Clinical study on antifungal drug resistance among cases of dermatophytosis in patients reporting to multiple tertiary care hospitals.

Background: In a tropical country like India, the warm and humid climate plays an important role in the increased incidence of superficial fungal infections. This is a study to identify the causative fungi of dermatophytosis and their in vitro antifungal susceptibility pattern among patients reporting to multiple tertiary care hospitals. Methods: Skin scrapping, nail clipping, and hair follicles were processed for microscopy, culture, and antifungal susceptibility testing as per standard guidelines. Antifungal susceptibility was performed as per published by Clinical Laboratory Standards Institute for yeasts (M27-A3) and filamentous fungi (M38-A2). Result: The study sample had a predominantly male population with the commonest age group being 21-30 years (39.57%) followed by 31-40 years (31.46%). Tinea corporis (57.30%) was the most common clinical presentation followed by tinea cruris (20.85%) and onychomycosis (14.73%). Microscopy positivity was 43.19%, while culture positivity was 23.97%. Dermatophytes accounted for the majority of isolates. All fungal isolates had high minimum inhibitory concentration (MIC) to fluconazole, suggesting that dermatophytes are possibly resistant to this drug. Conclusion: Trichophyton mentagrophytes is confirmed as the dominant pathogen of dermatophytosis in all three tertiary care hospitals.

Rapid detection of carbapenem resistance among gram-negative organisms directly from positive blood culture bottles.

Background: Carbapenemase producing gram-negative bacteria (GNB) has become a huge problem in majority of tertiary care centers worldwide. They are associated with very high morbidity and mortality rates, especially when they cause invasive infections. Therefore, rapid detection of these organisms is very important for prompt and adequate antibiotic therapy as well as infection control. The aim of this study was rapid detection of carbapenemase genes and thereby likely carbapenem resistance, 24-48 hours in advance, directly from the positive-flagged blood culture bottles using CHROMagar and Xpert® Carba-R. Methods: Aspirate from positively flagged blood culture bottles was subjected to differential centrifuge. All gram-negative bacilli on gram stain from the deposit were processed in Xpert® Carba-R and inoculated on CHROMagar. The presence of genes and growth on CHROMagar was compared with carbapenem resistance on VITEK-2 Compact. Results: A total of 119 GNB isolates were processed. One or more of the carbapenemase genes were detected in 80 isolates. On comparison with VITEK-2 result, 92 samples showed concordance for carbapenem resistance 48 hours in advance. There was discordance in 21 isolates with 12 major errors and 09 minor errors. The sensitivity of direct Xpert® Carba-R test for rapid detection of carbapenem resistance, 48 hours in advance, was 81.42%. The sensitivity of direct CHROMagar test for accurate detection of carbapenem resistance, 24 hours in advance, was 92.06%. Conclusion: The ability to detect carbapenem resistance with very high accuracy, 48 hours in advance, helps in appropriate antibiotic therapy and implementation of effective infection control practices.

Detection of dengue virus serotypes by single-tube multiplex RT-PCR and multiplex real-time PCR assay.

Background: All four dengue serotypes cause infection, with one of them predominantly reported from a particular geographical region. Coinfection by more than one serotype is reported from hyperendemic regions. These coinfections are clinically more severe than infection with a single serotype. This study was carried out to detect the predominant dengue serotype and presence of coinfections. Methods: Acute-phase serum samples of patients suffering from dengue infection were collected. They were screened for the presence of IgM, IgG and NS1Ag by a rapid test. Conventional multiplex reverse transcriptase polymerase chain reaction (RT-PCR) and multiplex real-time RT-PCR assays were carried out for detection and serotyping of the dengue virus. Results: A total of 196 samples were positive by the rapid card test. Of these, 139 were NS1Ag positive, 40 were positive only for IgM, 5 were positive only for IgG and 12 samples were positive for different combinations of antigen and antibodies. All four serotypes were detected in these samples by PCR. DENV-3 was found to be most common circulating serotype. A total of 22 cases were found to have coinfection with more than one dengue serotypes. Samples having only antibodies and no antigen on rapid card test were also positive for virus by PCR. Conclusion: Prevalence of dengue co-infections is increasing. Moreover, it is important to screen for dengue virus in those samples also which do not show NS1Ag on rapid tests and have either one or both the antibodies. Real-time multiplex RT-PCR is found to be more sensitive in detecting coinfection than conventional multiplex RT-PCR.

