Microbiology

IAMM recommended modification of MD microbiology curriculum to MD clinical microbiology as a speciality of medicine under consideration of MCI and Niti Ayog: Time has come to move on! Are we ready? Chand Wattal Indian Journal of Medical Microbiology 2018 36(4):453-457

Respiratory syncytial virus infections in India: Epidemiology and need for vaccine Shobha Broor, Shama Parveen, Megha Maheshwari Indian Journal of Medical Microbiology 2018 36(4):458-464 Respiratory syncytial virus (RSV) has been identified as a leading cause of lower respiratory tract infections in young children and elderly. It is an enveloped negative-sense RNA virus belonging to Genus Orthopneumovirus. The clinical features of RSV infection range from mild upper-respiratory-tract illnesses or otitis media to severe lower-respiratory-tract illnesses. Current estimates show that about 33.1 million episodes of RSV-acute lower respiratory infection (ALRI) occurred in young children in 2015, of these majority that is, about 30 million RSV-ALRI episodes occurred in low-middle-income countries. In India, the rates of RSV detection in various hospital- and community-based studies mostly done in children vary from 5% to 54% and from 8% to 15%, respectively. Globally, RSV epidemics start in the South moving to the North. In India, RSV mainly peaks in winter in North India and some correlation with low temperature has been observed. Different genotypes of Group A (GA2, GA5, NA1 and ON1) and Group B (GB2, SAB4 and BA) have been described from India. The burden of RSV globally has kept it a high priority for vaccine development. After nearly 50 years of attempts, there is still no licensed vaccine and challenges to obtain a safe and effective vaccine is still facing the scientific community. The data in this review have been extracted from PubMed using the keywords RSV and Epidemiology and India. The data have been synthesised by the authors.

Pneumococcal vaccines Anand Manoharan, Ranjith Jayaraman Indian Journal of Medical Microbiology 2018 36(4):465-474 Streptococcus pneumoniae continues to take a heavy toll on childhood mortality and morbidity across the developing world. An estimated 10.6 million invasive pneumococcal diseases (IPDs) occur every year, with nearly 1 million deaths in children under 5 years of age. Introduction of vaccines in the childhood immunisation programme in developed world has brought down the incidence of the disease considerably. However, childhood immunocompromising illnesses including HIV have increased the risk of IPD several folds. There is also a growing concern on the increasing antibiotic resistance among these invasive strains to penicillin, other beta-lactams and macrolides, making treatment difficult and expensive. It is estimated that about 62% of IPD worldwide is caused by the 10 most common serotypes. Although the ranking of individual pneumococcal serotypes causing serious disease varies among nations, the 7–13 serotypes included in pneumococcal conjugate vaccines (PCVs) may prevent 50%–80% of all paediatric pneumococcal diseases globally. The World Health Organization has recommended the use of PCV-10/13 in the national immunisation programmes (NIPs) of developing countries. Four doses of PCV-13 have been recommended by the US Association of Pediatrics and Centers for Disease Control and Prevention, at intervals of each 2 months for the first 6 months and by the 12th to 15th months after birth. This is expected to reduce the morbidity and mortality associated with IPD and simultaneously decrease colonisation with circulating antibiotic-resistant strains in immunized communities. Nevertheless, continued surveillance of antimicrobial resistance in non-vaccine serotypes is necessary to prevent the resurgence of resistance. Other virulence factors which are not serotype specific also need to be studied to overcome the drawbacks of serotype-specific pneumococcal vaccines. PCV-13 was launched during May 2017 under the NIP of five Indian states with the highest pneumococcal diseases in the country and is expected to be rolled out in the other parts of the country in the coming days.

