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Objectives: To investigate the genomic differences between two extensively drug resistant, ST16 strains of Klebsiella pneumoniae recovered from patients in the same ICU, one of which was colistin resistant. Methods: Antimicrobial susceptibilities of the isolates were determined using VITEK-2. Hybrid assemblies for both strains were generated using Oxford Nanopore and Illumina technologies. The sequence type, capsule type, O-locus type, antimicrobial resistance determinants and plasmids carried by the isolates were inferred from the genome sequence. The phylogenetic placement, antimicrobial resistance, and virulence determinants of the isolates relative to a collection (n = 871) of ST16 isolates were assessed. Results: Both BC16, a colistin-resistant blood stream isolate and U23, a colistin-sensitive urinary isolate displayed near-identical antimicrobial resistance profiles and genome sequences with varying plasmid profiles. The BC16 genome only had 21 SNPs relative to U23 and belonged to the same capsule, O-antigen locus and multi-locus sequence types. The mgrB locus in BC16 was disrupted by an IS5 element. Phylogenetically, U23 and BC16 were placed on a clade with 4 strains belonging to K-type K48 and O-type O2a as opposed to majority (n = 807) of the strains (K-type K51 and O-type O3b). Conclusions: BC16 was a colistin resistant derivative of U23, which evolved colistin resistance by an IS5-mediated disruption of the mgrB locus, likely during treatment of the index patient with colistin in the ICU. The strains belong to a rare subtype of ST16 with unique capsular and O-antigen types underscoring the utility of genomic surveillance networks and open-access genomic surveillance data in tracking problem clones.

Background: Enterococci are emerging nosocomial pathogen showing resistance to broad spectrum antibiotics. As reported by the center for disease control and prevention, enterococci (13.9%) are the second leading cause of urinary tract infection, after Escherichia coli. After the first report of vancomycin-resistant enterococci in England (1988), India reported its first vancomycin resistant enterococci isolate from New Delhi (1999). The prevalence of vancomycin resistant enterococci ranges from 1-9%, in India. To evaluate the prevalence of vancomycin resistant enterococci among urinary isolates and to check their antimicrobial resistance pattern. Methods: A retrospective observational study conducted at a tertiary care hospital. Data were analysed from November, 2017 to October, 2018. A total of 12,129 urine samples were received and subjected to culture on HiCrome UTI agar (Hi-Media laboratories, Mumbai) and incubated at 37 °C for a period of 18-24 hours. Antimicrobial susceptibility was performed using Kirby–Bauer disc diffusion method. Identification was done on the basis of colony colour and species identification was done by using biochemical test as per standard laboratory protocol. In one case automated siemens microscan walkaway identification system was used for confirmation. Results: Enterococci were isolated in 4.06% from urine cultures out of which 7.52% were vancomycin resistant. Most of the vancomycin resistant enterococci isolate (86.49%) were multi drug resistant. Conclusion: In vancomycin resistant enterococci related urinary tract infection, nitrofurantoin can be used as an appropriate first choice in uncomplicated cases and linezolid should be reserved for serious and complicated urinary tract infections.

Summary: Background: Carbapenem-resistant Enterobacterales (CRE) are a global health problem with a growing prevalence. India has a high prevalence of CRE. CRE infections are difficult to treat, and are associated with significant morbidity and mortality. Colonisation is generally a prerequisite for infection and the prevention of CRE colonisation is key to the prevention of CRE infection. Objectives: To determine the prevalence of CRE colonisation and subsequent infections in an adult intensive care unit (ICU) in India. Methods: We conducted a prospective observational study in which perirectal swabs were obtained along with relevant clinical details of consenting adult patients upon ICU admission between January 2019 and August 2020. Rectal screening was performed using MacConkey agar plates with ertapenem disks and further identification was performed using conventional microbiological techniques. Ertapenem minimum inhibitory concentration (MIC) was determined using an epsillometer (E) test. The modified carbapenem inactivation (mCIM) test and EDTA carbapenem inactivation test (eCIM) were performed to confirm carbapenem resistance using the Clinical Laboratory Standards Institute (CLSI) 2020 guidelines. Results: 192 ICU patients were screened for CRE. 37 patients were found to be colonised with CRE. Klebsiella pneumoniae (N=25; 67.6%) was the most frequent CRE isolate, followed by Escherichia coli (N=11; 29.7%) and one Enterobacter species (N=1; 2.7%). 89.2% (33/37) patients developed CRE infection. Pneumonia was the most common CRE infection identified in 12/33 (36.4%) patients.during the hospital stay. The median duration of hospital stay was longer (17 days) for CRE colonised compared to CRE non-colonised patients (9 days) (P