One-step single-tube accelerated quantitative nucleoprotein gene-specific reverse transcription loop-mediated isothermal gene amplification (RT-LAMP) assay for rapid, real-time & reliable clinical detection of Ebola virus.

Background & objectives: Due to the absence of specific drugs or vaccines for Ebola virus disease, rapid, sensitive and reliable diagnostic methods are required to control the transmission chain of the disease and for better patient management. Isothermal amplification of nucleic acids has emerged as a promising alternative in which rapid and efficient amplification is achieved at a constant temperature without the thermal cycling required in PCR. Methods: A one-step single-tube accelerated quantitative reverse trascription loop-mediated isothermal amplification (RT-LAMP) assay was developed by targeting the NP gene of 2014 Zaire Ebola virus (ZEBOV). The RT-LAMP assay was found to be specific for ZEBOV, without having any cross-reactivity with related haemorrhagic fever viral agents. Results: The comparative evaluation of Ebola virus NP gene-specific RT-LAMP assay with reverse transcription (RT) - PCR and TaqMan real-time RT-PCR demonstrated that RT-LAMP was 10-1000 folds more sensitive than TaqMan real-time RT-PCR and conventional RT-PCR, respectively, with a detection limit of 1 copy number. In the absence of real-world clinical samples, the feasibility of Ebola virus RT-LAMP assay for clinical diagnosis was evaluated with different body fluids including serum, urine, saliva, semen and stool samples from healthy human volunteers spiked with gamma-irradiated ZEBOV 2014 obtained from Robert Koch Institute, Berlin, Germany, through the European Network for Diagnostics of Imported Viral Diseases. The Ebola virus RT-LAMP assay could correctly be picked up the spiked samples up to 1 copy of viral RNA without having any matrix interference. The monitoring of gene amplification can also be visualized with the naked eye by using SYBR Green I fluorescent dye. Interpretation & conclusions: Thus, due to easy operation without a requirement of sophisticated equipment and skilled personnel, the RT-LAMP assay reported here is a valuable tool as a point-of-care diagnosis for the rapid and real-time detection of Ebola virus in resource-limited healthcare settings of developing countries.

Evaluation of ceftriaxone-sulbactam-disodium edetate adjuvant combination against multi-drug resistant Gram-negative organisms.

BACKGROUND: Multi-drug resistant (MDR) Gram-negative bacteria are an emerging threat, both in hospital and community settings. As very few antibiotics are effective against such infections, the need of the hour is a new antibiotic or drug combination which can overcome the effect of extended-spectrum ß-lactamases (ESBL) and metallo ß-lactamases (MBL). A new antibiotic combination of ceftriaxone, sulbactam and disodium edetate (CSE) has recently been proposed to tackle the MDR organisms. OBJECTIVE: Our study was carried out to assess the susceptibility of ESBL- and MBL-producing Gram-negative organisms to CSE. METHODS: The study was conducted in a tertiary-care hospital in Delhi, India, from February 2017 to June 2017. A total of 179 MDR (85 ESBL + 94 MBL) Gram-negative isolates from various clinical samples, identified by an automated system (Vitek 2) were tested against CSE using the Kirby-Bauer disc diffusion method. Susceptibility to CSE was recorded based on interpretative zone sizes of ceftriaxone as per 2017 Clinical and Laboratory Standards Institute guidelines. RESULTS: The most common isolate was Escherichia coli (76/179; 42.4%) followed by Klebsiella pneumoniae (53/179; 29.6%) and Acinetobacter baumanii (27/179; 15.1%). The in vitro susceptibility of ESBL- and MBL-producing Gram-negative isolates to CSE was found to be 58/85 (68.2%) for ESBL and 37/94 (39.4%) for MBL. CONCLUSION: The in vitro susceptibility results obtained for CSE against ESBL-producing organisms is promising. It has the potential to emerge as a carbapenem-sparing antibiotic, active against ESBL-producing strains. Further clinical studies are required to establish the clinical efficacy of CSE against MDR pathogens.

Endogenous endophthalmitis secondary to Burkholderia cepacia: A rare presentation.

