Utility of a multiplex pathogen detection system directly from respiratory specimens for treatment and diagnostic stewardship

The availability of syndrome-based panels for various ailments has widened the scope of diagnostics in many clinical settings. These panels can detect a multitude of pathogens responsible for a particular condition, which can lead to a timely diagnosis and better treatment outcomes. In contrast to traditional identification methods based on pathogen growth on culture, syndrome-based panels offer a quicker diagnosis, which can be especially beneficial in situations requiring urgent care, such as intensive care units. One such panel is the Biofire Filmarray Pneumonia plus Panel (BFP), which we have compared against microbiological culture and identification. The lower respiratory samples from patients were tested with BFP, culture, and identification with culture considered the gold standard. The phenotypic antibiotic susceptibility results (Vitek 2) were compared with the antimicrobial resistance (AMR) genes detected in BFP. Statistical analysis was carried out using GraphPad 7.0 and MS Excel (Microsoft Inc.). The results showed a positive percent agreement of 100% and a negative percent agreement of 47.8% with an overall agreement of 76.72% compared to culture. BFP was better at identifying fastidious bacteria, and the agreement with culture was higher for high bacterial identification numbers (107 and 106). There was also a correlation between the number of pathogens detected and growth in culture. Carbapenemase genes were detected in around 80% of phenotypically resistant samples and correlated with in-house PCR 60% of the time. Hence, BFP results need to be interpreted with caution especially when multiple pathogens are detected. Similarly, the presence or absence of AMR genes should be used to guide the therapy while being watchful of unusual resistance or susceptibility. The cost constraints and low throughput call for patient selection criteria and prioritization in emergency or resource-limited conditions.IMPORTANCEApplication of syndrome-based panels in clinical microbiology is of huge support in infectious conditions requiring urgent interventions, such as pneumonia. Interpreting the results requires caution; hence, we have compared the results obtained from Biofire Filmarray Pneumonia plus Panel with standard microbiological methods.

Kodamaea ohmeri: A rare yeast causing invasive infections in immunocompromised patients

INTRODUCTION

Kodamaea ohmeri is a rare, recognized pathogen that has previously been isolated from environmental sources. The patients commonly affected by this yeast include immunocompromised as well as immunocompetent patients having several associated risk factors.

METHODOLOGY

We report three cases in which K. ohmeri was isolated from blood using Bact T/ALERT. Identification was carried out by MALDI-TOF MS (Vitek-MS, BioMérieux, Marcy-l'Etoile, France) in addition to color characteristics on chromogenic media. The patients had diminished immune response on account of a multitude of comorbidities.

RESULTS

K. ohmeri can be misidentified as Candida tropicalis, Candida albicans, or Candida hemolounii by conventional methods; correct and timely identification can be achieved by MALDI-TOF MS. Antifungal susceptibility breakpoints for K. ohmeri are currently not defined. An Echinocandin was added to the treatment regimen of all three of the cases.

CONCLUSIONS

Identification of K. ohmeri using conventional methods is difficult and unusual yeasts should be carefully observed, especially upon prolonged incubation.

Microbiological Profile and the Resistance Pattern of Pathogens in Neurosurgical Patients from a New Delhi Trauma Center

BACKGROUND

Neurosurgical patients are considered to be at higher risk for infections including nosocomial infections compared with other critically ill individuals. Empirical antimicrobial therapy is of utmost importance for the survival of infected neurosurgical patients.

METHODS

The microbial distribution and antimicrobial resistance patients from January 2012 to December 2021 (10 years) were analyzed retrospectively. Identification was done using VITEK-2 and MALDI-TOF systems. Antimicrobial susceptibility testing was determined by the Kirby Bauer Disk Diffusion Agar method (Clinical and Laboratory Standards Institute) and VITEK-2.

