intervals was estimated for the dichotomous outcomes. The random-effect model was applied for all the studies in the analysis. Statistical Analysis Used: The meta-analysis was computed in RevMan Version 5.3, Copenhagen, Denmark. Results: In the first analysis, NAATs significantly improved the chances of detection in comparison to the standard culture and final RR was 1.24 (1.05–2.51), which put the diamond on the right of no-effect axis, indicating more positives by NAATs. In the second analysis, AMPLICOR had the more positive results, which may have indicated better detection rate, as well as less specificity and final RR was 0.809 (0.737–0.888), which put the diamond on the left of the non-effect axis, indicating more positives by AMPLICOR. Conclusions: In a resource-limited scenario like India, the syndromic management of STIs are considered to be the norm. A positive diagnosis is only given if the tests are confirmed by Culture, as it is still considered to be the gold standard of diagnosis. However, in many cases, due to suboptimal transportation and lack of proper handling, culture in unable to grow even if the patient is infected. In such cases, Nucleic Acid Tests should be able to detect an infection.
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Assessment of antibacterial activity of levonadifloxacin against contemporary gram-positive clinical isolates collected from various Indian hospitals using disk-diffusion assay p. 307
Shrikala Baliga, Dhruv K Mamtora, Varsha Gupta, Priyadarshini Shanmugam, Sanjay Biswas, DN Mukherjee, Suchitra Shenoy
DOI:10.4103/ijmm.IJMM_20_307  
Objectives: Levonadifloxacin is a novel benzoquinolizine subclass of quinolone with broad-spectrum activities against problematic pathogens such as methicillin-resistant Staphylococcus aureus, quinolone-resistant S. aureus, vancomycin intermediate S. aureus, and vancomycin-resistant S. aureus. Levonadifloxacin and its oral prodrug, alalevonadifloxacin, have been recently approved in India for the treatment of acute bacterial skin and skin structure infections, including concurrent bacteraemia and diabetic foot infections. The aim of the study is to assess the activity of levonadifloxacin against Gram-positive clinical isolates collected from various Indian hospitals using the disc-diffusion method. Materials and Methods: Nonduplicate isolates of S. aureus and other Gram-positive isolates collected from June 2019 to March 2020 were subjected to levonadifloxacin susceptibility testing (disk diffusion method) as per the Clinical and Laboratory Standards Institute guidelines (Year 2019). Levonadifloxacin 10 μg impregnated disks were used during the testing. Results: A total of 664 diverse Gram-positive clinical isolates collected from six different hospitals in India were analyzed. Majority (65.5%) of the isolates were S. aureus. All the S. aureus and other Gram-positive isolates were found to be susceptible to levonadifloxacin as per the prespecified interpretive criteria identified based on population pharmacokinetic model and Monte Carlo simulation enabled probability of pharmacodynamic target attainment analysis. Conclusions: The present study showed that levonadifloxacin was highly active against contemporary Gram-positive pathogens and furthermore demonstrated that levonadifloxacin susceptibilities can be reliably determined using the disc-diffusion method.
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Expected plazomicin susceptibility in India based on the prevailing aminoglycoside resistance mechanisms in Gram-negative organisms derived from whole-genome sequencing p. 313
Agila Kumari Pragasam, S Lydia Jennifer, Dhanalakshmi Solaimalai, Dhiviya Prabaa Muthuirulandi Sethuvel, Tanya Rachel, Divyaa Elangovan, Karthick Vasudevan, Karthick Gunasekaran, Balaji Veeraraghavan
DOI:10.4103/ijmm.IJMM_20_384  
Background: Aminoglycoside resistance is a growing challenge, and it is commonly mediated by the aminoglycoside-modifying enzymes (AMEs), followed by 16S rRNA methyl transferase. Plazomicin, a novel aminoglycoside agent approved by the Food and Drug Administration for complicated urinary tract infections is proven to overcome resistance mediated by AMEs but not due to 16S rRNA methyl transferase (16SRMTases). We undertook this study to predict the efficacy of plazomicin in India based on the antimicrobial resistance profile derived from whole-genome sequencing (WGS). Methodology: A total of 386 clinical isolates of Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii subjected to WGS were screened for aminoglycoside-resistance mechanisms such as AMEs and 16SRMTases and its association with carbapenemases. Results: AMEs was present in all E. coli, A. baumannii and in 90% of K. pneumoniae. In addition, up to 47% of E. coli and 38% of K. pneumoniae co-carried 16SRMTases with AMEs genes. However, A. baumannii showed 87% of isolates co-harbouring 16SRMTase. bla NDM, bla Oxa-48-like and bla Oxa-23-like were the most predominant carbapenemases in E. coli, K. pneumoniae and A. baumannii, respectively. Notably, 48% of NDM-producing E. coli and 35% of Oxa-48-like producing K. pneumoniae were identified to co-harbour AMEs + RMTAses, where plazomicin may not be useful. Conclusion: Overall, 53%, 62% and 14% of carbapenemase-producing E. coli, K. pneumoniae and A. baumannii harbours only AMEs, indicating the role of plazomicin use. Plazomicin can be used both for ESBLs as “carbapenem-sparing agent” and carbapenemase producers as “colistin-sparing agent.” For optimal use, it is essential to know the molecular epidemiology of resistance in a given geographical region where plazomicin empirical therapy is considered.
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Detection of chlamydia trachomatis infection among the pregnant women attending a tertiary care hospital in Kerala - South India by polymerase chain reaction p. 319
A Neena, R Deepa
DOI:10.4103/ijmm.IJMM_19_429  
Background: Chlamydia trachomatis infection is the most prevalent bacterial sexually transmitted infection and may influence pregnancy outcome. Aims and Objectives: This study was conducted to assess Chlamydial infection during pregnancy by PCR. Materials and Methods: Study group consists of patients who are attending the antenatal clinics. Endocervical swabs were collected from 300 patients. Results: Off the 300 samples tested, 29 were positive as per PCR which used CT F : 5' CGT GTC GGC AAT CCT GCT GAT 3' and CT R : 5' GTC GAT AAC ATA GTC ACG ATA GTC 3'as the primers. Conclusion: This suggests there is a prevalence of Chlamydia trachomatis in our population which is 10%. Hence, it should be noted as a significant public health problem especially among sexually active young women of child bearing age. Timely detection and prompt treatment of Chlamydial infection during pregnancy can eliminate its adverse outcomes.
