Insight into the Burden of Antimicrobial Resistance among Bacterial Pathogens Isolated from Patients Admitted in ICUs of a Tertiary Care Hospital in India.

Intensive care unit (ICU) patients are prone to develop infections by hospital prevalent organisms. The aim of the study was to determine the bacteriological profiles and their drug resistance pattern among different infections in ICU patients of a tertiary care hospital. The record-based retrospective data of culture reports of the patients admitted to all the ICUs of a tertiary care hospital during the period from January 2020 to May 2022 were analyzed. A total of 3,056 samples were obtained from 2308 patients. The infection rate among ICU patients was found to be 53.40%. Isolates belonged equally to males (50.86%) and females (49.14%). The most common culture-positive clinical specimen received was blood (39.08%) followed by respiratory samples (29.45%). Acinetobacter sp. (33.02%) was the most common organism isolated from various clinical specimens, followed by Klebsiella pneumoniae (20.89%), and Escherichia coli (13.8%). More than 80% of Acinetobacter species were found to be resistant to third-generation cephalosporins, aminoglycosides, and carbapenems, whereas minocycline (56.31% S) and colistin (100% S) were the most effective drugs. Klebsiella sp. was found to be more resistant than E.coli, and the least resistance was observed to be tetracycline (43.97%) and doxycycline (55.84%). Among Staphylococcus aureus, 82.78% of strains were methicillin-resistant (MRSA). Vancomycin-resistant Enterococci (VRE) sp. accounted for 16.67% of the isolates. Evidence-based knowledge regarding the local bacterial organisms and their antimicrobial resistance pattern is pivotal in deciding empirical drug therapy, ultimately leading to the management of antimicrobial resistance (AMR).

Antifungal Resistance Profile of Fungal Isolates from Fungal Rhinosinusitis Patients: A Study from Tertiary Care Hospital.

Objective Fungal rhinosinusitis is on the rise worldwide and it is endemic especially in North India. The main purpose of this study was to determine the antifungal resistance profile of fungal isolates from the cases of fungal rhinosinusitis. Methods Antifungal susceptibility testing of isolated fungi to fluconazole, amphotericin B, itraconazole, and voriconazole was determined by standard CLSI broth microdilution method. Results Sixty-eight fungal isolates of Aspergillus spp . ( n = 49), Rhizopus spp. ( n = 9), Candida spp . ( n = 4), Penicillium spp . ( n = 2), Mucor spp . ( n = 2), Bipolaris spp . ( n = 1), and Alternaria spp . ( n = 1) were obtained from 60 different clinical samples as exudate from nasal mucosa ( n = 28), allergic mucin ( n = 8), nasal lavage ( n = 2), tissue biopsy from nasal polyps ( n = 14), and intraoperative nasal mucosa ( n = 8). Of the 68 isolates, 75% were resistant to fluconazole, 13.23% were resistant to itraconazole, 2.94% to amphotericin B, and none were resistant to voriconazole. Aspergillus flavus (5%) was the only fungi found resistant to amphotericin B, while against itraconazole, A. flavus (7.5%) and A. niger (100%) were found resistant. All the isolates of A. flavus , A. fumigatus , A. niger , and Penicillium spp. were resistant to fluconazole. Conclusion Although amphotericin B stills remains to be the most effective drug, more prospective studies are needed for the requirement of knowledge of the sensitivity pattern for optimal treatment and reduction in morbidity in the long run.

Is Omicron really mild? - Comparative analysis of comorbidities and disease outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants.

PURPOSE: Multiple variants of SARS-CoV-2 from Alpha to Omicron have an estimated 6.1 million deaths globally till date. These variants have been found to vary in transmissibility and severity. The present study deals with comparison of morbidity and mortality with SARS-CoV-2 Omicron (B.1.1.529) and Delta (B.1.617.2) variants. MATERIALS AND METHOD: An observational retrospective cohort study was conducted on a cohort of laboratory confirmed patients of SARS-CoV-2 diagnosed by qRT-PCR of nasopharyngeal swabs in periods; April-2021 and January-2022; that were sequenced and variants were recorded. Patients were invited for a telephonic interview after voluntary and informed consent was obtained from each participant wherein, the demographics, co-morbidities, oxygen requirement and mortality outcomes of the patients were enquired about. RESULTS: A total of 200 patients, with 100 from each period were included in the study. Major comorbidities in patients included hypertension, diabetes mellitus and pulmonary disease. Patients who succumbed to the Delta variant (26%) were higher as compared to the Omicron variant (10%); with the elderly (68 â€‹± â€‹9.7 â€‹years) having significant mortality during the Omicron variant. The mortality was increased in patients with comorbidities as with hypertension (53.8%, 70%), diabetes mellitus (26.9%, 40%), chronic pulmonary disease (30.8%, 20%), and smoking (15.4%, 40%) in the patients infected with both Delta and Omicron variants, respectively. CONCLUSION: The study concluded that the newer strains of SARS-CoV-2 have potential of high transmissibility and milder disease for the population by large, however, for patients with comorbidities have a higher proportion of adverse outcomes, irrespective of the variant.