RESULTS

A total of 48,474 samples were received, out of which 10,134 (21%) had growth. Respiratory specimens showed the maximum isolation of pathogens (42% n = 4292). The predominant bacterial pathogens were gram negative (n = 8972; 88.5%), whereas gram positives were only 11.5% (n = 1162) of the total organisms. Among the gram positives, the most common was Staphylococcus aureus (64.6%), and among gram negatives, the most common pathogen was Acinetobacter baumanni (38.6%). The weighted average of the drug-resistance profile across all gram positives was >50% for fluoroquinolones (levofloxacin, ciprofloxacin), gentamicin, erythromycin, and ampicillin, and in the case of gram negatives it was >90% for ampicillin-sulbactam, ticarcillin, cefazolin, cefotaxime, and ceftriaxone. Thirty-two patients were found to have candidemia, out of which 6 were C. albicans and the rest were nonalbican. Six neurosurgery patients had infection with C. auris, 4 from blood samples and 2 from urine.

CONCLUSIONS

This study will add to the current knowledge and provide a better understanding of pathogen profile and resistance patterns in traumatic brain injury patients.

Prognostic relevance of NPM1, CEBPA, and FLT3 mutations in cytogenetically normal adult AML patients

BACKGROUND

Acute myeloid leukemia with normal cytogenetics (CN-AML) is the largest group of AML patients with very heterogenous patient outcomes. The revised World Health Organization classification of the hematolymphoid tumours, 2022, has incorporated AML with Nucleophosphmin1 (NPM1) and CCAAT/enhancer binding protein-alpha (CEBPA) mutations as distinct entities. Despite the existing evidence of the prognostic relevance of FMS-like tyrosine kinase-3 internal tandem duplication (FLT3-ITD) in AML, it has not been included in the revised classification.

METHOD

In this prospective study, we determined the prevalence of NPM1, CEBPA, and FLT3 gene mutations in 151 de novo CN-AML adult patients (age ≥18 years) in a tertiary care hospital in north India. Additionally, the prognostic relevance of these mutations was also evaluated.

RESULTS

NPM1, FLT3-ITD, and CEBPA mutations were found in 33.11%, 23.84%, and 15.77% of CN-AML patients, respectively. CEBPA mutations were found at 3 domains: transactivation domain 1 (TAD1) in 10 (6.62%), transactivation domain 2 (TAD2) in 5 (3.31%), and basic leucine zipper domain (bZIP) in 11 (7.82%) patients. Patients with NPM1 mutation had better clinical remission rate (CR) (P=0.003), event-free survival (P=0.0014), and overall survival (OS) (P=0.0017). However, FLT3-ITD and CEBPA mutations did not show any association with CR (P=0.404 and 0.92, respectively). Biallelic CEBPA mutations were found in 12 (7.95%) patients and were associated with better OS (P=0.043).

CONCLUSIONS

These findings indicate that NPM1 and CEBPA mutations can be precisely used for risk stratification in CN-AML patients.

E. hirae Causing Biliary Tract Infection in a Patient with Cholangiocarcinoma: A Case Report

INTRODUCTION

E. faecium and E. faecalis are the common species of Enterococcus responsible for the majority of infections. Earlier, species other than the common ones were usually unidentified and reported as Enterococcus species. However, modern equipment, like MALDI-TOF and VITEK2, have been utilitarian, helping us to identify the previously unidentified species. E. hirae is an organism seldom reported to cause human infections. Here, we report a case of a biliary tract infection in a female patient with cholangiocarcinoma caused by E. hirae.

CASE

A 56-year-old female presented with fever and abdominal pain. Bile aspirated during the ERCP was received in our laboratory. The gram stain of the bile sample revealed abundant polymorphonuclear leucocytes along with gram-positive diplococci. The organism failed to grow on MacConkey agar. On blood agar, non-hemolytic colonies grew. The organism was identified as E. hirae by MALDI-TOF MS. The antibiotic susceptibility performed using VITEK2 revealed it to be resistant to high-level gentamicin and susceptible to all remaining drugs. She was successfully treated with oral ciprofloxacin for the infection.

DISCUSSION

Bile is colonized with bacteria due to obstruction in the biliary tree, leading to cholangitis. This causes bacterial proliferation and translocation of bacteria into the systemic circulation. Our case was resistant to high-level gentamicin, while all previously reported cases were susceptible. The resistant isolates of E. hirae being isolated from cattle and their surroundings amidst the rampant use of antibiotics in livestock can pose a difficult situation for humans. Thus, there should be regulations on antibiotic usage in livestock. Cases like these should be reported and recognized for their potential to cause outbreaks if they remain unreported.