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Genetic sequencing of influenza A (H1N1) pdm09 isolates from South India, collected between 2011 and 2015 to detect mutations affecting virulence and resistance to oseltamivir p. 324
P Nandhini, Sujatha Sistla
DOI:10.4103/ijmm.IJMM_20_83  
Background: Influenza A viruses evolve continuously and the two surface antigens, hemagglutinin (HA) and neuraminidase (NA) have been the target proteins for research as they are vital components in determining the virulence, immune effectiveness, pathogenicity, transmission and resistance. Methods: Both HA and NA (partial genes) of 45 pandemic influenza A(H1N1)pdm09 isolates were sequenced. Phylogenetic analysis was performed with reference to representative global isolates retrieved from Influenza Virus Resource (IVR), GISAID EpiFluTM and GenBank and evolutionary analyses. Nucleotide and amino acid sequences were aligned using ClustalW/ Clustal Omega/MEGA version 6 with reference to vaccine strain (A/California/07/2009). Results: All the isolates clustered along with the clade 7 virus, irrespective of the year of isolation. The study isolates exhibited 98.5% and 98.8% nucleotide homology to the reference strain A/California/07/2009(H1N1) for HA and NA, respectively. Overall, there was limited genetic diversity observed over a period of 3 years (2012-2015). Two samples collected from expired patients had D239N (D222G or D225G) mutation in HA. This mutation which is associated with dual-binding specificity of the virus has been well-correlated with severe disease outcomes. All the study isolates possessed H274 residue and 7 strains had N295S, the next most common mutation found in oseltamivir-resistant variants. Conclusion: In this study, although H274Y mutation associated with oseltamivir resistance has not been noted, significant mutations have been noted in both HA and NA genes including D239N, N295S, V106I, Q136K, N248D, V267A. In both HA and NA gene analysis, multiple mutations were found more in 2015 strains when compared to 2012 strains. Hence such accumulation of mutations has to be monitored continuously to determine the efficacy of annual flu vaccines and anti-influenza drugs.
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Chlamydia pneumoniae infection in patients hospitalised for community-acquired pneumonia in Southern Jordan p. 338
Tahany Saleem Al-Hajaya, Wael Ali Al-Zereini, Hesham Mahmoud Al-Younes
DOI:10.4103/ijmm.IJMM_20_63  
Purpose: Chlamydia pneumoniae is associated with human respiratory diseases. Few reports examined the involvement of this bacterium in community-acquired pneumonia (CAP) in Jordan. This study investigates for the first time the role of C. pneumoniae in the establishment of CAP among nationals residing the southern part of Jordan. Materials and Methods: Nasopharyngeal and sera samples were collected from 70 hospitalised CAP patients and 63 healthy controls from Al-Karak Governorate and examined using the microimmunofluorescence and polymerase chain reaction techniques. The overall prevalence of C. pneumoniae infection was estimated by detecting the chlamydial immunoglobulin G (IgG) antibodies at a titre of 1:16. Rate of acute infection was estimated by detecting chlamydial DNA in nasopharyngeal samples and IgG and IgM at titres of 1:512 and 1:16, respectively. Results: A higher overall seroprevalence of C. pneumoniae IgG was detected in CAP patients than controls (44.3% vs. 30.2%). The rate of acute infection in the entire CAP patients, based on IgG titre of 1:512, was 7.14% compared to 1.58% in the controls. Approximately, three-fold increase in the rate of acute infection was observed in CAP cases, seropositive at IgG titre of 1:16, compared to seropositive controls (16.1% vs. 5.3%). Interestingly, chlamydial IgM antibodies were detectable in 27.1% compared to only 3.2% of the controls. The presence of chlamydial nucleic acids was confirmed in 40% of CAP patients and in 7.9% of controls. Conclusions: The present findings clearly suggest a role of C. pneumoniae in the aetiology of CAP in Southern Jordan. However, coinfections with other respiratory pathogens should not be excluded.
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Predominance of multidrug-resistant Gram-negative organisms as cause of surgical site infections at a private tertiary care hospital in Mumbai, India p. 344
Sweta Shah, Tanu Singhal, Reshma Naik, Pooja Thakkar
DOI:10.4103/ijmm.IJMM_20_284  
Background: This study aims to study the incidence, microbial aetiology and antimicrobial susceptibility of surgical site infections (SSIs) at a private tertiary care hospital in Mumbai, India, and compare it with previously published data from the same institute as well as literature. Methods: This is a prospective observational study done over 6 years (January 2013–December 2018) at a 750-bed private multi-specialty hospital in Mumbai, India, among all patients undergoing clean and clean-contaminated surgeries. Standard guidelines for preventing, diagnosing and classifying SSIs were followed. The incidence rates of SSI (overall and specialty specific), microbial aetiology and antibiotic susceptibility of SSI were calculated and expressed as percentages. Results: A total of 55,553 patients underwent clean and clean-contaminated surgeries during the study period. The overall SSI rate was 1.0% (555 cases). The SSI rate in clean surgeries was 0.97% and in clean-contaminated surgeries was 1.03%. Sixty-five per cent of SSIs were due to Gram-negative bacilli, 30% were due to Gram-positive cocci and 4% were due to Candida. Klebsiella pneumoniae (19%), Escherichia coli (17%), Pseudomonas aeruginosa (13%), Staphylococcus aureus(12%) and Enterococcus (10%) were the top five organisms. The overall susceptibility rate of the Gram-negative isolates to beta-lactam–beta-lactamase inhibitor combinations was 60% and carbapenems was 73%. The prevalence of methicillin resistance in S. aureus was 44% and coagulase-negative Staphylococcus was 84%. The crude mortality rate was 1%. Conclusions: Although the SSI rate is comparable to established international benchmarks, the predominance of multidrug-resistant Gram-negative organisms is a matter of serious concern.