Comparative Diagnostic of Cervical Tuberculous Lymphadenitis: PCR is a Fast, Efficient, and Improved Diagnostic Approach.

Methods: The study included 100 clinically suspected cases of TBLN. Fine needle aspirate (FNA) samples were processed for cytology staining and cultured on LJ & BACTEC 12B media. The biochemical tests were performed to identify the isolates at the species level. Additionally, for PCR, DNA was extracted and used for the diagnosis and identification of mycobacterial species. Results: Patients ranged from 2 to 45 years with a mean age of 24.96 ± 9.10 years. Out of 100 patients, 73% had clinical symptoms of weight loss, followed by fever (72%), anorexia (66%), and night sweats (58%). 24% of patients were found to be smear-positive after Ziehl-Neelsen (ZN) staining and statistically highly significant with PCR. On LJ medium 34% and on BACTEC radiometric 45% of samples were smearing positive. Overall, 48% of cases were PCR-positive for TBLN. When compared with culture, the sensitivity and specificity of PCR were 93.75% and 100%, respectively, which are higher than cytology. The true positive predictive value (PPV) and negative predictive value (NPV) were 83.3% and 61.5%, respectively. Conclusion: This study suggests that PCR is a rapid, sensitive, and specific tool for correct diagnosis of TBLN cases as compared to staining and culture which lead to the early and proper management of mycobacterial diseases.

Nitrofurantoin Susceptibility Pattern in Gram-Negative Urinary Isolates: In Need of Increased Vigilance.

Nitrofurantoin is the first-line drug in the treatment of uncomplicated urinary tract infections (UTIs) and its use has increased exponentially in recent years. Objectives This study aims to determine the susceptibility pattern of nitrofurantoin in gram-negative urinary isolates and to evaluate their bacteriological and epidemiological profile along with co-existing resistance to other important urinary antimicrobials. Material and Methods This was a retrospective study conducted in a tertiary care hospital in New Delhi in which 500 gram-negative bacterial urinary isolates were evaluated. Records of antimicrobial susceptibility were reviewed from July to September 2019. Antimicrobial susceptibility was performed using the Kirby-Bauer disk diffusion method on Mueller Hinton agar and interpreted using CLSI 2019. Test for extended spectrum ß-lactamase (ESBL) producers was done using double disk approximation test. Statistical Analysis Data analysis was performed using the SPSS windows version 25.0 software. Results Out of total 500 isolates, 20.17% (94) isolates were resistant (R) to nitrofurantoin and 9.01% (42) were found to be intermediate (I). Highest resistance was seen in Klebsiella sp. (44.61%) and Escherichia coli (8.12%). About 28.82% of the I/R isolates were of the pediatrics age group and most of the isolates belonged to females (64.69%). High resistance was also seen against ampicillin (92.30%), cefazolin (88.46%), ceftazidime (73.0%), and fluoroquinolones (65.38%). Carbapenemase co-resistance was seen in 57.15% isolates whereas ESBL production was seen in 30.76% of E. coli and 12.06% of Klebsiella sp. Conclusion Increase in multidrug resistance uropathogens along with a near absence of novel oral antibiotics has led to increased consumption of nitrofurantoin since its resistance has increased.

Comparative evaluation of cost effective extraction free molecular technique for detection of SARS-CoV-2 with reference to standard VTM based RT-qPCR method.

BACKGROUND AND OBJECTIVES: The entire globe is undergoing an unprecedented challenge of COVID-19. Considering the need of rapid and accurate diagnostic tests for SARS-CoV-2, this study was planned to evaluate the cost effective extraction free RT-PCR technique in comparison to the standard VTM based RT-qPCR method. MATERIALS AND METHODS: Paired swabs from nasopharynx and oropharynx were collected for SARS-CoV-2 testing, from 211 adult patients (≥18 years) in VTM and plain sterile tubes (dry swabs). These samples were processed and RT-qPCR was carried out as per standard protocols. RESULTS: 54.5% of the patients were females and 45.5% were males with sex ratio 1:1.19 (M: F). 38.86% were symptomatic, of which fever (86.59%), cough (79.23%) and breathlessness (46.34%) were the most common symptoms. The positivity by VTM based method and index method was 31.27% and 13.27% respectively. Of the 27 inconclusive results from index method, 37.04% were positive, 48.15% were negative by VTM based method. However, in 40 inconclusive results by VTM based method, 90% were negative and rest remained inconclusive by index method. The sensitivity and specificity of the index method were 39.39% and 85.71% respectively. The overall agreement between VTM based method and index method was 49.59% with estimated Kappa value of 0.19. CONCLUSION: VTM based method showed higher sensitivity compared to the index method. The higher positivity by VTM based method, suggests that VTM based method could plausibly be a better detection method of SARS-CoV-2. Still, the index method might add value in a resource limited setups for detection of SARS-CoV-2.