CONCLUSION

Thus, E. hirae, when encountered, should not be ignored but considered a pathogen and reported. The presence of drug-resistant organisms in cattle and their surroundings, their zoonotic potential to cause infections in humans, and the uncontrolled usage of antibiotics in livestock are causes for concern. Thus, we need to be more vigilant regarding it in the future.

P282 Bacterial co-infections in Mucormycosis infected COVID-19 patients: experience from a tertiary care center in India

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM

During the second wave of COVID-19 in India, there was a deluge in Mucormycosis cases; which posed a serious threat as both conditions require extended hospital stay thus serving as an ideal setting for secondary infections.

Objectives

1. To ascertain the prevalence and anti-microbial profile of hospital-acquired secondary infections in COVID- 19 patients with Mucormycosis.

2. To evaluate the outcome in these patients and compare it with the outcome of COVID-19 patients with Mucormycosis but without any other secondary infection.

Methods

A 2-month retrospective observational study was conducted, where we compared outcomes in two groups of COVID-19 patients with Mucormycosis, one group being patients with secondary infections and the other group including patients without secondary infections.

A total of 180 samples from suspected cases of Mucormycosis, that underwent evaluation by conventional methods, KOH mount and cultures on SDA, were included. Fungal pathogens were identified from the positive cultures, based on macroscopic and microscopic features, as per standard Mycological methods.

Secondary infections inpatients were studied based on conventional bacteriological culture, microbiological profile, along-with identification and antibiotic susceptibility by VITEK 2. PCT and CRP values were also compared. The outcome was then evaluated. Data analysis was done using SPSS V-20.

Results

A total of 55 patients out of 140 patients, tested positive for Mucormycosis, either by KOH, culture or both. Rhizopus arrhizus was the most common isolate identified.

A total of 12/55 (21.8%) people with Mucormycosis developed secondary infections during their stay in the hospital, bloodstream infection being the most common (7/15; 46.67%). Overall, gram-negative (GN) organisms were more common (11/16; 68.75%), in comparison to Gram Positives (GP) (5/16; 31.25%), but the most common organism isolated was Enterococcus faecium (5/16; 31.25%), followed by Klebsiella pneumoniae (4/16) and E. coli (4/16). A total of 4/5 isolates (80%) of Enterococcus faecium were multi-drug resistant (MDR) and two of them were vancomycin-resistant. In all, 10/11 GN isolates (90.9%) were MDR, high resistance to carbapenems was observed, nine out of 11(81.81%) isolates were resistant to imipenem and eight (72.72%) were resistant to meropenem. A total of 3/12 (25%) patients succumbed to their infection in the group with secondary infections, after an average length of stay of 23.33 days. The most common cause of death in these patients was septic shock. A total of 8/43 (18.6%) succumbed to their infection in the group without any secondary infection at an average stay of 9.12 days in the hospital. CRP was found to be consistently elevated, this biomarker might not have a predictive value for bacterial infections in COVID-19 but PCT had a positive predictive value for the secondary bacterial infections overall (P-value <.001). Length of stay in hospital co-related with the development of secondary infection and mortality (P-value <.001).

Conclusion

Culture-based testing should be carried out before the administration of anti-microbials. PCT can be used as a guiding tool. Controlled use of antibiotics along with periodic surveillance and hand hygiene practices will immensely contribute to infection control.

P296 The role of Candida in acute pancreatitis: A disregarded pathogen

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM

 

Background

Acute pancreatitis is often complicated by infection of peri-pancreatic necrotic tissue. The infectious etiology commonly involves gram negative enteric bacilli and enterococci. Role of Candida species has remained debatable, despite being isolated in pure or mixed cultures in specimens. We evaluated patients with acute pancreatitis with Candida infection over a duration of 4 years for assessment of risk and prognostic factors.

Objectives

To determine the prevalence and role of Candida infection in patients of acute pancreatitis and ascertain the species distribution and risk factors.