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Epidemiological pattern of Malassezia, its phenotypic identification and antifungal susceptibility profile to azoles by broth microdilution method p. 351
Packia Nancy Romald, Anupma Jyoti Kindo, V Mahalakshmi, U Umadevi
DOI:10.4103/ijmm.IJMM_20_106  
Background: Malassezia though known for its cutaneous infections can potentially cause invasion. The skin infections caused by Malassezia have poor patient compliance due to its chronicity and recurrent nature of the disease. There is also a lack of standardised antifungal susceptibility profile for Malassezia due to its complex growth requirement. Objective: This study was performed to understand the epidemiological pattern of disease and to study the antifungal susceptibility testing (AFST) profile so as to choose the appropriate drug/drugs to treat the infections caused by Malassezia. Materials and Methods: Samples were collected and processed, species were identified by conventional method and AFST was done by broth microdilution method. Results: The epidemiological pattern showed adolescent females commonly affected in torso. The most common lesion was pityriasis versicolor. The systemic antifungal of choice was itraconazole with the lowest minimum inhibitory concentration (MIC) of 0.125–1 μg/ml. The best topical drug with the lowest MIC value was clotrimazole 0.03–0.5 μg/ml. Conclusion: AFST is important as it will help the dermatologist to choose the appropriate antifungal agents for the patient and thereby reduce the chronicity of the disease with good patient compliance
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Group B Streptococcus in Indian pregnant women: Its prevalence and risk factors p. 357
Neeraj Goel, Chand Wattal, Kanwal Gujral, Nehal Dhaduk, Chandra Mansukhani, Pankaj Garg
DOI:10.4103/ijmm.IJMM_20_333  
Purpose: To study the prevalence of group B streptococci (GBS) in Indian pregnant women and associated risk factors. Methods: Four hundred and fifty pregnant women attending antenatal outpatient/inpatient department between 35-38 weeks of gestation were enrolled in the study. All enrolled subjects were assessed by a predefined proforma for their demographics, socio-economic characteristics, education, toilet habits, obstetric history and clinical outcome. Two cotton swabs each from lower vagina and rectum were collected and plated on selective solid media CHROM agar Strept B (CHROMagarTM) and selective Enrichment Broth LIM RambaQUICK StreptB broth (CHROMagarTM). Presumptive identification of GBS was growth of 1-3 mm grayish white β-hemolytic colonies on BAP or mauve coloured colonies on CHROM agar Strept B. All presumptively identified GBS were confirmed as group B streptococcus by automated identification system-Vitek MS (Bio Merieux). Results: The recto vaginal colonization rate of GBS in this study was observed as 3.3% (n=15). GBS colonization was significantly associated with nulliparous women (p= 0.026) and use of western style toilet (p=0.017). GBS urinary tract infections was also seen more commonly in women with GBS rectovaginal colonization (p=0.002). Conclusion: Due to the low GBS prevalence and no significant association with major risk factors, we recommend to institute universal screening of GBS in pregnant women, instead of risk based screening. Since this was a single centric study with low prevalence of GBS, its applicability may be limited, therefore further larger multi-centric prospective studies are required to understand the true GBS prevalence in Indian society.
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The impact of antimicrobial stewardship programme on regulating the policy adherence and antimicrobial usage in selected intensive care units in a tertiary care center - A prospective interventional study p. 362
Sushmita Sana Chowdhury, Apurba Sankar Sastry, Sathasivam Sureshkumar, Anusha Cherian, Sujatha Sistla, Deepashree Rajashekar
DOI:10.4103/ijmm.IJMM_20_326  
Purpose: Antimicrobial resistance (AMR) presents a significant threat to human health. The root cause for this global problem is irrational antimicrobial usage. Antimicrobial stewardship (AMS) emphasises on the appropriate use of antibiotics and ensures strict implementation of antimicrobial policy guidelines. This study was conducted to evaluate the impact of auditing of AMS programme on regulating the antimicrobial policy adherence and antimicrobial usage in hospital intensive care units. Materials and Methods: This was a prospective interventional study. It consisted of pre-implementation and implementation phases 6 months each. Two hundred and eighty patients were enrolled. Details of antibiotic consumption, surgical prophylaxis, culture/sensitivity patterns, de-escalation rates, etc., were collected in both phases. The implementation phase, in addition, included stewardship audit rounds. Results: In pre-implementation phase and implementation phases: policy adherence rates were 23.7% and 41.8%, respectively, de-escalation rates were 22.73% and 43.48%, respectively. Cultures were sent before the initiation of antimicrobials in 36.73% cases during the pre-implementation phase, which improved to 60.41% during the implementation phase. Defined daily dose (DDD) for the antibiotics was 98.66 DDD 100BD during the pre-implementation phase, which reduced to 91.62 DDD 100BD in the implementation phase. Total days of therapy (DOT) in the pre-implementation phase were 561 DOT1000BD, which reduced to 463 DOT1000BD during the implementation phase. Conclusions: Implementation of continuous monitoring of the AMS programme, therefore, has a definite role in reducing the antimicrobial consumption and improving the compliance to the policy guidelines. A more robust study for a prolonged period is, however, necessary to have a better analysis of the outcome.
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Antimicrobial activity of biosynthesised silver nanoparticles against multidrug-resistant microbes isolated from cancer patients with bacteraemia and candidaemia p. 371
Gamal Mohamed El-Sherbiny, Mohamed Kasem Lila, Yousseria Mohamed Shetaia, Marwa M F. Elswify, Samar Samer Mohamed
DOI:10.4103/ijmm.IJMM_20_299  
Background: In the past years, saprophytic bacteria and candida have been emerging as potential human pathogens causing life-threatening infections in patients with cancer. This study was designed to determine the bacteria and candida species, causing bloodstream infections in cancer patients and the assessment of their susceptibility to antibiotics and biosynthesised silver nanoparticles. Materials and Methods: Ninety-seven microbial pathogens recovered from blood samples of cancer patients were included in the present study. The microbial isolates were collected in a duration period extending from December 2016 to July 2018 at National Cancer Institute, Cairo, Egypt. The clinical samples were collected using microbiological methods and were cultivated on MacConkey agar, blood agar media and Sabouraud dextrose agar media. The microbial isolates were identified using both standard microbiological methods and VITEK 2 compact automated system. The antibiotic resistance pattern was determined by the VITEK 2 compact automatic system and disk diffusion method, according to the Clinical and Laboratory Standards Institute. The characterisation of nanoparticles was carried out using ultraviolet spectroscopy and electron microscope. The antimicrobial activity of bio (AgNPs) was evaluated. Results: A total of 97 microbial isolates recovered from collected blood samples from cancer patients were included in the study. Pathogenic bacteria and Candida were represented by 74 isolates (76.22%) and 23 isolates (23.69), respectively. Among the 74 bacterial isolates, Escherichia coli constituted (27.81%), Klebsiella pneumoniae (24.72%), Acinetobacter baummannii (11.33%), Pseudomonas aeruginosa (4.12%), Enterobacter spp. (3.09%) and) Staphylococcus aureus (2.06%). Cedecea davisae (1.03%), Burkholderia cepacia (1.03%) and Pantoea agglomerans (1.03%). Among the 23 Candida isolates, Candida tropicalis constituted (9.27%), Candida albicans (5.15%), Candida glabrata (5.15%) and Candida krusei (4.12%) from the total microbial isolates. The antibiotic susceptibility results revealed that amikacin and gentamycin were the most effective antibiotics against Gram-negative bacteria, while vancomycin and linezolid were most effective against S. aureus. Caspofungin was the most effective against candida species. The obtained stable biosynthesised silver nanoparticles ranged in size from 10 nm to 100 nm and were mostly spherical in shape. These biosilver nanoparticles showed the highest antimicrobial activity against most of the microbial isolates (bacteria and Candida). The in vitro cytotoxicity of biosynthesised AgNPs on HeLa cell lines revealed a dose-dependent potential. The IC50 value of AgNPs was found 6 and 5.6 μg/ml, respectively. Conclusion: The present study revealed a significant distribution of multidrug-resistant microbes, which may increase the burden of healthcare to prevent infections in cancer patients. Biosilver nanoparticles exhibit antimicrobial activity against multidrug-resistant microbes and could be considered as effective agents against these strains.