Pneumocystis Jirovecii detection and comparison of multiple diagnostic methods with quantitative real-time PCR in patients with respiratory symptoms.

Pneumocystis jirovecii (PCP) remains a significant cause of mortality and morbidity in patients with respiratory infections. Accurate diagnosis of PCP is still a diagnostic challenge. Hence, the main objectives were to study the incidence of Pneumocystis Jirovecii pneumonia infection among respiratory problems patients and to compare the real-time quantitative PCR technique with various diagnostic methodologies. Patients who have respiratory symptoms of PCP like breathlessness, cough, and fever were enrolled. Bronchoalveolar lavage (BAL) samples were collected and homogenized, and then smears were prepared for examination by Gomorimethanamine silver staining (GMSS), Immunofluorescent staining (IFAT), Toludine blue O (TBO), and Giemsa staining. Further, RT-PCR was also performed for the detection of PCP. The mean patients' age was 52 (SD ±â€¯16) years. 41% were female, and 59% of the patients were male. Weight loss (80%), fever (92%), cough (100%), and dyspnea (76%) were the most common complaints. Twenty-eight patients have been diagnosed with pulmonary infiltrates using chest X-ray. Out of 100 patients, 35% were positive for PCP. The organism was detected using IFAT in all the 35 specimens, 15 of 35 (42.86%) by GMSS, 8 of 35 (17.6%) by Giemsa stain, and 1 of 35 (2.8%) was detected by TBO stains. RT-PCR showed that 39 patients was found to be positive for PCP. Thirty-five of these 39 patients had a positive IFAT (89.74%); the IFAT was negative or undefined in 4 samples. All 39 patients (100%) had signs and symptoms for PCP. Our results suggest that RT-PCR is still the most highly sensitive method for Pneumocystis Jirovecii detection. In poor resource settings where RT-PCR and IFAT is not available, diagnosis of Pneumocystis jirovecii pneumonia remains a complicated issue. In settings where RT-PCR & IFAT are not available, GMSS staining may be the next best choice to detect PCP.

Clinico-mycological analysis and antifungal resistance pattern in human immunodeficiency virus-associated candidiasis: An Indian perspective.

OBJECTIVES: Candidiasis is a common human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome-associated opportunistic mycoses. The present study ascertained the species spectrum of Candida strains recovered from different clinical samples from symptomatic HIV-positive individuals and determined the antifungal susceptibility profile of the isolates. MATERIALS AND METHODS: A variety of specimens were collected from 234 symptomatic HIV seropositive individuals depending on their clinical manifestations and subjected to direct microscopic examination. Blood samples were inoculated in biphasic blood culture medium and all other specimens on Sabouraud dextrose agar with chloramphenicol and incubated at 35°C-37°C. Species identification of the recovered Candida isolates was attempted on the basis of germ tube production, micromorphology on corn meal agar, color and morphology on HiCrome Candida Differential agar, and carbohydrate fermentation and assimilation tests. Susceptibility testing of the isolates was performed employing the VITEK 2 system. RESULTS: A total of 167 Candida isolates were obtained; Candida albicans (136), Candida tropicalis (13), Candida krusei (8), Candida parapsilosis (5), Candida glabrata (4), and Candida kefyr (1). Fluconazole resistance was more frequent among nonalbicans species, and significantly higher 5-fluorocytosine resistance compared to C. albicans was also observed. Eight Candida strains (six C. krusei, one C. kefyr, and one C. albicans) were multidrug resistant. CONCLUSION: Although C. albicans continues to be the leading etiological agent of candidiasis, the incidence of nonalbicans species among HIV-positive Indian individuals is rising. Antifungal resistance was higher among nonalbicans Candida species. Another issue of therapeutic concern is the possible emergence of multidrug-resistant Candida strains among these patients.

Pulmonary aspergillosis as opportunistic mycoses in a cohort of human immunodeficiency virus-infected patients: Report from a tertiary care hospital in North India.