Burkholderia cepacia (previously known as Pseudomonas cepacia) is low virulent, gram negative bacilli, known to cause infections in immunocompromised hosts. There are reports about this organism causing keratitis, acute or delayed postoperative, or post traumatic endophthalmitis. Persistence of infection and poor visual outcome are well known complications of infection caused by this organism. Endogenous endophthalmitis due to Burkholderia cepacia is rare. There is no such case report available of endogenous endophthalmitis caused by these bacteria in the literature, where it is presented as retinal abscess and retinal vasculitis. Our aim is to report such a rare case from our hospital, which was treated with systemic and intravitreal antibiotics, with control of infection.

Direct antimicrobial susceptibility testing from positive blood culture bottles in laboratories lacking automated antimicrobial susceptibility testing systems.

BACKGROUND: Timely initiation of appropriate antimicrobial can improve the outcome in terms of reduced morbidity and mortality in addition to reduced health-care costs. Availability of early preliminary Antimicrobial Susceptibility Test (AST) report will be useful in directing antimicrobial therapy. The aim of the study was to correlate AST by disc diffusion method, directly from positively flagged blood culture bottles, with the AST by automated method. METHODS: A total of 144 aerobic blood culture bottles flagged positive by the automated blood culture system were processed. The bacteria were pelleted by two-step centrifugation of the broth from the bottle and used to make a smear for Gram stain as well as an inoculum for antimicrobial sensitivity testing by Kirby Bauer disc diffusion method. Automated identification and AST were also carried out. RESULTS: On direct staining, 94 samples showed gram-negative bacilli, 39 showed gram-positive cocci, and 11 showed yeasts or polymicrobial growth. In the case of gram-negative bacteria, there was 99% categorical agreement between direct sensitivity testing and automated sensitivity testing with 1% disagreement. Among the gram-positive cocci, there was 96% categorical agreement with 4% disagreement between the two methods. CONCLUSION: High degree of agreement between the two methods is promising and applicable to situations where automated sensitivity testing is not available. Even if the systems are available, this method would prove useful as an adjunct to standard AST reporting. This sensitivity report can be generated earlier than the conventional AST, enabling choice of appropriate antimicrobial.

Molecular characterization and phylogenetic analysis of Chikungunya virus from Delhi, India.

BACKGROUND: Chikungunya virus is an alpha virus with high similarity to Dengue and Zika viruses, both in transmission cycle and in clinical presentation. Chikungunya is a re-emerging mosquito-borne infection known to cause small to very large outbreaks/epidemics at frequent intervals. In 2016, India witnessed a large outbreak of Chikungunya infection affecting more than 58,000 people. This study was undertaken to look at the genotypic phylogeny to know the relatedness with previously reported strains. METHODS: During the 2016 outbreak, samples from all patients clinically suspected to have Chikungunya were collected and subjected to testing for IgM antibody by ELISA and viral RNA detection by RT-PCR. Sequencing of the E1 gene segment was done to create a phylogenetic tree comparison with other strains. RESULTS: Serum samples were collected from 142 patients of clinically suspected Chikungunya infection. Majority of the patients were in the age group of 31-50 years accounting for more than 35% of the total cases. Twenty eight samples were positive for IgM antibody. Thirty seven samples were positive for viral RNA by RT-PCR. Only 06 cases were positive by both tests. Mutations in the amino acids K211E, M269V and D284E in the E1 gene segment of the Chikungunya virus were observed in the seven strains that were sequenced. On phylogeny tree, all the strains were found to belong to the ECSA genotype. CONCLUSION: Actively searching for the potential epidemic causing mutations and reporting of novel mutations may help in better understanding and probably forecasting of future CHIKV outbreaks and its nature.

Emergence of human West Nile Virus infection among pediatric population in Madhya Pradesh, India.

Human infections caused by West Nile virus (WNV) mostly remain subclinical and self-limited. However, nearly 20% infected people suffer from febrile illness and very few of them (<1%) may get neuroinvasive illness. Mortality has been reported among children. India somehow has reported very less number of WNV cases in the past. We collected cerebrospinal fluid (CSF) samples from 75 pediatric age group patients clinically suffering from acute encephalitis syndrome. Three of these samples were positive by reverse transcriptase polymerase chain reaction using pan flavivirus primers. On sequencing of the 212 bp long-amplified fragment, it was found to be WNV belonging to lineage 1. This is probably the first report of WNV causing encephalitis from this central part of India.