Objectives Urinary tract infection (UTI) is one of the most common diagnoses in patients visiting urology clinics. Rampant use of empiric and inadequate doses of antibiotics leads to an increase in resistance and poses a huge financial burden. We evaluated UTI in relation to antibiotics used, frequency, susceptibility, and resistance pattern of different pathogens at a tertiary care center and made some important observations. Methods Prospectively 729 patients diagnosed with UTI attending a urology outpatient department from July 2018 to January 2020 were managed accordingly. Antibiotics were started on the basis of urine culture and sensitivity (c/s) or empirically and changed according to subsequent urine c/s. Repeat urine c/s was performed after 5 to 7 days of starting therapy and 10 days after completion of therapy. Results Out of 729 subjects, 417 (57.2%) were males and 312 (42.8%) were females. The most common symptom at diagnosis was dysuria 512 (70.2%), whereas 221 (30.3%) patients presented with fever. Escherichia coli was the most common organism isolated, 453 (62.1%). Among 729 patients, 239 took antibiotics without c/s report, whereas in 490 patients antibiotics were prescribed after the report. A total of 431 (59.1%) patients required one antibiotic session for clearance of pathogen, whereas 135 (18.5%) required two sessions, and three sessions were required in 66 (9%) cases. Among 239 patients whose culture came out to be positive, 145 (60.6%) were found to be resistant to the previously given antibiotic and the common pathogens isolated were E. coli (61 [42%]), Pseudomonas (28 [19.3%]), Enterococcus (22 [15.1%]), Klebsiella (14 [9.6%]), and others. Conclusion Unchecked, rampant, and inadequate use of antibiotics leads to complicated UTI with the increasing share of Pseudomonas, Klebsiella, or other dangerous microbes, which are difficult to treat as well as pose threat in the future.

The annual cystic echinococcosis (CE) incidence in endemic countries is between 1 and 200 per 100,000 population. The clinical manifestations of CE are associated with damage or dysfunction of target organs and affect primarily the liver in around 70% of cases and lungs in around 20% of cases. The involvement of the spleen is rarely seen, representing 2 to 6% of all CE cases. We describe a 60-year-old female patient who presented with 15 days' history of intermittent fever and abdominal distension, having significant hepatosplenomegaly. CE was diagnosed involving the liver, spleen, and lungs and was confirmed radiologically and microbiologically. CE is caused by the larval or cystic stage of the zoonotic dog-tapeworm. Humans can be infected by ingestion of contaminated food or water. At present, there are nine species under the genus Echinococcus with E. granulosus sensu stricto having worldwide distribution, while the rest are focally distributed. CE involving multiple organs is rare. CE should be taken into consideration in patients with these symptoms in endemic areas.

Background: Asymptomatic carriers are responsible for the consistent spread of coronavirus disease 2019 (COVID-19) in the community. The Government of India has deputed house-to-house survey teams to aid in identifying asymptomatic individuals and their susceptible contacts. We selected door-to-door survey teams of a COVID-19 red zone in western India and determined their infectioncontrol practices and anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobin G (IgG) status. Materials and Methods: This single-day prospective cross-sectional study was conducted by the Department of Microbiology of a tertiary care hospital of Jodhpur, in collaboration with the Rajasthan State Health Services. Participants were asked to fill out a questionnaire regarding personal protective equipment (PPE) use after written informed consent. Venous blood samples were collected and Kavach enzyme-linked immunosorbent assay (ELISA) (J Mitra and Co.) was performed to determine anti-SARS-CoV-2 IgG status. Results: Out of the total 39 participants, IgG antibody was detected in four. Of them, three reported mild symptoms in the past. Out of two previously real-time polymerase chain reaction (RT-PCR) SARS-CoV-2-positive participants, only one had detectable IgG antibodies (Ab) in serum. Cloth mask was used by 24, N95 mask by 11, and surgical masks by four. Conclusion: Anti-SARS-CoV-2 IgG Abs were detected among four members of house-to-house COVID-19 survey teams in Jodhpur. Most of the team members used cloth masks, whereas the Government of India guidelines has recommended triple-layered surgical masks as minimum essential PPE for healthcare workers in India. More such studies should be conducted to ascertain infection prevention and control practices among such vulnerable frontline workers in our country.

Objectives The 2019 novel coronavirus (2019-nCoV) has spread across the globe with more than 6 lakh deaths. Clinical autopsies are important to understand the pathobiology of the disease. Materials and Methods Autopsy techniques have been modified to be minimally invasive autopsies in all COVID-19 positive cases, and tissue biopsies were sampled from lungs, liver, and bone marrow within an hour after death. Detailed histological analysis was performed in the sampled tissues, along with immunohistochemistry. Patients’ clinical records were collected. Statistical Analysis Descriptive statistics were used to summarize data. Results Of the 21 cases studied, 76.2% patients were ≥ 60 years of age, 80.9% were males, and 85.7% had co-morbidities. Histopathological analysis revealed diffuse alveolar damage (including exudative and organizing phase) in 88.9% cases. Microthrombi were seen in 44.4% cases. Additional findings include viral cytopathic changes, metaplastic change in the epithelium, intra-alveolar hemorrhage, and pulmonary edema. Liver showed centrizonal congestion with hepatocytic loss, lobular inflammation, steatosis, Kupffer cell hypertrophy, and sinusoidal neutrophilic infiltration, while significant portal infiltrate and cholestasis were absent to minimal. Bone marrow revealed hemophagocytosis in 60% cases. Conclusion Incorporation of minimally invasive autopsies provides an effective method to study the pathological findings in COVID-19 deaths in resource-constrained settings. Presence of pulmonary microthrombi in a significant number of cases supports the vascular events, apart from the characteristic diffuse alveolar damage, as an important pathogenic mechanism for lung injury in COVID-19 infections. Histopathological findings in the liver and bone marrow suggest indirect insult to these organs, related to circulatory and/or hyperinflammatory response to viral infections.