Methods

This study was conducted including adult patients who were admitted to gastro-surgery department and had clinical suspicion of peri-pancreatic fungal infection. Specimens included peri-pancreatic fluid collection obtained intra-operatively or aspirated USG-guided, drain fluid and blood. In addition to aerobic bacterial culture, fungal cultures were performed availing standard mycological procedures. Candida infections were categorized into true and possible as per Chakraborty et al. with some modifications.

True Candida infection of pancreatic tissue was considered when yeast cells were seen and grown in pure or mixed culture from

Possible Candida infection of pancreatic tissue was considered when Candida spp were isolated from

Relevant patient information was obtained from hospital information system. Data were analyzed by SPSS 20 statistical software and MS Excel.

Results

A total of 14 cases were identified amongst which 6/14 (42.9%) had true Candida infection whereas possible Candida infection was seen in 8/14 (57.1%) patients. Out of these, C. tropicalis was the predominant species seen in 9/14 (64.3%) whereas C. albicans was seen in 4/14 (28.6%). One isolate of C. auris was identified. Patients with C. tropicalis infection showed higher mortality (6/9, 66.7%) as compared with patients with other Candida species, in whom 20% (1/5) mortality was noted. Acknowledging limitations inherent to retrospective data extraction, we delineated some of the possible risk factors predisposing to Candida infection, given in Table 1.

Conclusion

Role of Candida species in the pathogenesis of adjacent tissues in case of acute pancreatitis has been neglected in past, but now being increasingly recognized. C. tropicalis is the commonest isolate in our study and carries very high mortality. Screening for Candida spp should be carried out in these patients in view of starting antifungal treatment at the earliest possible so that proper diagnosis and management can be undertaken.

P222 Epidemiology of Candida emia at level-1 trauma care cent er in North India

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM

 

Objective

Patients affected by trauma who get admitted to critical care units experience prolonged hospitalization and thereby acquire several infections. This retrospective observational study was done from 2014 to 2021 to observe Candidaemia affecting this population. A total of 4816 patients admitted with traumatic injuries and hospitalized for treatment at ICU in our 190 bedded Level-1 Trauma center underwent this study.

Methods

Paired blood samples were collected from patients showing signs of sepsis and incubated and monitored regularly by the BacT/ALERT system (bioMe´rieux InC., Marcy l'Etoile, France). All the positive signal samples exhibiting budding yeast cells on Gram stain were subcultured on Chrome agar and Sabouraud dextrose agar. Pure growths obtained were subjected for identification and susceptibility by MALDI-TOF and VITEK 2 system.

Results

Out of the 4816 patients, 61 were affected by Candidaemia. Out of 61, the maximum was in the age group of 31-40 years (19.7%). Male preponderance (50/61, 82%) was exhibited compared to females. To ascertain Candidaemia, samples collected were blood (63/66, 95.5%) and CVP tip (3/66, 4.5%). Candidaemia was primarily observed in patients who suffered major orthopedic trauma (14/61, 21.2%). A total of 66 Candida species were isolated from samples of these patients. Out of these, Candida tropicalis (43.9%) was the most common, followed by C. parapsilosis (22.7%), C. albicans (21.2%), C. haemulonii (4.5%), C. glabrata (3%), C. rugosa (3%), and C. guilliermondii (1.5%). Concerning antifungal resistance, fluconazole resistance was 16.6% (11), flucytosine 1.5% (1), amphotericin B 6% (4), and micafungin 3% (2). Voriconazole was resistant to none but intermediate to 12.1% (8), caspofungin was intermediate to 3% (2), and resistant to none. A total of 47% (31/61) of patients succumbed to their injuries which were observed highest in the age group of 61-70 years (8/61, 25.8%). The most common injuries that the deceased suffered were polytrauma (9/61, 29%) and blunt trauma abdomen (9/61, 29%). Maximum mortality was also observed in patients with Candidaemia due to Candida tropicalis (15/61, 48.3%).