OBJECTIVE: The incidence of pulmonary aspergillosis in human immunodeficiency virus (HIV)-infected persons is rising. This study was designed to determine the prevalence of pulmonary aspergillosis in a cohort of HIV-positive patients (n = 71) presenting with lower respiratory tract infection at a tertiary care medical center in India. METHODS: Sputum samples were collected, and potassium hydroxide mount, cultural characteristics, and lactophenol cotton blue preparations were employed to aid in the identification of Aspergillus species. In addition, serum galactomannan antigen testing was also performed. RESULTS: Pulmonary aspergillosis was diagnosed in 7 patients, five of whom showed a positive antigenemia indicating invasive form of disease. The prevalence of pulmonary aspergillosis was highest in individuals 21-40 years of age (13.3%). The gender-wise prevalence of pulmonary aspergillosis was 18.7% and 7.7% in females and males, respectively. The common chest radiographic findings noted in patients with pulmonary aspergillosis included a normal chest radiograph in 3 (42.8%), infiltrates in 2 (28.6%), and pleural effusion in 2 (28.6%). The common Aspergillus species recovered from sputa of these patients were Aspergillus flavus (4; 57.1%); Aspergillus fumigatus (2; 28.6%), and Aspergillus niger (1; 14.3%). A predisposing lung condition in the form of pulmonary tuberculosis was identified in 2; Pneumocystis carinii pneumonia in 2 and a dual tubercular and P. carinii infection in one. The mean CD4 count of these patients was 155.86 ± 119.33 cells/µl (median = 117 cells/µl; range = 18-329 cells/µl). CONCLUSION: Our findings suggest that Aspergillus species be considered possible etiological agents in HIV-positive patients with pulmonary infection.

Fungal Opportunistic Pneumonias in HIV/AIDS Patients: An Indian Tertiary Care Experience.

INTRODUCTION: Opportunistic pneumonias are a major cause of mortality and morbidity in Human Immunodeficiency Virus (HIV) reactive patients. Despite the significant role that fungi play in causation of this opportunistic mycoses, very few Indian studies have attempted to investigate the burden and aetiological spectrum of HIV/AIDS-associated fungal pneumonias. AIM: To document the prevalence of fungal aetiology in HIV/AIDS-related opportunistic pneumonias in an Indian setting; and to elucidate the various fungal opportunists responsible for the same. MATERIALS AND METHODS: The present study was a prospective, cross-sectional analysis conducted at Maulana Azad Medical College and associated Lok Nayak Hospital, New Delhi from October 2008 to September 2011. Expectorated sputa were collected from 71 HIV reactive patients with a clinical diagnosis of pneumonia and subjected to direct microscopic examination employing Gram stain, 10% KOH wet mount and India ink preparation. In addition, direct immunofluorescence of sputum samples was performed for detection of cysts and trophozoites of Pneumocystis carinii. Also, each sputum sample was inoculated in duplicate onto Sabouraud Dextrose Agar (SDA) for culture. A blood sample was drawn from each patient and a battery of serological tests was performed, including Cryptococcal Antigen Latex Agglutination System (CALASTM) for detection of cryptococcal capsular polysaccharide antigen; Platelia™ Aspergillus EIA for detection of Aspergillus galactomannan antigen; SERION ELISA antigenCandida for detection of Candida antigen and Histoplasma DxSelect™ for detecting antibodies to Histoplasma species. Descriptive statistics were employed to depict results as proportions and figures. Further, arithmetic mean and standard deviation were calculated for central tendencies and median for non-normal/skewed distributions. RESULTS: A definite fungal aetiology was established in 25 (35.2%) of 71 HIV reactive patients with pneumonic involvement. Of these, sputa of 21 patients yielded single fungal isolates, while mixed fungal isolates were reported in four patients. Pneumocystis carinii was the predominant fungal pathogen isolated in our study and was reported in 14 (19.7%) patients. Pulmonary aspergillosis was reported in 7 (9.9%) patients, with Aspergillus flavus (4), Aspergillus fumigatus (2) and Aspergillus niger (1) being the commonly recovered Aspergillus species. Candida pneumonia was documented in 6 (8.5%) patients and the Candida species isolated included Candida albicans in four, Candida glabrata in one and Candida tropicalis in one of these six patients respectively. Pulmonary cryptococcosis was diagnosed in 2 (2.8%) patients; a coexisting cryptococcal meningitis was documented in one of them. Furthermore, antibodies against Histoplasma species were detected in 21 (29.6%) cases suggesting its possible aetiological role. CONCLUSION: Fungal opportunistic pneumonias are common in HIV reactive patients in Indian setting and warrant a prompt and accurate diagnostic evaluation in the form of a combination of microbiological, serological and histopathological techniques, for an effective prophylactic and therapeutic management.