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Prevalence of torch infections and its associated poor outcome in high-risk pregnant women of Central India: Time to think for prevention strategies p. 379
HV Manjunathachar, Kavita N Singh, Vivek Chouksey, Ravindra Kumar, Ravendra K Sharma, Pradip V Barde
DOI:10.4103/ijmm.IJMM_20_136  
Introduction: The TORCH infections during pregnancy are associated with adverse congenital abnormalities, poor foetal outcome and subsequent reproductive failures. The absence of baseline data on status of TORCH infections and associated foetal outcomes prompted us to conduct the current study in Central India. Materials and Methods: A total of 144 high-risk pregnant women attending tertiary care unit, suspected for TORCH infections were enrolled from August 2017 to December 2018. All the participants were tested for the presence of IgM and IgG antibodies and followed up to record the foetal outcome. Results: The overall TORCH infection (IgM positivity) positivity rate was 61.1% (88/144). Rubella was the most prevalent infection (46.5%) followed by herpes simplex virus (HSV) 1 and 2 (41%) and cytomegalovirus (CMV) (34.7%). The highest IgG sero-positivity was recorded against CMV (88.6%), followed by Rubella (86.8%), HSV 1 and 2 (28.4%), and toxoplasmosis (15.2%). Follow-up of IgM TORCH positive pregnant women revealed that majority of the neonates/infants are having congenital cardiac abnormalities (39.2%), followed by microcephaly/hydrocephaly (25%), low birth weight (10.7%), and deafness (3.6%). Thirty-two percent of neonatal mortality was associated to multiple TORCH infections. Conclusion: A high prevalence of IgM seropositivity of TORCH infection was noted in the present study with the increased rate of poor foetal outcome warrants the need of proper prenatal counselling, universal immunisation and nutritional supplements during pregnancy.
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Comparison of two real-time polymerase chain reaction assays for the detection of severe acute respiratory syndrome-CoV-2 from combined nasopharyngeal-throat swabs p. 385
Oves Siddiqui, Vikas Manchanda, Abhishek Yadav, Tanu Sagar, Sanchita Tuteja, Nazia Nagi, Sonal Saxena
DOI:10.4103/ijmm.IJMM_20_279  
Context: In the absence of effective treatment or vaccine, the current strategy for the prevention of further transmission of severe acute respiratory syndrome (SARS) CoV-2 (COVID-19) infection is early diagnosis and isolation of cases. The diagnosis of SARS-CoV-2 is done by detecting viral RNA in the nasopharyngeal and throat swabs by real-time polymerase chain reaction (PCR). Many commercial assays are now available for performing the PCR assay. Aims: The aim was to evaluate the performance of the SD Biosensor nCoV real-time detection kit with the real-time PCR kit provided by the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune (NIV Protocol). Subjects and Methods: A total of 253 pairs of nasopharyngeal-oropharyngeal swabs combined in a single viral transport medium were tested for viral RNA by both the protocols. The sensitivity and specificity of the SD Biosensor were calculated considering the ICMR-NIV kit as the gold standard. Matched pairs of recorded cycle threshold values (Ct values) were compared by Pearson's correlation coefficient. Results: Concordant COVID-19 negative and positive PCR results were reported for 113 and 77 samples, respectively. The SD Biosensor kit additionally detected 62 cases, which were found negative by the NIV protocol. In all discordant positive results by the SD Biosensor kit, the average Ct values were higher than the concordant positive results. A total of forty samples tested positive for E gene by SD Biosensor and having Ct values <25 had 100% concordance with NIV protocol results and 39 samples tested positive for E gene by SD Biosensor having Ct value >32 were all found negative by the NIV protocol. Conclusions: The results highlight the need for careful evaluation of commercial kits before being deployed for screening of COVID-19 infections.
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Detection of various beta-Lactamases in Escherichia coli and Klebsiella sp.: A study from Tertiary Care Centre of North India p. 390
Varsha Gupta, Meenakshi Singh, Priya Datta, Anku Goel, Sanjay Singh, Kashinath Prasad, Jagdish Chander
DOI:10.4103/ijmm.IJMM_20_253  
Objective: The emergence of carbapenem-resistant Escherichia coli and Klebsiella species is a global threat. We aimed to compare two phenotypic methods and evaluate the genotypic method for the detection of beta-lactamases produced by E. coli and Klebsiella spp. Materials and Methods: One hundred and twenty-six E. coli and Klebsiella isolates were examined for phenotypic production of beta-lactamases by using disc diffusion, combined disc test (CDT) and modified carbapenem inactivation method (mCIM). All strains were also studied for the presence of various genes by polymerase chain reaction. Results: Out of 126 isolates, 96% of the isolates were extended-spectrum β-lactamase (ESBL) producers based on the presence of various ESBL genes. CDT method showed higher number of total (89%) carbapenemases in comparison to mCIM (81%). Among carbapenemases none of the isolates were Klebsiella pneumoniae carbapenemase producer by CDT, while 69% isolates were metallo-beta-lactamase (MBL) producers. Another method, mCIM/ethylene diamine tetraacetic acid mCIM showed 100% agreement for MBL detection. As regards, AmpC and class D carbapenemases; 0.04% and 16% positivity was detected, respectively, based on CDT method. Molecular analysis revealed 91% of the isolates harbouring carbapenemase genes. blaNDMwas the most common gene detected followed byblaOXA-48. Nine of the blaNDM-positive isolates also possessed blaOXA-48gene. Conclusion: Our finding shows high percentages of ESBL and carbapenemases in E. coli and Klebsiella spp. Among phenotypic methods, CDT seems to be a better choice as prevalence of carbapenemases shows lots of variation in our country. For Class B enzymes, both CDT and mCIM/eCIM can be used in the routine laboratories.