ABSTRACT Klebsiella pneumoniae can be broadly classified into classical strains that cause drug-resistant, hospital-associated infections and hypervirulent strains that cause invasive, community-acquired, drug-susceptible infections. Hypermucoviscosity in Klebsiella pneumoniae has been associated with immune evasion and hypervirulence. A string-test-positive, hypermucoviscous strain of Klebsiella pneumoniae, P34, was isolated from the cystic lesion of a patient who reported to a tertiary care hospital in Jodhpur, Rajasthan, India. Given the antibiotic-susceptible and hypermucoviscous nature of the isolate, it was suspected to belong to the hypervirulent lineage of Klebsiella pneumoniae. However, P34 did not overproduce capsular polysaccharides and also remained susceptible to the antimicrobial effects of human serum when tested alongside strains that were non-hypermucoviscous. Sequencing of the genome of P34 revealed the absence of any large virulence plasmids or integrative conjugative elements that usually carry hypermucoviscosity- and hypervirulence-associated genes. P34 also lacked key virulence determinants such as aerobactin, yersiniabactin, and salmochelin biosynthesis clusters. In addition, P34 lacked homologs for genes associated with enhanced capsule synthesis and hypermucoviscosity, such as rmpA, rmpA2, rmpC, and rmpD (regulator of mucoid phenotype). These observations suggest that P34 may harbor novel genetic determinants of hypermucoviscosity independent of the indirectly acting rmpA and the recently described rmpD. IMPORTANCE Hypermucoviscosity is a characteristic of hypervirulent Klebsiella pneumoniae strains, which are capable of causing invasive disease in community settings. This study reports phenotyping and genomic analysis of an unusual clinical isolate of Klebsiella pneumoniae, P34, which exhibits hypermucoviscosity and yet does not harbor rmp (regulator of mucoid phenotype) genes, which are known determinants of hypermucoviscosity (rmpA and rmpD). Similar clinical isolates belonging to the K. pneumoniae complex that are hypermucoviscous but do not harbor the rmp loci have been reported from India and abroad, indicating the prevalence of unknown determinants contributing to hypermucoviscosity. Therefore, strains like P34 will serve as model systems to mechanistically study potentially novel determinants of hypermucoviscosity in the K. pneumoniae complex.

The coronavirus pandemic is a global health crisis of recent times and the biggest threat we have faced after the Second World War. This viral infection (COVID-19) is not the only cause of deaths in this pandemic. A usual complication of viral infections is a secondary superimposed bacterial infection or a superinfection. Based on limited published data, the relatively high incidence of severe infection and mortality in COVID-19 patients is attributed to these infections. It is reasonable to anticipate that nearly half of the patients who have died from COVID-19 had superinfection. Patients who have severe form of the disease and those requiring prolonged stay in intensive care units (ICUs) are more prone to developing super added infection by nosocomial pathogens. The most common type of infection observed among COVID-19 patients is ventilator-associated pneumonia (VAP), followed by bacteremia with sepsis and urinary tract infections (UTIs). Antibiotics are commonly prescribed to keep these infections at bay which is promoting antimicrobial resistance (AMR). In developing countries like India, where there is well-established high burden of multidrug-resistant organisms in hospital settings, superinfections in COVID-19 patients can pose a biggest challenge in the treatment leading to increase mortality. There is a need of prospective studies, which should include clinical, microbiological, and epidemiological data on superinfections that can be used in forming effective antimicrobial stewardship strategies; which can have a crucial role in optimal antimicrobial prescribing.

On 31st December, 2019, an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was declared in Wuhan, China. On 24 March 2020, there was a nationwide lockdown for 21 days, followed by Janata curfew on 22nd March. As the pandemic has developed and spread across continents, everyone including policy makers have realized shortage of personal protective equipment (PPE) such as N95 respirators, coverall, and face shields. This is one of the major factors putting healthcare workers not only at risk of infection but also to various side effects of prolonged use of PPE. Based on international experiences, new ideas in procuring and mass manufacturing, rational use of PPE equipment is the need of hour, especially for developing nations which lack adequate resources and infrastructure for manufacturing PPEs.

Aims: The indigenously developed Indian Council of Medical Research (ICMR)-NIV COVID Kavach IgG enzyme linked immunosorbent assay (ELISA) has been recommended for seroprevalence among vulnerable populations in India, which provided essential services throughout the lockdown. The staff working in the High Court was one such group. We compared anti-SARS-CoV-2 IgG seropositivity among the staff of Jodhpur and Jaipur High Courts, Rajasthan, India. Methods: Asymptomatic judiciary staff of Jodhpur and Jaipur benches of High Courts were enrolled after informed written consent. A questionnaire was filled and 3–5 ml venous blood was collected from participants. The ICMR-NIV COVID Kavach IgG ELISA and EUROIMMUN IgG ELISA were used for detection of Anti-SARS-CoV-2 IgG antibodies. Results: A total of 63 samples (41 from Jodhpur and 22 from Jaipur) were collected between 28th July to 4th August 2020. The overall anti-SARS-CoV-2 IgG seroprevalence was found to be 6.35%. Seropositivity was higher among the staff from Jaipur (13.64%) as compared to Jodhpur (2.44%). The Kavach ELISA results were in complete agreement with EUROIMMUN ELISA. The infection control measures were deemed effective. Conclusion: Seroprevalence among the staff of Jodhpur High Court was found to be lower than Jaipur, reflecting higher susceptibility to COVID-19 in the former. Many offices worldwide are closed till mid 2020 but need to come up with pre-emptive policies eventually. This study may help to anticipate the possible challenges when other government/private offices start functioning. The infection control practices of one workplace may help formulate guidelines for other offices.