Prosthetic joint infection: A major threat to successful total joint arthroplasty Sujeesh Sebastian, Rajesh Malhotra, Benu Dhawan Indian Journal of Medical Microbiology 2018 36(4):475-487 Total joint arthroplasty (TJA) is one of the most common and reliable orthopaedic procedures that has significantly improved the quality of life of patients with degenerative joint diseases. Following the increase in the ageing population, availability of trained orthopaedic surgeons and advances in implantation procedures, demand for TJA both globally and in India is significantly increasing. Though TJA is one of the most cost-successful orthopaedic procedures, prosthetic joint infection (PJI) is one of the major complications of joint arthroplasty. Accurate diagnosis of PJI is challenging. Since total hip and knee arthroplasties comprises the majority of TJAs, this review focuses on the current understanding of incidence, risk factors, pathogenesis, causative microorganisms, diagnosis, treatment and prevention of PJI related to these two procedures.

Multidrug-resistant Enterobacteriaceae colonising the gut of adult rural population in South India Sherly Antony, Kandasamy Ravichandran, Reba Kanungo Indian Journal of Medical Microbiology 2018 36(4):488-493 Background: Multidrug-resistant (MDR) colonisers act as a reservoir for transmission of antibiotic resistance and are a source of infection. Exposure to antibiotics by the commensal flora renders them resistant. Antibiotic consumption and hospitalisation are two major factors influencing this. We studied, antibiotic-resistant bacteria colonising rural adult population who had restricted access to health care and presumably had low consumption of antibiotics. Aim: Detection of multidrug resistance genes of extended spectrum β-lactamase (ESBL-CTX-M), AmpC β-Lactamase (CIT), Klebsiella pneumoniae carbapenemase (KPC) and New Delhi Metallo β-lactamase (NDM) in Enterobacteriaceae colonising the gut of adult population in a South Indian rural community. Methodology: Faecal samples of 154 healthy volunteers were screened for Enterobacteriaceae resistant to commonly used antibiotics by standard methods, followed by phenotypic detection of ESBL by double disk synergy method, AmpC by spot inoculation and carbapenemases by imipenem and ethylenediaminetetraacetic acid + imipenem combined E-test strips and modified Hodge test. Polymerase chain reaction was done to detect blaCTX-M,blaCIT,blaKPC-1 and blaNDM-1 genes coding for ESBL, AmpC, KPC and NDM, respectively. Results: Colonisation rate of enteric bacteria with MDR genes in the community was 30.1%. However, phenotypically, only ESBL (3.2%) and NDM (0.65%) were detected. While the genes coding for ESBL, AmpC and NDM were detected in 35.6%, 17.8% and 4.4% of the MDR isolates, respectively. Conclusions: Carriage of MDR strains with a potential to express multidrug resistance poses a threat of dissemination in the community. Awareness for restricted use of antibiotics and proper sanitation can contain the spread of resistant bacteria.

Characterization of In vitro inhibitory effects of consensus short interference RNAs against non-structural 5B gene of hepatitis C virus 1a genotype Imran Shahid, Waleed Hassan Almalki, Munjed M Ibrahim, Sultan Ahmad Alghamdi, Mohammed H Mukhtar, Shaia Saleh R. Almalki, Saad Ahmed Alkahtani, Mohammad S Alhaidari Indian Journal of Medical Microbiology 2018 36(4):494-503 Purpose: Chronic hepatitis C has infected approximately 170 million people worldwide. The novel direct-acting antivirals have proven their clinical efficacy to treat hepatitis C infection but still very expensive and beyond the financial range of most infected patients in low income and even resource replete nations. This study was conducted to establish an in vitro stable human hepatoma 7 (Huh-7) cell culture system with consistent expression of the non-structural 5B (NS5B) protein of hepatitis C virus (HCV) 1a genotype and to explore inhibitory effects of sequence-specific short interference RNA (siRNA) targeting NS5B in stable cell clones, and against viral replication in serum-inoculated Huh-7 cells. Materials and Methods: In vitro stable Huh-7 cells with persistent expression of NS5B protein was produced under gentamycin (G418) selection. siRNAs inhibitory effects were determined by analysing NS5B expression at mRNA and protein level through reverse transcription-polymerase chain reaction (PCR), quantitative real-time PCR, and Western blot, respectively. Statistical significance of data (NS5B gene suppression) was performed using SPSS software (version 16.0, SPSS Inc.). Results: siRNAs directed against NS5B gene significantly decreased NS5B expression at mRNA and protein levels in stable Huh-7 cells, and a vivid decrease in viral replication was also exhibited in serum-infected Huh-7 cells. Conclusions: Stable Huh-7 cells persistently expressing NS5B protein should be helpful for molecular pathogenesis of HCV infection and development of anti-HCV drug screening assays. The siRNA was effective against NS5B and could be considered as an adjuvant therapy along with other promising anti-HCV regimens.