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Use of fluorescence foldscope as an effective tool for detection of biofilm formation in Pseudomonas aeruginosa p. 397
Chandrayee Deshamukhya, Bhaskar Jyoti Das, Shiela Chetri, Deepjyoti Paul, Debadatta Dhar Chanda, Tuhina Banerjee, Amitabha Bhattacharjee
DOI:10.4103/ijmm.IJMM_20_118  
Purpose: Pseudomonas aeruginosa is an opportunistic pathogen with biofilm-forming ability, by the virtue of which they can evade the immune response and antimicrobial chemotherapy. Several methods have been designed for the detection of biofilms but require sophisticated instrumentation and expertise. The present study, therefore, used an improvised device, 'fluorescence foldscope' which is an origami-based fluorescence microscope as an easy and effective tool to detect biofilm formation. Methodology: Three representatives of P. aeruginosa of clinical origin were taken for the study along with two reference strains PA01 and ATCC27853. The strains were cultured in Luria Bertani (LB) broth with and without carbapenem (imipenem and meropenem) and cephalosporin (ceftazidime, cefotaxime and ceftriaxone) pressure, respectively. The cultures were diluted to 1:100 in LB; seeded with sterile glass slides at 90° angle and incubated for 5 consecutive days. The slides were observed with fluorescence foldscope. Results: Fluorescence emission was observed in two test isolates CD1 and CD2 at 48 and 72 h, respectively, whereas no fluorescence was observed in CD3. The fluorescence observed in the isolates was not affected by 2 μg/ml carbapenem pressure, while with 2 μg/ml ceftazidime stress, a change in fluorescence was observed in CD2 in comparison to the fluorescence observed under normal growth condition. Conclusion: Fluorescence foldscopy is an effective and reliable tool for the detection of biofilm formation in clinical isolates of P. aeruginosa under different laboratory conditions. Biofilm-forming P. aeruginosa worsens the medical condition and is difficult to eradicate. The present study came up with an effective and reliable tool for the detection of biofilm formation in clinical isolates of P. aeruginosa.
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Molecular diversity of dengue virus serotypes 1–4 during an outbreak of acute dengue virus infection in Theni, India p. 401
Amudhan Murugesan, Dhanasezhian Aridoss, Swarna Senthilkumar, Lallitha Sivathanu, Ramalingam Sekar, Esaki M Shankar, Elanchezhiyan Manickan
DOI:10.4103/ijmm.IJMM_20_89  
Background: Dengue fever (DF) is caused by an arthropod-borne dengue virus (DENV), has four serotypes and several genotypes. Although having clinical and epidemiological significance, the information on the circulating serotypes/genotypes is scarce in India. Materials and Methods: Blood specimens were collected from the patients suspected of DF and they are tested for DENV NS1 antigen and DENV IgM by ELISA. Antigen-positive samples were further serotyped by reverse transcriptase polymerase chain reaction. Representative samples from each serotype were sequenced to identify the genotypes. Results: All the four DENV serotypes were detected with the pre-dominance of DENV-1 (n = 49; 41.9%). Cases with multiple DENV serotype infections were also identified. Genotyping showed that DENV-1 belonging to genotype I, DENV-2 cosmopolitan (IV), DENV-3 genotype III and DENV-4 genotype I were active in the circulation during the outbreak in 2017. Conclusion: Our study documents the molecular characteristics of DENV circulating in our geographical locality. The detection of heterologous DENV serotypes highlights the importance of regular molecular monitoring for the early recognition of any switch in pre-dominant serotype.
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Microsporidia infection in patients with autoimmune diseases p. 409
Khadiga Ahmed Ismail, Yousry A Hawash, Taisir Saber, Emad M Eed, Amany S Khalifa, Khalaf F Alsharif, Saleh A Alghamdi, Ahmed M Khalifa, Osama Mahmoud Khalifa, Hatem K Althubiti, Gala M Alsofyani
DOI:10.4103/ijmm.IJMM_20_325  
Purpose: Microsporidium is a spore-forming intracellular parasite that affects a wide range of hosts including humans. The tumor necrosis factor alpha (TNF-α) plays a key role in the immunity to infection with microsporidia. Recently, the TNF-α antagonists have proven successful in treating variable autoimmune diseases. In the current study, we aimed to investigate the impact of using TNF-α antagonists as a therapeutic regimen in the prevalence of infections with microsporidia. Materials and Methods: Diarrheal patients with distinct autoimmune diseases (n = 100) were assigned to the study. Patients taking anti-TNF-α medications (n = 60) were allocated to Group 1A and those undergoing non-TNF-α inhibitor treatment (n = 40) to Group 1B. Furthermore, patients with diarrhea without autoimmune disorders (n = 20) were allocated as controls. Stool specimens, 3 per patient, were collected and microscopically examined for microsporidia spores. A microsporidia-specific stool polymerase chain reaction was used to confirm the microscopic findings. Results: Microsporidia infection was identified in 28.3% (17/60), 10% (4/40), and in 5% (1/20) of patients in Group 1A, Group 1B, and in the control group, respectively. Overall, infection was significantly high in cases compared to the controls and in patients receiving TNF-α antagonists compared to patients not given TNF-α inhibitors (P < 0.05). Finally, infection was significantly higher in cases treated with TNF-α antagonists for ≥2 months compared to cases treated for <2 months of duration (P < 0.05). Conclusion: There was a significant increase in microsporidia infection in autoimmune disease patients undergoing treatment with TNF-α antagonists, and the duration of treatment is one of the risk factors. The study highlights the importance of microsporidia testing in immunocompromised patients, particularly those undergoing treatment with anti-TNF-α drugs and emphasises the need for awareness among clinicians regarding this opportunistic parasite.