Background: Chronic suppurative otitis media (CSOM) is a major cause of hearing disability and morbidity in poor socioeconomic developing countries with prevalence of 4%. Indiscriminate use of antibiotics and poor follow up of patients has resulted in treatment failure, emergence of resistant strains, super infection, intra-cranial and extra-cranial complications in CSOM patients. Staphylococcus aureus, P. aeruginosa, Proteus spp. and Klebsiella spp. are most common organisms causing infection. Knowledge of microbial profile and susceptibility pattern is essential for efficacious treatment of this disorder. Objective: To determine the clinico-bacteriological profile of CSOM, to analyze the susceptibility pattern of various antibiotics and to evaluate the in vitro efficacy of aminoglycosides over fluoroquinolones against the aerobic bacterial isolates from CSOM. Methods: We studied 153 clinically suspected CSOM cases from March 2018 to October 2018 in Microbiology and Otorhinolaryngology department. The ear swabs were aerobically cultured and identification of the isolate was done by standard bacteriological methods. Results: Safe type CSOM was a major cause of disease. Moderate (35.3%) and mild degree (32.7%) of hearing loss was seen in most of the CSOM cases. The culture positivity rate was 82.4% and the most common isolate was P. aeruginosa (55.8%) followed by S. aureus (27.5%). P. aeruginosa, A. baumannii and Enterobacteriaceae spp. showed high sensitivity to colistin, piperacillin-tazobactam, ceftazidime-tazobactam and good sensitivity for cefepime and amikacin; 33.3% S. aureus isolates were Methicillin-resistant which was sensitive to gentamicin, vancomycin and linezolid. Conclusion: Knowledge of the spectrum of microorganisms causing ear discharge is important for effective treatment.

SARS-CoV-2 belongs to genus Betacoronavirus subgenus Sarbecovirus of the family Coronaviridae, which originated as a global public health problem. The disease caused is termed as Coronavirus Disease (COVID-19). The virus spread in more than 213 countries and territories all over the world and disease was declared as a pandemic. SARS-CoV-2 is an enveloped positive-sense single- stranded ribonucleic acid (ssRNA) virus. Severe infection and high-mortality are seen in patients with comorbid conditions like diabetes, hypertension, cancer, old age, malnutrition, children, and pregnancy. In India, strategy for testing of COVID-19 has been framed and revised over the course of time by the Indian Council of Medical Research (ICMR), Department of Health Research (DHR), Ministry of Health and Family Welfare (MOHFW), Government of India. ICMR has created a network of viral research and diagnostic laboratories (VRDLs) all over the country, and COVID-19 testing has also been undertaken by ICMR. AIIMS Jodhpur is a regional level VRDL, mentoring 38 government and private laboratories for molecular diagnosis of COVID-19 in the states of Rajasthan and Gujarat. Currently, real-time reverse transcription polymerase chain reaction (rRT-PCR) assay is used all over the country for diagnosis of COVID-19. It uses the TaqMan fluorogenic probe-based chemistry and 5′- nuclease activity of Taq DNA polymerase. It targets specific genes like the RdRp gene, HKU-Orf1ab gene, E gene, and N gene. Apart from rRT-PCR, other isothermal nucleic acid test (NAT)-like transcription-mediated amplification (TMA), loop-mediated isothermal amplification (LAMP), etc. are emerging diagnostic tools to detect COVID-19. Cepheid Xpert Xpress SARS- CoV-2 test and Truenat betaCoV are point-of-care molecular assays which gives results in less than 1 hour, and helps to provide rapid and accurate results. Automated molecular assays like Cobas SARS-CoV-2 and Multiplex NAAT BioFire Respiratory Panel 2.1 (RP2.1) are newer techniques to curb the disease. Sherlock CRISPR SARS-CoV-2 kit is a highly specific and sensitive assay developed to diagnose COVID-19. rRT-PCR has been combined with techniques like bead hybridization, digital droplet PCR, microarray, etc. for improving the correct diagnosis. Recent molecular assays are the future pillars for containment of COVID-19 outbreaks all over the world.

Development of rapid, reliable, and easy diagnostic tests with high-throughput is the need of the hour for laboratories combating the COVID-19 pandemic. While real-time polymerase chain reaction (RT-PCR) is the gold standard for diagnosing active infections, it is expensive and time-consuming. Serological diagnostic assays with a premise to aid rapid contact tracing, immune status determination, and identification of potential convalescent plasma donors hold great promise. Timely diagnosis, effective treatment, and future prevention are key to management of COVID-19.

Through this manuscript, we would like to share our experience with building a COVID hospital, allocating duties, planning and managing supplies during COVID-19 pandemic. This manuscript is prepared by the Doctors of various specialties with vast experience involved in actual planning of the infrastructure and resources. This comprehensive manuscript will help teams to prepare and train, stockpile necessary equipment and prepare their staff to deal with current crisis if there is a surge in infected cases.

Background: Leprosy is a chronic granulomatous infectious disease, which mainly involves skin, peripheral nerves, mucosa of the upper respiratory tract, and eyes. According to National Leprosy Eradication Programme 2017–18 annual report, the annual new case detection rate from Rajasthan is 1.27 per 1 lakh population and prevalence rate is 0.14. Aims and Objective: The main objective of this study was to determine the spectrum of Mycobacterium leprae infections among suspected cases attending a teaching hospital in western Rajasthan, India. Materials and Methods: This is a retrospective study conducted in the Department of Microbiology, in a teaching hospital, western Rajasthan, between the period of January 2017 and April 2019. The records of modified Ziehl–Neelsen staining during the study period were analyzed. The demographic data like age and sex along with clinical diagnosis were also recorded from laboratory register and hospital information system. Results: Out of total 91 suspected cases, 30.77% was microbiologically confirmed cases of leprosy. Out of total positive cases, 71.43% were male and 28.57% were female. A maximum number of positive (50%) were found in the age group of 31–50 years. Conclusion: Present study gives an insight about the spectrum of leprosy in the region. The large number of positive cases signifies that leprosy awareness and programs aimed at elimination need to be more vigorously implemented. To achieve complete eradication from this menace, newer strategies like effective vaccine development and drug-resistance testing should be implemented.