Validation of pneumococcal iron acquisition (piaA) gene for accurate identification of Streptococcus pneumoniae Sreeram Chandra Murthy Peela, Sujatha Sistla, Kadhiravan Tamilarasu, Sriram Krishnamurthy, B Adhishivam Indian Journal of Medical Microbiology 2018 36(4):504-507 Purpose: The pneumococcal iron acquisition (piaA) gene is found to be highly specific and hence proposed as a diagnostic marker for identification of pneumococci. The objective of the present study was to evaluate the piaA gene as a genetic marker for the identification of pneumococci. Methods: Twenty isolates were initially sequenced for lytA gene using published primers. PiaA-PCR (piaA polymerase chain reaction) was performed using in-house primers and protocol. Based on the sensitivity and specificity results, a final sample of 30 pneumococcal isolates and 11 non-pneumococcal isolates confirmed with lytA- sequencing were selected. Statistical analyses were performed using OpenEpi v3.01 and GraphPad Quickcalc at P < 0.05 as the level of statistical significance. Results: Of the initial 20 samples tested, piaA PCR was positive in only 71.43% (10/14) of the pneumococcal isolates but was 100% specific (0/6 non-pneumococcal isolates) P = 0.011. When the PCR was performed on 41 samples, the sensitivity increased to 73.33% (95% of confidence interval [CI] = 55.55–85.82) and specificity remained the same P < 0.001. The level of agreement between the PCR and lytA-sequencing was found to be moderate (κ = 0.694; 95% CI = 0.432–0.955). Conclusions: PiaA-PCR can be used as a specific marker for the identification of pneumococcus, though it is less sensitive. As the level of agreement was moderate, further analyses on a large number of samples can give conclusive evidence for its use as a diagnostic marker for pneumococcus.

A road less travelled: Clinical comparison of HIV seropositive and seronegative patients with cystoisosporiasis – An 11-year experience from a tertiary care centre in Northern India Ujjala Ghoshal, Vidhi Jain, Nidhi Tejan, Sonali Khanduja Kalra, Prabhat Ranjan, Richa Sinha, Dinesh Gangwar, Uday C Ghoshal Indian Journal of Medical Microbiology 2018 36(4):508-512 Background: Cystoisospora is a well-known opportunistic enteric parasite among human immunodeficiency virus (HIV) seropositive patients but there is a paucity of data among HIV negative patients. This study investigated Cystosporiasis on both HIV positive and negative patients, with or without diarrhea, presenting to a tertiary care and super specialty center of northern India. Methodology: Oocysts of Cystoisospora were detected on light microscopy, by modified Kinyoun staining of stool specimens, over an 11-year study period. Results: Of the 10,233 stool specimens evaluated, Cystoisospora was detected in 64 patients, 37 (57.81%) of whom were HIV positive. Year-wise analysis showed an overall declining trend of cystoisosporiasis. Maximum cases were detected in May and June in HIV positive patients and February and September among HIV negative patients. Among HIV positive patients, the mean CD4 count was 152.04 ± 81.12cells/μL, mean absolute eosinophil count (AEC) was 229.16 ± 175.62 cells/μL and 12.5% patients had mild eosinophilia. Tuberculosis was the most common co-morbidity. Dual infections of Cystoisospora with Cryptosporidium and Giardia were also seen. Among HIV negative patients, eight had primary autoimmune disorders, seven were solid organ transplant recipients and the rest had chronic bowel diseases. The mean AEC was 485.47 ± 414.88 cells/μL, with 14.81% patients showing mild and 11.11% showing marked eosinophilia. Dual infection with Giardia was seen. Recurrent cystoisosporiasis was noted, despite cotrimoxazole treatment in a single case. Conclusion: The epidemiology of cystoisosporiasis differs between HIV seropositive and seronegative patients in terms of year-wise and month-wise trends, co-infections and most importantly, AECs.