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Characteristics and outcomes of critically ill patients with influenza A (H1N1) in the Western Balkans during the 2019 post-pandemic season p. 415
Pedja Kovacevic, Jovan Matijasevic, Sasa Dragic, Biljana Zlojutro, Srdjan Gavrilovic, Milka Jandric, Ana Andrijevic, Tijana Kovacevic, Vladimir Carapic, Maja Travar, Ljubisa Preradovic, Danica Momcicevic
DOI:10.4103/ijmm.IJMM_20_169  
Background: This study looked at the characteristics and outcomes of critically ill patients with confirmed influenza A (H1N1) pdm09 infection in the Western Balkans in the post-pandemic period. Materials and Methods: This retrospective observational study of medical records and associated data collected during the post-pandemic period included all mechanically ventilated adult patients of two university-affiliated hospitals of the Western Balkans between 1 January and 31 March 2019 who had influenza A (H1N1) pdm09 infection confirmed by real-time reverse transcriptase-polymerase chain reaction from nasopharyngeal swab specimens and respiratory secretions. Results: The study included 89 patients, 49 males (55.1%), aged 56.09 ± 12.64 years. The median time from shift from hospital time to intensive care unit was 1 day (range: 1–2). In the post-pandemic period, cases observed in this study were found to have the following comorbidities: cardiovascular diseases in 44 (49.4%) patients and diabetes in 21 (23.6%) patients. Thirty-one patients (34.8%) in this study were obese. All 89 patients (100%) experienced some degree of acute respiratory distress syndrome, and 39 (44%) had multiorgan failure. Eighty-three patients (93%) were intubated and mechanically ventilated, 6 (7%) received non-invasive mechanical ventilation, 12 (13%) were treated with vvECMO and 36 (40%) received renal replacement therapy. Vasoactive support was needed by 56 (63%) patients. The median duration of mechanical ventilation was 9 (6–15.5) days. The hospital mortality rate was 44%. Conclusion: Critically ill patients with confirmed influenza A (H1N1) pdm09 infection in the post-pandemic season were older, required vasoactive drugs more often, and there was a trend of higher survival compared to H1N1 infection patients in the previous pandemic seasons.
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Molecular, phylogenetic and antibiotic resistance analysis of enteroaggregative escherichia coli/uropathogenic Escherichia coli hybrid genotypes causing urinary tract infections p. 421
Vinay Modgil, Harpreet Kaur, Balvinder Mohan, Neelam Taneja
DOI:10.4103/ijmm.IJMM_20_365  
Background: Horizontal gene transfer of virulence genes (VGs) from different Escherichia coli pathotypes results in the evolution of hybrid strains. Hybrid genotypes of enteroaggregative E. coli and uropathogenic E. coli (EAEC/UPEC) have been reported in sporadic infections and outbreaks of extraintestinal origin. Yet, their association with routine infections is still underrated. Materials and Methods: In this study, we analysed 163 isolates of E. coli from cases of urinary tract infection seeking hybrid (EAEC/UPEC) strains. Using multiplex polymerase chain reaction, we investigated VGs (adhesive and toxin genes) of UPEC along with EAEC marker genes (aap and agg R), ast A (toxin genes) and serine protease autotransporters of Enterobacteriaceae, pet (plasmid-encoded toxin) and pic (mucinase gene). Those UPEC strains which had characteristic defining genes of EAEC (agg R/aap or their combination) were considered UPEC/EAEC hybrids. Results: Molecular predictors of EAEC (aap and aggR) were detected in 20.2% (33/163) of the strains. The pap C was also detected in 36% of the EAEC/UPEC hybrid strains. Phylogenetic analysis revealed that hybrid strains belonged to Group D (60.6%). Nearly 73.8% of UPEC and 75.7% of UPEC/EAEC hybrid strains were multidrug-resistant. Among UPEC isolates, 72.3% and in hybrid UPEC/EAEC, 78.7% isolates were able to produce biofilm. Conclusions: Our results indicated a closer relationship among EAEC and UPEC, which suggested that some EAEC strains can be potential uropathogens. Ours is a first study documenting the existence of EAEC pathotypes VGs in UPEC strains of nosocomial origin; further studies are required to understand the diarrhoeagenic potential of these hybrids.
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Two novel genomic DNA sequences as common diagnostic targets to detect Cryptosporidium hominis and Cryptosporidium parvum: Development of quantitative polymerase chain reaction assays, and clinical evaluation p. 430
Arpit Kumar Shrivastava, Swagatika Panda, Subrat Kumar, Priyadarshi Soumyaranjan Sahu
DOI:10.4103/ijmm.IJMM_20_114  
Introduction: Cryptosporidium is an intestinal parasite responsible for gastroenteritis. Conventional diagnosis of Cryptosporidium is made by microscopy. The most frequent molecular detection method for this parasite is polymerase chain reaction (PCR). The objective of the present study was to identify the novel DNA targets and development of PCR-based assays for the specific detection of two major human infecting species Cryptosporidium parvum and Cryptosporidium hominis. Methodology: Sensitive and specific SYBR green quantitative PCR (qPCR) and TaqMan qPCR assays were developed and validated at both diagnostic and analytical level using the new identified targets TU502HP-1 and TU502HP-2. Results: Assay validation results showed that the newly developed real-time PCR assays are 100% specific with a reliable limit of detection. Overall repeatability and reproducibility of these assays showed good quality results over intra- and inter-laboratory analysis. Conclusion: Novel target-based qPCR assays can be rapid an efficient tool for simultaneous detection of a C. parvum and C. hominis. These genes could also be utilized for the development of innovative DNA-based Point-of-Care test development.
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Characterisation of colonisation properties of vaginal lactobacilli from healthy Indian women: Implications for identification of potential probiotic candidates p. 440
Arati Mane, Ishrat Khan, Madhuri Thakar
DOI:10.4103/ijmm.IJMM_20_108  
The ability of probiotic bacteria to colonise the target site is considered of utmost importance and used for preliminary screening of potential probiotic candidates. Thirty-eight vaginal Lactobacillus strains isolated from healthy women and characterised by 16S RNA sequencing were assessed for colonisation characteristics including adherence to human vaginal epithelial cells, auto-aggregation and hydrophobicity. No significant difference in adherence (P = 0.384), auto-aggregation (P = 0.282) and hydrophobicity (P = 0.084) abilities between Lactobacillus species was observed, however, significant difference in colonisation characteristics between strains of the same species was noted (P < 0.001). We identified seven Lactobacillus strains that may serve as best candidates for vaginal probiotic development.
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Staphylococcus aureus colonisation in HIV-infected patients: Incidence, risk factors and subsequent skin- and soft-tissue infections p. 444
Aashirwad Panigrahy, Sanjeev Sinha, Bimal Kumar Das, Arti Kapil, Sreenivas Vishnubhatla, Benu Dhawan
DOI:10.4103/ijmm.IJMM_20_5  
We evaluated the incidence and risk factors of Staphylococcus aureus colonisation in 300 treatment-naïve HIV patients. Swabs from anterior nares and pharynx were cultured. Eighty-eight patients (29.3%) were colonised with S. aureus (47.7% nasal, 23.8% pharyngeal and 28.5% at both sites), which yielded 112 isolates. Methicillin-resistant S. aureus was detected in 25.9% (29/112) of isolates. Panton–Valentine leucocidin gene was present in 18.8% (21/112) of isolates. Multiple logistic regression analysis identified CD4 count <200 cells/mm3, public bath use, alcohol intake and other sexually transmitted infections as independent predictors for S. aureus colonisation. On follow-up, 22.7% of patients with S. aureus colonisation developed skin- and soft-tissue infections. Strategies for behavioural changes would be helpful in controlling S. aureus colonisation and subsequent infection.