This study was planned to estimate the proportion of confirmed multi-drug resistance pulmonary tuberculosis (TB) cases out of the presumptive cases referred to DTC (District Tuberculosis Center) Jodhpur for diagnosis; to identify clinical and socio-demographic risk factors associated with the multidrug-resistant pulmonary TB and to assess the spatial distribution to find out clustering and pattern in the distribution of pulmonary TB with the help of Geographic Information System (GIS). In the Jodhpur district, 150 confirmed pulmonary multi-drug resistant tuberculosis (MDR-TB) cases, diagnosed by probe-based molecular drug susceptibility testing method and categorized as MDR in DTC's register (District Tuberculosis Center), were taken. Simultaneously, 300 control of confirmed non-MDR or drug-sensitive pulmonary TB patients were taken. Statistical analysis was done with logistic regression. In addition, for spatial analysis, secondary data from 2013-17 was analyzed using Global Moran's I and Getis and Ordi (Gi*) statistics. In 2012-18, a total of 12563 CBNAAT (Cartridge-based nucleic acid amplification test) were performed. 2898 (23%) showed M. TB positive but rifampicin sensitive, and 590 (4.7%) showed rifampicin resistant. Independent risk factors for MDR TB were ≤60 years age (AOR 3.0, CI 1.3-7.1); male gender (AOR 3.4, CI 1.8-6.7); overcrowding (AOR 1.6, CI 1.0-2.7); using chulha (smoke appliance) for cooking (AOR 2.5, CI 1.2-4.9), past TB treatment (AOR 5.7, CI 2.9-11.3) and past contact with MDR patient (AOR 10.7, CI 3.7-31.2). All four urban TUs (Tuberculosis Units) had the highest proportion of drug-resistant pulmonary TB. There was no statistically significant clustering, and the pattern of cases was primarily random. Most of the hotspots generated were present near the administrative boundaries of TUs, and the new ones mostly appeared in the area near the previous hotspots. A random pattern seen in cluster analysis supports the universal drug testing policy of India. Hotspot analysis helps cross administrative border initiatives with targeted active case finding and proper follow-up.

Doctors, nurses, house cleaning staff and hospital ward attendants are at increased risk of acquiring coronavirus disease 2019 (COVID-19) if there is a breach in the personal protection equipment. A new simple, easy to implement scoring system has been developed by our Suraksha Chakra team which can be used by the policy makers and hospital administrators. The scoring system is not to discourage anyone but constantly reinforce the healthcare workers for safe practices during patient care.

In the COVID-19 pandemic, global health care systems have become overwhelmed with potentially infectious patients seeking testing and care. Preventing spread of infection to and from health care workers (HCWs) and patients relies on effective use of personal protective equipment(PPE). The most critical part in due course of managing this pandemic is adequate supply of PPEs. We have customized a PPE which is economical and reusable after proper disinfection. This customized PPE can be a solution to conservation of supply during this pandemic.

Introduction: About 20–25% of the world's populations are infected with dermatophyte and the incidence of the disease is increasing steadily. In India, the cause of dermatophytoses is adversely influenced by economic factors such as poverty, poor hygiene and social conditions like overcrowding. The main objective of this study was to determine the prevalence, etiological agents, and distribution patterns of the disease among the patients attending a teaching hospital, Jodhpur. Materials and Methods: This is a retrospective study conducted in the Department of Microbiology and Department of Dermatology of a teaching hospital, Jodhpur from January 2017 to May 2018. The microbiological records of potassium hydroxide (KOH) mount examination and the fungal culture report of skin, hair, and nail samples during the study period were analyzed. Results: A total 363 skin, hair, and nail samples were received for fungal culture as investigations requested by dermatologist. Out of total 363 samples, KOH mount was positive in 58.4% and the culture was positive in 44.07% cases. Dermatophyte was isolated in 40.22% cases. Trichophyton mentagrophytes was the predominant dermatophyte (55%) isolated followed by T. tonsurans (22.5%) and T. rubrum (6.25%). Conclusion: The present study gives an insight about the prevalence and distribution pattern of dermatophytoses in Jodhpur, India. Tinea corporis was the most commonly diagnosed clinical condition followed by Tinea cruris. T. mentagrophytes was implicated as the predominating species.