Dual therapy with lopinavir/ritonavir plus lamivudine could be a viable alternative for antiretroviral-therapy-naive adults with HIV-1 infection regardless of HIV viral load or subgenotype in resource-limited settings: A randomised, open-label and non-inferiority study from China Linghua Li, Haolan He, Yun Lan, Jinfeng Chen, Huolin Zhong, Jingmin Nie, Xiejie Chen, Fengyu Hu, Xiaoping Tang, Weiping Cai Indian Journal of Medical Microbiology 2018 36(4):513-516 Backgrounds: This randomised controlled, open-label, non-inferiority trial was conducted in antiretroviral-naïve HIV-1-infected patients to assess the efficacy and safety of 48-week dual therapy of LPV/r plus 3TC (DT group) compared with Chinese first-line triple-therapy regimen (TT group). Methods: 198 were randomised to DT (n = 100) or TT (n = 98). Results: Ninety-two DT patients (92%) and 88 TT patients (89.8%) achieved HIV-1 RNA <50 copies/ml at week 48 (P = 0.629). Moreover, the safety profile was similar between two groups, and no secondary HIV resistance was observed. Conclusion: The results suggest that dual therapy of LPV/r plus 3TC is non-inferior to the first-line triple-therapy regimen in China.

Human papillomavirus prevalence and genotype distribution among Turkish women with or without cervical lesion Mehmet Demirci, Aylin Dag Guzel, Aynur Adeviye Ersahin, Eda Yorulmaz, Suat Suphan Ersahin, Baris Ata Borsa Indian Journal of Medical Microbiology 2018 36(4):517-521 Context: Human papillomavirus (HPV) infection is the main cause of cervical cancer, but the risk is associated with the various HPV genotypes which may be found in women with or without clinical findings. Aims: We aimed to identify HPV prevalence and genotype distribution in women with or without cervical lesions admitted to Gynaecology and Obstetrics Clinics of one of the largest private hospitals in Istanbul between 2013 and 2017. Subjects and Methods: In the present study, cervical cytobrush samples collected from 2464 women with different cytological conditions, and investigated for the presence of HPV, and the different genotypes. Results were evaluated based on the HPV positivity in different cytological findings, and ages. Furthermore, distribution of high-risk (HR) and low-risk (LR) genotypes in different groups was investigated. Results: Among all participants, 1925 (78.1%) was with the normal cytological condition, 354 (14.4%) with ASC-US; 151 (6.1%) with low-grade squamous intraepithelial lesion (LSIL), and 34 (1.4%) with high-grade squamous intraepithelial lesion (HSIL). Our results showed that 649 out of 2464 patients (26.3%) were positive, and 1815 (73.7%) were negative for the presence of HPV. Among 649 positive patients, 223 (34.3%) were found positive for more than one genotype. HPV 16 was found the most common HR-HPV type in ASC-US and LSIL whereas HPV 18 was the most common in HSIL. HPV 6 was found the most common LR-HPV type in ASC-US and LSIL whereas HPV 11 was the most common in HSIL. 26.9% of women <50 years old, and 22.3% of women ≥50 years old was positive for HPV. The most common HR-HPV genotype was 16 in both groups with (19%) or without (17%) abnormal cytology. Conclusions: We concluded that HPV prevalence and genotype distribution in women with or without clinical findings is an important predictor of cervical cancer.