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E-tutorials to accentuate – Clinical microbiology learning p. 448
Sheetal U Harakuni
DOI:10.4103/ijmm.IJMM_20_100  
Competency-based medical education has challenged the educators to adopt new teaching modalities to instil self-directed learning among children. E-learning in the form of blended learning is studied to facilitate clinical microbiology learning. A class of 200 students was introduced to the process of Google Classroom. Two topics were discussed in online classrooms. The students attempted online tests on the topics, that were later discussed in small groups in offline class. Students found that analytical/interpretive questions accentuated learning. E-tutorials facilitate students' preparedness for small-group discussion.
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Analysis of multi-sample pools in the detection of SARS-CoV-2 RNA for mass screening: An Indian perspective p. 451
Sangeeta Deka, Deepjyoti Kalita, Amit Mangla, Ravi Shankar
DOI:10.4103/ijmm.IJMM_20_273  
In the current COVID-19 crisis, many national healthcare systems are confronted with a huge demand for mass testing and an acute shortage of diagnostic resources. Considering group testing as a viable solution, this pilot study was carried out to find the maximum number of samples that can be pooled together to accurately detect one positive sample carrying the severe acute respiratory syndrome-coronavirus 2 viral RNA from different pools. We made different pool sizes ranging from 5 to 30 samples. Three positive samples, covering the common range of polymerase chain reaction (PCR) threshold cycle values (an indirect indicator of viral load) observed in our patients, were selected, and different pools were made with known negative samples. The pools underwent real-time qualitative PCR for the determination of effective maximum pool size. It was observed that up to 20-sample pools of all positive samples could accurately be detected in terms of both E gene and RdRp gene, leading to considerable conservation of resources, time and workforce. However, while deciding the optimal pool size, the infection level in that particular geographical area and sensitivity of the test assay used (limit of detection) have to be taken into account.
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Arterial blood gas as a prognostic indicator in patients with sepsis p. 457
Sayan Mukherjee, Suvrajyoti Das, Sudipta Mukherjee, Pralay Shankar Ghosh, Sanjay Bhattacharya
DOI:10.4103/ijmm.IJMM_19_478  
Abnormal arterial blood gas (ABG) among patients with sepsis is an important prognostic indicator. All-cause mortality was the highest among patients with respiratory acidosis (4/9 = 44.4%), followed by those having metabolic acidosis (3/8 = 37.5%). Median length of hospital and intensive care unit stay was 15.75 days and 6.25 days for those with abnormal ABG and 11 and 3.5 days among those with normal ABG. Median health-care expenditure at the time of discharge or death of the patient was the highest in patients with respiratory acidosis ($14,473) and least in patients with normal ABG ($3,384) (average expenditure among patients with abnormal ABG was [$10,059]).
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Prevalence of COVID-19 antibodies in healthcare workers at the peak of the pandemic in Mumbai, India: A preliminary study Highly accessed article p. 461
Tanu Singhal, Sweta Shah, Reshma Naik, Amreen Kazi, Pooja Thakkar
DOI:10.4103/ijmm.IJMM_20_308  
Healthcare worker (HCW) infections due to COVID-19 are of serious consequence. Testing for antibodies against COVID-19 in HCWs has been previously recommended. We conducted a serosurvey in HCWs at a private hospital in Mumbai which is treating COVID patients. A total of 244 HCWs were tested. The prevalence of infection in asymptomatic HCWs was 4.3% and in previously symptomatic untested HCWs was 70%. We recommend that HCWs with a previous history of COVID symptoms who were not tested/tested negative by reverse transcription–polymerase chain reaction should be tested for antibodies at least 2 weeks after onset of symptoms.
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A real-time polymerase chain reaction-based approach for qualitative estimation of viral RNA in organ tissues of coxsackievirus A-16-infected neonatal mice p. 464
Sanjaykumar Sidram Tikute, Shailesh Dattatraya Pawar, Samruddhi Satish Kawale, Deepa Kailash Sharma, Varanasi Gopalkrishna
DOI:10.4103/ijmm.IJMM_20_117  
Hand, foot and mouth disease (HFMD) is a paediatric disease associated with enteroviruses (EVs). Among EVs, coxsackievirus A-16 (CVA-16) strain is currently in circulation and causing outbreaks in India. Neonatal mice (Institute of Cancer Research) strains were infected with CVA-16 strain isolated from HFMD patients to conduct pathological and molecular studies. Infected organs were harvested as per time points. A real-time polymerase chain reaction was used for qualitative estimation of viral RNA in organ tissues of infected mice. Skeletal muscle, brain tissue and cardiac tissues were the major target sites of CVA-16 tropism. The first-ever study was conducted on CVA-16 strains using the current approach in India.
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INFECTIOUS DISEASE GRAND ROUND Top

False-positive blood cultures: The need for follow-up p. 469
Suverna Kirolikar, Ambreen Pandrowala, Sangeeta Joshi, Ruchira Misra, Sujata Mushrif
DOI:10.4103/ijmm.IJMM_20_402  
The diagnosis of blood-borne infections in immunocompromised patients is a major challenge for the clinical microbiology laboratory. Isolation of bloodborne pathogens in these patients has profound clinical implications, yet is fraught with technical problems, including the presence of unusual and difficult to isolate pathogens. Coupled with this is the problem of false-positive blood culture signals from automated blood culture systems which further delays the definitive diagnosis. Here, we present a case of an 8-year-old boy with Ph +ve acute lymphoblastic leukaemia who has repeated 'false positive' blood cultures and later grew an uncommon organism.
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Mycotic keratitis due to Cylindrocarpon lichenicola: Successful salvage of the eye p. 472
M Suchitra Shenoy, Rajesh R Nayak, Vijay Pai, K Archana Bhat
DOI:10.4103/ijmm.IJMM_20_399  
We hereby report a successfully salvaged eye due to mycotic keratitis by Cylindrocarpon lichenicola in a 60-year-old female from Kasaragod (Kerala). The patient came with a history of pain, photophobia and decreased vision of the right eye. The microbiological investigations of the corneal scraping revealed C. lichenicola. C. lichenicola is a soil saprophyte. Since the ulcer worsened paracentesis followed by therapeutic keratoplasty and adjunct therapy with natamycin drops, voriconazole drops and oral ketoconazole was given. We stress that evidence-based timely medical and surgical intervention helped in the restoration of the vision in an infected eye.