INTRODUCTION: The crude mortality rate due to infectious diseases in India is approximately 417 per one lakh persons and pyogenic infections are one of the significant contributor. Poor antimicrobial stewardship in India has led to an increase in multidrug resistant superbugs in both community as well as hospital settings. The aim of this study was to identify the bacterial etiology of pyogenic infections and to evaluate their antimicrobial resistance profile. METHODS: this is a retrospective observational study from January, 2018 to December, 2018. A total 1851 samples, collected as a part of patient care were included in this study. Specimens were subjected to culture on Blood agar and MacConkey agar media and incubated at 37°C for 48 hours. Species identification was done as per standard laboratory protocol. Antimicrobial susceptibility testing was performed using Kirby-Bauer disc diffusion according to Clinical and Laboratory Standards Institute guidelines. RESULTS: of total 1851 samples, culture was positive in 61.54%. A total 70.59%, Gram negative organisms were isolated followed by Gram positive cocci in 45.48%, yeast in 1.05%, coryneform bacteria in 0.79% and in one case, non-tubercular mycobacteria was isolated. Staphylococcus aureus (30.9%) was the predominant organism isolated. Most common multi drug resistant isolates were Klebsiella spp. (74.79%) and Acinetobacter spp. (74.32%). CONCLUSION: this study gives an insight about the prevalence and common etiology of pyogenic infections along with their antimicrobial resistance profile in north western region of India. This study will contribute in formulating antibiotic stewardship program by selecting the antibiograms of pyogenic isolates.

Group C Streptococci comprises of Streptococcus dysgalatiae that is further divided into two subspecies, namely S. dysgalactiae subspecies equisimilis and S. dysgalactiae subspecies dysgalactiae. S. dysgalactiae subspecies dysgalactiae is mainly an animal pathogen but few cases of human infections have been described in the literature. A 40 year old patient presented to the hospital with complaints of pain in pelvis and suprapubic area. Urine sample of the patient was subjected to microscopy and culture for isolation and identification of the etiological agent. S. dysgalactiae subspecies dysgalactiae was identified from the clinical specimen of the patient by conventional and automated methods. The patient was successfully treated with third generation cephalosporin. With newer or rarely reported pathogens causing human diseases and increase in number of immunocompromised individuals in the population, the pathogenic potential of such isolates should not be undermined and a careful correlation with the clinical profile should help guide a clinician in optimum treatment of the patient.

Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in the Wuhan City of China in December 2019 and evolved into a global pandemic. To date, there are no proven drugs or vaccines against this virus. Hence, the situation demands an urgent need to explore all potential therapeutic strategies that can be made available to prevent the disease progression and improve patient outcomes. In absence of clinically proven treatment guidelines, several repurposed drugs and investigational agents are currently being evaluated in clinical trials for their probable benefits in the treatment of COVID-19. These include antivirals (remdesivir, lopinavir/ritonavir, umifenovir, and favipiravir), interferon, antimalarials (chloroquine/hydroxychloroquine), antiparasitic drugs (ivermectin and nitazoxanide), biologics (monoclonal antibodies and interleukin receptor antagonist), cellular therapies (mesenchymal stem cells and natural killer cells), convalescent plasma, and cytokine adsorber. Though several observational studies have claimed many of these agents to be effective based on their in vitro activities and extrapolated evidence from SARS and Middle East respiratory syndrome (MERS) epidemics, the currently available data remains inconclusive because of ill-defined patient selection criteria, small sample size, lack of concurrent controls, and use of intermediary outcomes instead of patient-relevant outcomes. Moreover, there is a need to clearly define the patient populations who warrant therapy and also the timing of initiation of treatment. Understanding the disease pathology responsible for the clinical manifestations of COVID-19 is imperative to identify the potential targets for drug development. This review explains the pathophysiology of COVID-19 and summarizes the potential treatment candidates, which can provide guidance in developing effective therapeutic strategies.

Coronavirus disease 2019 (COVID-19), an acute onset pneumonia caused by a novel Betacoronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly evolved into a pandemic. Though its origin has been linked to the Wuhan City of China’s Hubei Province in December 2019, recent reports claim that the original animal-to-human transmission of the virus probably happened sometime between September and October 2019 in Guangdong Province, rather than Hubei. As of July 3, 2020, India has reported a case positivity rate of 6.5% and a fatality rate of 2.8%, which are among the lowest in the world. Also, the severity of the disease is much less among Indians as evidenced by the low rate of ICU admission (15.3%) and the need for mechanical ventilation (4.16%). As per the World Health Organization (WHO) situation report 165 on July 3, 2020, India has one of the lowest deaths per 100,000 population (1.32 deaths against a global average of 6.04). Several factors related to the pathogen, host and environment might have some role in reducing the susceptibility of Indians to COVID-19. These include some ongoing mutations that can alter the virulence of the circulating SARS-CoV-2 strains, host factors like innate immunity, genetic diversity in immune responses, epigenetic factors, genetic polymorphisms of ACE2 receptors, micro RNAs and universal BCG vaccination, and environmental factors like high temperature and humidity which may alter the viability and transmissibility of the strain. This perspective -highlights the potential factors that might be responsible for the observed low COVID-19 fatality rate in Indian population. It puts forward several hypotheses which can be a ground for future studies determining individual and population susceptibility to COVID-19 and thus, may offer a new dimension to our current understanding of the disease.