Recovery of Five Complete Influenza A(H1N1)pdm09 Genome Sequences from the 2015 Influenza Outbreak in India by Metagenomic Sequencing.

Five complete (H1N1)pdm09 viral sequences were recovered from hospitalized individuals during the 2015 influenza outbreak by metagenomic sequencing. Four of the genomes are from oropharyngeal swabs, and one is from an isolate. All five sequences belong to an emerging 6B clade. Studying them further is critical for outbreak preparedness.

Simultaneous detection and serotyping of dengue infection using single tube multiplex CDC Dengue Real-Time RT-PCR from India.

Four antigenically different dengue virus serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) are known to cause infections in humans. Some of these are known to cause more severe disease than the others. Chances for developing Dengue hemorrhagic fever-dengue shock syndrome (DHF-DSS) increases significantly with history of previous infection with one of the four serotypes. Therefore, early diagnosis, serotyping and providing early warning of dengue fever epidemics to concerned authorities becomes very important for better patient outcome and to curb the rapid spread in the community. During the 2014 outbreak, a total of 100 samples from suspected cases of dengue were collected. NS1 antigen based rapid test was used for serological diagnosis. Dengue complex one step reverse transcription-polymerase chain reaction was performed to look for presence of viral RNA. Single tube multiplex RT-PCR was also performed to look for infecting serotype. CDC Dengue Multiplex Real Time PCR assay was performed for rapid diagnosis and simultaneous serotyping of the dengue virus. Out of the 100 samples screened, 69 were found to be positive by NS1Ag Rapid test. 34 samples were found positive by dengue consensus RT-PCR assay. 22 samples were found to be positive by single tube Dengue multiplex RT-PCR assay. Serotype DEN-2 was present in maximum numbers followed by DEN-3. 44 samples were found positive by DENV CDC Multiplex Real time PCR assay. DEN-2 was found in maximum numbers followed by DEN-1. Dengue remains to be an important health problem in India and across the globe. Few serotypes of dengue are more dangerous than the others. Rapid diagnosis and serotyping remains the key for better patient management and prevention of disease spreading in the community. Highly sensitive, specific and rapid CDC real time RT-PCR assay was found to be most promising tool among all available molecular diagnostic methods. This will serve a rapid and reliable simultaneous dengue virus detection as well serotyping assay in near future for rapid identification of dengue suspected sample screening.

Oseltamivir-resistant influenza A(H1N1)pdm09 virus associated with high case fatality, India 2015.

Influenza A viruses has been associated with severe global pandemics of high morbidity and mortality with devastating impact on human health and global economy. India witnessed a major outbreak of influenza A(H1N1)pdm09 in 2015. This study comprises detailed investigation of cases died of influenza A(H1N1)pdm09 virus infection during explosive outbreak of 2015, in central part of India. To find out presence of drug resistant virus among patients who died of influenza A(H1N1)pdm09 virus infection and to find out presence of other mutations contributing to the morbidity and mortality. Twenty-two patients having confirmed influenza A(H1N1)pdm09 infection and subsequently died of this infection along with 20 non fatal cases with influenza A(H1N1)pdm09 infection were included in the study. Samples were investigated through RT-PCR/RFLP analysis, followed by nucleotide cycle sequencing of whole NA gene for detection of H275Y amino acid substitution in NA gene responsible for oseltamivir drug resistance. Out of 22 fatal cases, 6 (27.27%) were found to harbor oseltamivir resistant virus strains, whereas the H275Y mutation was not observed among the 20 non fatal cases. Amino acid substitution analysis of complete NA gene revealed V241I, N369K, N386K substitution in all strains playing synergistic role in oseltamivir drug resistance. High morbidity and mortality associated with influenza A(H1N1)pdm09 viruses can be explained by presence of drug resistant strains circulating in this outbreak. Presence of Oseltamivir resistant influenza A(H1N1)pdm09 viruses is a cause of great concern and warrants continuous screening for the circulation of drug resistant strains.

Zika virus: A public health threat.