Identification and Antifungal Susceptibility Testing of Candida Species: A Comparison of Vitek-2 System with Conventional and Molecular Methods.

BACKGROUND: Candida infection is a major cause of morbidity and mortality in immunocompromised patients; an accurate and early identification is a prerequisite need to be taken as an effective measure for the management of patients. The purpose of this study was to compare the conventional identification of Candida species with identification by Vitek-2 system and the antifungal susceptibility testing (AST) by broth microdilution method with Vitek-2 AST system. MATERIALS AND METHODS: A total of 172 Candida isolates were subjected for identification by the conventional methods, Vitek-2 system, restriction fragment length polymorphism, and random amplified polymorphic DNA analysis. AST was carried out as per the Clinical and Laboratory Standards Institute M27-A3 document and by Vitek-2 system. RESULTS: Candida albicans (82.51%) was the most common Candida species followed by Candida tropicalis (6.29%), Candida krusei (4.89%), Candida parapsilosis (3.49%), and Candida glabrata (2.79%). With Vitek-2 system, of the 172 isolates, 155 Candida isolates were correctly identified, 13 were misidentified, and four were with low discrimination. Whereas with conventional methods, 171 Candida isolates were correctly identified and only a single isolate of C. albicans was misidentified as C. tropicalis. The average measurement of agreement between the Vitek-2 system and conventional methods was >94%. Most of the isolates were susceptible to fluconazole (88.95%) and amphotericin B (97.67%). The measurement of agreement between the methods of AST was >94% for fluconazole and >99% for amphotericin B, which was statistically significant (P < 0.01). CONCLUSION: The study confirmed the importance and reliability of conventional and molecular methods, and the acceptable agreements suggest Vitek-2 system an alternative method for speciation and sensitivity testing of Candida species infections.

An Unusual Case of Cystic Fibrosis Associated Pneumocystis jiroveci Pneumonia in an Infant.

Pneumocystis jiroveci pneumonia (PJP) is one of the major infections in patients with impaired immunity. The entity is common in HIV-seropositive individuals but quite very rare in HIV-seronegative individuals especially children. We report here a case of 16-week-old HIV-seronegative infant with chief complaint of chronic cough of one month of evolution. Sweat chloride test for diagnosis of cystic fibrosis was positive. Bronchoalveolar lavage (BAL) fluid was collected and Pseudomonas aeruginosa was isolated on culture. Empirical antibiotic regimen comprising ceftriaxone and azithromycin was initiated that was switched to meropenem as per antimicrobial susceptibility report, but the patient did not improve. Subsequently, an immunofluorescence staining of BAL fluid was performed and P. jiroveci cysts were detected. Following a laboratory confirmation of Pneumocystis pneumonia, cotrimoxazole was added and the clinical condition of the patient significantly improved. This is an unusual case wherein unsuspected PJP occurred and since signs and symptoms of the patient persisted even after the initiation of antimicrobial therapy for Pseudomonas infection and resolved only after treatment for PJP was started, it suggests a causative role of P. jiroveci rather than colonization/contamination.

Pneumocystis pneumonia in HIV patients: a diagnostic challenge till date.

HIV has become a major health problem in India, patients commonly succumb to opportunistic infections (OIs), respiratory infections being an important cause of morbidity and their accurate diagnosis is still a challenge. Our aim was to study the occurrence of Pneumocystis pneumonia (PCP) in HIV/AIDS patients with respiratory complaints attending ART clinic and to compare various diagnostic methodologies. One hundred and twenty five HIV/AIDS patients presenting with respiratory symptoms like cough, fever, breathlessness etc, were enrolled, and induced sputum samples were collected. Samples were homogenized using glass beads and Dithiothretol. Smears were prepared and examined by Immunoflourescent staining (IFAT), Gomori methanamine silver staining (GMSS), Toludine blue O staining (TBO) and Giemsa staining for Pneumocystis jiroveci. Among the 125 patients who presented with respiratory complaints, 34 cases (27.2%) were diagnosed as having PCP. All 34 cases were detected by IFAT followed by GMSS, Giemsa and Toludine blue O staining in decreasing order. The mean CD4 count was 67.27cells/µl. PCP has become an important health problem in HIV/AIDS patients with low CD4 counts in India. IFAT remains the most sensitive method for the detection of this uncultivable organism. In resource poor settings where an immunoflourecent microscope is not available, diagnosis of PCP still remains problematic.