BACKGROUND:Government of India is committed to eliminate measles and control rubella/congenital rubella syndrome (CRS) by 2020. In 2016, CRS surveillance was established in five sentinel sites. We analyzed surveillance data to describe the epidemiology of CRS in India. METHODOLOGY/PRINCIPAL FINDINGS:We used case definitions adapted from the WHO-recommended standards for CRS surveillance. Suspected patients underwent complete clinical examination including cardiovascular system, ophthalmic examination and assessment for hearing impairment. Sera were tested for presence of IgM and IgG antibodies against rubella. Of the 645 suspected CRS patients enrolled during two years, 137 (21.2%) were classified as laboratory confirmed CRS and 8 (1.2%) as congenital rubella infection. The median age of laboratory confirmed CRS infants was 3 months. Common clinical features among laboratory confirmed CRS patients included structural heart defects in 108 (78.8%), one or more eye signs (cataract, glaucoma, pigmentary retinopathy) in 82 (59.9%) and hearing impairment in 51. (38.6%) Thirty-three (24.1%) laboratory confirmed CRS patients died over a period of 2 years. Surveillance met the quality indicators in terms of adequacy of investigation, adequacy of sample collection for serological diagnosis as well as virological confirmation. CONCLUSIONS/SIGNIFICANCE:About one fifth suspected CRS patients were laboratory confirmed, indicating significance of rubella as a persistent public health problem in India. Continued surveillance will generate data to monitor the progress made by the rubella control program in the country.

Background: Occupational exposure to bloodborne pathogen is a significant risk to health-care workers. In any teaching hospital apart from regular health-care workers and employees, there are significant population of students and trainee. It is important to assess the health-care worker in hospital which has maximum chances of exposure to these pathogens. The aim of this study is to determine the most susceptible job group for needlestick injury (NSI) reported in a newly established teaching medical institute in the Western part of Rajasthan, India. Methods: This is a retrospective analysis of data of NSI occurred during September 2014 to January 2017. Results: Sixty three NSIs were reported during the study. Nursing students were the most vulnerable group who reported maximum number of NSI. Among the nursing students, 72% were completely vaccinated against hepatitis B virus. Conclusions: Nursing students are at utmost risk for NSIs, the prevention of which requires regular training and education.

Corynebacterium diphtheriae is a toxin producing, classically noninvasive bacteria that causes diphtheria a vaccine-preventable disease mainly in children. With increasing vaccine cover, new spectrum of infections is increasingly seen involving invasive infections and nontoxigenic strains of C. diphtheriae. Here, we present a case of Ludwig's angina caused by C. diphtheriae in a 45-year-old female. Only Corynebacterium spp. have been previously reported in Ludwig's angina patients.

Nontuberculous mycobacteria (NTM) infections are ever more important in recent years for leading causes of morbidity and mortality worldwide. Clinical appearance of Mycobacterium tuberculosis (TB) complex and NTM is same, but the treatment regimen is always different. NTM is challenging for both diagnostic and therapeutic with reason that it mimic pathological, microbiological, immunological, and radiological findings of TB. Newer molecular diagnostic methods allow for a better identification of NTM infections in patients not responding to antitubercular treatment and falsely categorized as drug-resistant TB. This article will explore the recent methods for the diagnosis and identification of NTM infections in clinical practice. In the future, the molecular-based diagnosis will significantly reduce the turnaround time of the diagnosis and thereby improving patient outcome.

Background: Acinetobacter species are the major cause of nosocomial infection especially in intensive care unit settings. This organism also gains its importance for its nature of showing resistance towards various classes of antibiotics. Methods: Conventional biochemical test and Microscan walkway automated system was used for identification of the isolate. Results: Here, we report an unusual finding of multidrug resistant Acinetobacter baumanii, isolated from cerebrospinal fluid due to the post antibiotics effect. Conclusion: Microbiologist should be vigilant while reporting the unusual morphology of bacteria as antibiotic pressure effect may change the morphology and important findings may miss by microbiologist so antibiotic history should evaluated.

Background: We describe here two rare case of Ralstonia pickettii infection associated with tonsillitis and wound infection. Ralstonia pickettii is a gram negative bacteria, usually isolated from the soil and water. Infection-associated Ralstonia species though rare, has become an emerging nosocomial pathogen due to its capability to survive in harsh conditions like antiseptic solutions. Both of our reported cases presented to the outdoor patient unit and thus possibility of community acquired Ralstonia picketti infection cannot be ruled out. Methods: Isolates were subjected to Siemens MicroScan WalkAway 96 Plus (Beckman Caulter Diagnostics, USA) for identification and antimicrobial susceptibility testing. Results: Ralstonia pickettii was identified as a rarely detected pathogen. Conclusion: Ralstonia pickettii though rarely associated with wound infections and tonsillitis, could be a potential hospital acquired pathogen.

Disseminated Aspergillosis though rare is usually seen among immunocompromised and neutropenic patients. Aspergillus spp are usually considered to be a laboratory contaminants until its association with the disease is established on repeated isolation. The present is of Aspergillus nidulans associated with pericarditis post Anti-Tuberculous Treatment (ATT) initiation in a 67-year-old male patient with known case of Pulmonary Tuberculosis (PTB). Aspergillus nidulans was identified on the basis of culture on Sabouraud Dextrose Agar (SDA) and Lacto-Phenol Cotton Blue (LPCB) wet mount preparation.

Chronic non healing ulcers are caused by various aetiologies ranging from infections, autoimmune disorders to neoplasms. Fungal infections are important yet neglected cause of non healing ulcers. In most of these instances there is a history of direct inoculation due to minor trauma. Presence of immuno-compromised state is an important risk factor. In this case report, we are discussing a case of 48-year-old immunocompetent female patient, who had undergone local debridement at a rural hospital about eight months back on her left foot, later she developed a chronic non healing ulcer at the site. Chronic non healing ulcers should always be investigated for bacterial as well as fungal aetiologies despite patient’s normal immune status to prevent misuse of antibiotics along with prolonged disability of the patient.