The resurgence of Zika virus as public health emergency of an international concern with increased incidence of microcephaly has drawn attention of scientific community for its detailed understanding with regard to virus evolution, epidemiology, geographical spread, pathogenesis, etc. The scope of the present review is to discuss the detailed updated information in respect of Zika virus evolution since its inception.

Species distribution and antimicrobial resistance pattern of Coagulase-negative Staphylococci at a tertiary care centre.

BACKGROUND: Coagulase-negative Staphylococci (CoNS), previously dismissed at contaminants, have now emerged as an important cause of nosocomial infections especially in patients with implants and prosthetic devices. They are a well-known cause of bloodstream infections, urinary tract infections, wound infections, prosthetic valve endocarditis and eye infections. This study was conducted with an aim to identify CoNS at the species level from various clinical samples and determine the antimicrobial resistance pattern of these isolates. METHODS: This cross sectional study was carried out from September 2011 to February 2014 in which 150 non-repetitive clinical isolates of CoNS were identified at the species level by conventional phenotypic methods. Complete antimicrobial susceptibility profile was also determined by Kirby Bauer disc diffusion method. Susceptibility testing to vancomycin was done by E-test method. RESULTS: Only three species of CoNS were isolated, the most common being Staphylococcusepidermidis (60%) followed by Staphylococcussaprophyticus (27.3%) and Staphylococcushemolyticus (12.7%). Most S. epidermidis were isolated from blood and intravascular catheter tip samples, whereas all S. saprophyticus were isolated from urine samples of female patients. All isolates were found to be resistant to penicillin, but were susceptible to glycopeptides and linezolid and showed variable resistance to fluoroquinolones, aminoglycosides and macrolides. CONCLUSION: CoNS are emerging nosocomial pathogens and should not always be overlooked as contaminants. However, growth of CoNS from blood cultures and intravascular catheter tips should be clinically correlated and carefully interpreted. As many CoNS strains exhibit drug resistance, antimicrobial susceptibility profile should be determined prior to treatment of these infections.

Emergence of influenza A (H1N1)pdm09 genogroup 6B and drug resistant virus, India, January to May 2015.

To investigate the aetiology of the 2015 A(H1N1)pdm09 influenza outbreak in India, 1,083 nasopharyngeal swabs from suspect patients were screened for influenza A(H1N1)pdm09 in the state of Madhya Pradesh. Of 412 positive specimens, six were further characterised by phylogenetic analysis of haemagglutinin (HA) sequences revealing that they belonged to genogroup 6B. A new mutation (E164G) was observed in HA2 of two sequences. Neuraminidase genes in two of 12 isolates from fatal cases on prior oseltamivir treatment harboured the H275Y mutation.

Prevalence and molecular characterization of methicillin resistance among Coagulase-negative Staphylococci at a tertiary care center.

BACKGROUND: Methicillin-resistant Coagulase-negative Staphylococci (MR-CoNS) have emerged as an important cause of nosocomial infections especially in patients with prosthetic devices and implants. This study was conducted with an aim to determine the prevalence of methicillin resistance among CoNS isolates at a tertiary care center by both phenotypic and genotypic methods. METHODS: This cross sectional study was carried out from September 2011 to February 2014 in which 150 non-repetitive clinical isolates of CoNS were identified at the species level by conventional phenotypic methods. Cefoxitin disk (30 µg) diffusion testing was used to determine methicillin resistance and confirmed by detection of mecA gene by polymerase chain reaction (PCR). RESULTS: Out of 150 CoNS isolates, 51 were methicillin resistant by cefoxitin disk diffusion method. Out of these 51 isolates, mecA gene was detected only in 45 isolates. Moreover, mecA gene was also detected in 4 isolates, which were cefoxitin sensitive. Thus, the prevalence of methicillin resistance among CoNS was found to be 32.7% by PCR. CONCLUSION: The prevalence of methicillin resistance among Coagulase-negative Staphylococci (CoNS) was 32.7% by PCR detection of mecA gene. The sensitivity and specificity of cefoxitin disk diffusion method against mecA gene detection by PCR were found to be more than 90%. It can be concluded from this study that cefoxitin disk diffusion test can be used as a useful screening method to detect methicillin resistance among CoNS isolates. However, detection of mecA gene by PCR remains a more accurate method of detecting methicillin resistance among CoNS.