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CASE REPORTS Top

A rare case of Colletotrichum truncatum keratitis in a young boy with complete healing after medical treatment p. 475
Josephine S Christy, A Balraj, Aditi Agarwal
DOI:10.4103/ijmm.IJMM_20_146  
Colletotrichum is a rare fungal pathogen, which is known to cause anthracnose in plants and keratitis or subcutaneous infections in humans. Among the seven Colletotrichum species reported in eye infections, truncatum species is usually virulent with poor visual prognosis even after surgical treatment. Here we report a case of Colletotrichum truncatum keratitis in a young boy with thorn injury that completely resolved with topical natamycin and voriconazole.
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An unexpected host in a soft-tissue lesion of thigh p. 478
Kavita Jain, SM Sarfaraj, Moumita Sengupta, Chhanda Datta, Uttara Chatterjee
DOI:10.4103/ijmm.IJMM_20_236  
Rhinosporidiosis is an enigmatic entity and poses a major health problem in the developing countries of South-East Asia. A soft friable polypoid nasal mass is the most common presentation, while sparse literature is available on extranasal involvement. We describe the case of a 35-year-old female patient who presented with a slow-growing soft-tissue swelling with ulceration over the thigh. On clinical and radiological examination, a provisional diagnosis of soft-tissue neoplasm was made. After resection, histopathological sections showed a closely packed cyst with innumerable endospores. The present case report documents the rare occurrence of an incidentally detected cutaneous rhinosporidiosis causing diagnostic difficulty.
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Streptococcus dysgalactiae septic arthritis of sternoclavicular joint with bacteraemia p. 481
Pruthu Narendra Dhekane, Ram Gopalakrishnan, V Lakshmi Sree, V Dedeepiya Devaprasad
DOI:10.4103/ijmm.IJMM_20_257  
Invasive infections due to Streptococcus dysgalactiae are uncommon in the adult population, and sternoclavicular joint septic arthritis (SCSA) is usually caused by other organisms such as Staphylococcus aureus and Pseudomonas aeruginosa. We hereby report a case of SCSA caused by this organism. The patient responded well to intravenous antibiotics and recovered fully without any surgical intervention.
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Adrenal histoplasmosis in immunocompetent individuals a case series from the North-Western part of India, Rajasthan province: An emerging endemic focus p. 485
Balram Sharma, Hardeva Ram Nehara, Vijay Kumar Bhavi, Pratibha Maan, Sanjay Saran
DOI:10.4103/ijmm.IJMM_20_280  
Histoplasmosis is a fungal infection caused by Histoplasma capsulatum and very few cases reported from North-West India. Adrenal histoplasmosis is an even more uncommon mycotic disease. We describe five immunocompetent men with adrenal histoplasmosis presenting with constitutional symptoms. Four patients had bilateral adrenal involvement, whereas one had unilateral adrenal mass. Three patients had adrenal insufficiency at presentation and the other two developed adrenal insufficiencies during follow-up. All the patients received amphotericin B and itraconazole treatment which led to symptomatic improvement but adrenal insufficiency persisted in all patients at the end of the follow-up.
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First report of Vibrio cholerae O9, novel st520, isolated from a child with bacteraemia-associated sepsis p. 489
Nandita Shashindran, Lekshmi Narendrakumar, Suhas Udayakumaran, Divya Mavanavila Vijayakumar, Sabu Thomas, Anil Kumar
DOI:10.4103/ijmm.IJMM_20_283  
Vibrios have been identified to cause extra-intestinal complications apart from the occasional cholera-like diarrhoeal outbreaks. The non-O1/O139 Vibrio cholerae strains are ubiquitous in environmental water bodies and hence pose a threat to people even without obvious risk factors. We describe a case of sepsis in a child with spinal dysraphism caused by a V. cholerae O9 strain belonging to a novel sequence type (ST520). The present case highlights the need of considering V. cholerae non-O1/O139 as one of the pathogens while dealing with sepsis cases, and also, the study expounds the importance of proper characterisation of the pathogen for an effective treatment.
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Aspergillus mediastinitis in a post-operative immunocompetent child p. 492
Anand Kumar Mishra, Vidur Bansal, Gradlin Roy, Vikram Halder, Parakritii Gupta, Arunaloke Chakrabarti
DOI:10.4103/ijmm.IJMM_20_267  
Post-operative Aspergillus mediastinitis is regarded to be a devastating infection, usually affecting patients undergoing cardiothoracic surgery with specific predisposing factors characterised by a high mortality and chronic morbidity. Patient outcome after such a complication is extremely poor despite antifungal therapy and surgery. We describe the case of an immunocompetent 2-month-old child with obstructed supracardiac total anomalous pulmonary venous circulation (TAPVC) and severe pulmonary artery hypertension, who underwent TAPVC repair through median sternotomy and developed post-operative mediastinitis due to Aspergillus flavus.
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Burkholderia vietnamiensis causing a non-lactational breast abscess in a non-cystic fibrosis patient in Tamil Nadu, India p. 496
Anusha Rohit, M Shraddha Rani, N Suresh Anand, Cynthia Chellappa, P Mohanapriya, Indrani Karunasagar, Iddya Karunasagar, Vijaya Kumar Deekshit
DOI:10.4103/ijmm.IJMM_20_329  
Burkholderia cepacia complex is a Gram-negative opportunistic pathogen usually found in people with an immunocompromised condition such as cystic fibrosis (CF). In a tropical country like India, this organism has been associated with a number of hospital-acquired infections including sepsis. We present here a report of a case of Burkholderia vietnamiensis causing a non-lactational breast abscess in a non-CF patient. The pathogen was identified as B. cepacia using Vitek system and matrix-assisted laser desorption ionisation–time of flight. This was confirmed by polymerase chain reaction (PCR) using recA genus-specific gene and sequencing of the PCR amplicons. recA-restriction fragment length polymorphism and recA gene sequencing revealed that the isolate is B. vietnamiensis. This is the first description of B. vietnamiensis isolated from a clinical case from India.
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CORRESPONDENCE Top

Does Xpert Carba R assay detect carbapenemase-producing organism in Gram-negative sepsis in neonates? p. 500
R Usha Devi, Thangaraj Abiramalatha, Ashok Chandrasekaran, Shaik Mohammad Shafi Jan, Prakash Amboiram, Umamaheswari Balakrishnan
DOI:10.4103/ijmm.IJMM_20_290  
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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