Chromogenic media are being used now-a-days for identification of many microorganisms in the clinical microbiology laboratories. They are being used for screening purposes especially in case of urine cultures, environmental surveillance and also for detection of multidrug-resistant organisms like Methicillin-resistant Staphylococcus aureus (MRSA), Vancomycin-resistant Enterococci (VRE) and Carbapenem-resistant Enterobactericeae (CRE) etc. Organisms produce specific colour due to digestion of chromogenic substrates present in the medium. Thus the Organisms are identified on basis of colour production. These media are specific in detecting common pathogens which are isolated. But they can give different results when uncommon organisms are encountered. In this case report the uncommon organism that is Stenotrophomonas maltophilia produced colour similar to Klebsiella spp. on chromogenic media.

Introduction: Owing to the poor socioeconomic conditions and lack of sanitary hygiene, a large number of population in developing countries remain under constant threat of different parasitic infections causing severe morbidity and mortality. Enough measures to prevent and reduce the disease burden are still to be undertaken. Aim: Aim of the study was to determine the spectrum of parasitic infections in patients with complaints of diarrhoea and other gastrointestinal symptoms attending a tertiary care hospital in Western Rajasthan, India. Materials and Methods: It is a retrospective study conducted in the Department of Microbiology, All India Institute of Medical Sciences, Jodhpur, India, between the period of September 2014 and April 2016. The records of routine stool examination carried out during the study period, were analyzed. A total of 968 stool samples from the same number of patients complaining of diarrhoea and other gastrointestinal symptoms such as nausea, vomiting, flatulence, and pain abdomen were received from different outdoor and indoor wards of the hospital. Microscopic examination was performed after the concentration of stool samples by formol-ether concentration technique and their wet mount preparations. Modified Ziehl-Neelsen (ZN) staining was performed on 17 samples for the detection of coccidian parasites. Results: Out of 968 cases, 158 (16.3%) were found to be infected with either a parasite or a commensal or both. A maximum number of isolates (21.1%) were from the age group of 31-40 years. Overall, protozoans (95.38%) were detected in excess of helminths (4.62%). The most common protozoa isolated was Entamoeba histolytica (37.57%) followed by Giardia lamblia (23.12%), and the most common helminth isolated was Hymenolepis nana (2.9%) followed by Ascaris lumbricoides (1.15%). Out of 17 stool samples, where modified ZN staining was performed, Cryptosporidium spp., Isospora belli, and Cyclospora spp. were detected in one sample each. Conclusion: Intestinal protozoal infections are more prevalent as compared to helminthic infections in this study group.

Background Rapid diagnosis is essential to decrease the morbidity and mortality of Pott’s disease. The bacteriological methods are time-consuming or insensitive. Polymerase chain reaction (PCR) provides a rapid diagnostic tool and hope for early diagnosis of this disease. The aim of this study was to compare and assess of a rapid and effective method among diagnostic battery (Ziehl–Neelsen (ZN) microscopy, BACTEC culture and PCR) of Pott’s disease. Materials and Methods Sixty-five specimens from clinico-radiological suspected cases of Pott’s disease were included in this study. They were processed for ZN microscopy, BACTEC culture, and PCR IS6110. The tests tool’s efficiency, positive agreement K c (Kappa coefficient), and significance level (P value) were calculated for correlation between PCR and performed tests. Results The PCR sensitivity reached to 96% and 46.3% among positive and negative specimens on ZN microscopy. Further, 94% and 36.4% sensitivity were found among positive and negative specimens by BACTEC culture. The total 38 (58.5%) specimens were detected either ZN microscopy or by BACTEC culture. Thus, the overall sensitivity and specificity of PCR were 95% and 74.1%. The kappa coefficient and P value, calculated for PCR against BACTEC culture and combined results of performed bacteriological tests were (K c=0.60, (P

The breast tuberculosis (TB) is an extremely rare manifestation for the reason that mammary cells offer great resistance to the survival and multiplication of Mycobacterium infection. The diagnosis is difficult because of nonspecific clinical and radiological findings. It is usually suspected in a multiparous, reproductive woman. We report three cases of tubercular infection of breast confirmed by either mycobacteriology, pathology or both. We described their diagnostic confirmation and six month follow-up after antitubercular treatment (ATT).

Nontuberculous mycobacteria (NTMs) are ubiquitous and are being increasingly reported as human opportunistic infection. Cutaneous infection caused by mixed NTM is extremely rare. We encountered the case of a 46-year-old female, who presented with multiple discharging sinuses over the lower anterior abdominal wall (over a previous appendectomy scar) for the past 2 years. Microscopy and culture of the pus discharge were done to isolate and identify the etiological agent. Finally, GenoType Mycobacterium CM/AS assay proved it to be a mixed infection caused by Mycobacterium szulgai and M. intermedium. The patient was advised a combination of rifampicin 600 mg once daily, ethambutol 600 mg once daily, and clarithromycin 500 mg twice daily to be taken along with periodic follow-up based upon clinical response as well as microbiological response. We emphasize that infections by NTM must be considered in the etiology of nonhealing wounds or sinuses, especially at postsurgical sites.

Purpose Acinetobacter baumannii is a highly virulent bacteria in modern health care, with a high ability to acquire antimicrobial resistance. Carbapenemases production appears to be the most common mechanism involved in drug resistance to carbapenem. As the prevalence of carbapenem-resistant A. baumannii was high in intensive care unit (ICU) patients, this study was designed to find the frequency of oxacillinases (OXA) genes including OXA-23, OXA-24, OXA-51, and OXA-58.