Conclusion

Candidaemia is usually fatal. Mortality due to Candidaemia increases in patients with severe traumatic injuries and added risk factors such as extremes of age, immunocompromised state, and broad-spectrum antibiotics. When compared to a similar study done in our center from 2009 to 2012 (3 years) on Candidaemia in ICU patients, the incidence was lower in our study (12.6% per 1000 ICU admissions vs 14.9% per 1000 ICU admissions), but the mortality rate was higher (47% vs 43.3%). Therefore, a watchful eye on early signs of sepsis, strict hospital infection control measures and antimicrobial stewardship may alter their outcome.

Large granular lymphocytic leukemia: a brief review

LGL leukemia is a rare chronic lymphoproliferative disorder of cytotoxic lymphocytes which can be immunophenotypically either T cell or NK cell-derived. According to the World Health Organization classification, it can be divided into three subtypes: chronic T-cell leukemia and chronic natural killer cell lymphocytosis, and aggressive natural killer cell LGL leukemia. Clonal proliferation of large granular lymphocytes can be because of stimulation of various molecular pathways namely JAK-STAT3 pathway, FAS/FAS-L pathway, RAS-RAF-1-MEK1-ERK pathway, PI3K/AKT pathway, NF-KB pathway, and Sphingolipid Rheostat pathways. The most common clinical features presenting with this leukemia are neutropenia, anemia, thrombocytopenia. This leukemia is also associated with various autoimmune conditions. It usually has an indolent course except for the aggressive NK cell LGL leukemia. The cause of death in the indolent cases was mostly due to infectious complications related to the neutropenia associated with the disease. The rarity of the disease coupled with the availability of only a handful of clinical trials has been a hindrance to the development of a specific treatment. Most of the cases are managed with immunomodulators. The advances in the knowledge of molecular pathways associated with the disease have brought few targeted therapies into the limelight. We discuss here the evolution, epidemiology, demographic profile, pathophysiology, differential diagnosis, the available treatment options along with the survival and prognostic variables which may help us in better understanding and better management of the disease and hopefully, paving the way for a targeted clinical approach.

Medical postgraduate (MD) program in Laboratory Medicine in India: The Past, Present and Future

A medical postgraduate course in the field of Laboratory Medicine for the Bachelor of Medicine and Bachelor of Surgery (MBBS) degree holders has existed for more than two decades in India, initiated and offered by the All India Institute of Medical Sciences, New Delhi, which was created under the special Act of Parliament of India 1956. This course has recently been included in the draft of National Medical Commission’s Post Graduate Regulation 2021 list of medical courses, and the foundation guidelines have been laid for other medical colleges and teaching hospitals across the country to start this course. This article, written purely in academic interest, describes the past, present and future of this postgraduate training program in India with an aim to answer several doubts regarding this unique and holistic course with a view to providing a direction to those who are willing to become a laboratory physician through this post-graduation.

Application of Sysmex XN-Series Automated Haematology Analyser in the Rapid Detection of Malaria

Malaria, an important parasitic disease worldwide, still has diagnostic challenges in the laboratory. Many studies have been conducted on the detection ability of haematology analysers for malaria. We evaluated the Sysmex XN-series analyser as a tool for detection of malaria by analysing the leukocyte cell population data (LCPD), scattergrams and associated Flow Cytometry Standard (FCS) data from both the WNR (white cell nucleated) and WDF (white cell differential) channels. 1281 clinically suspected cases of malaria were screened for malaria by peripheral blood smear examination and were run in the Sysmex XN-1000 for analysis of haematological parameter data, LCPD, all the scattergrams and FCS data. 1281 clinically suspected cases of malaria were screened for malaria by peripheral blood smear examination and were run in the Sysmex XN-1000 for analysis of haematological parameter data, LCPD, all the scattergrams and FCS data. 48 cases had malarial parasite on microscopy; of which, 41 cases were of Plasmodium vivax, 6 cases of Plasmodium falciparum and 1 case of mixed infection. 46 malaria-positive samples showed certain patterns of clusters in the scattergrams of both WDF and WNR channels. A case with only a few ring forms of P. vivax and another with very low parasite load having only gametocyte of P. falciparum didn't show the distinctive cluster. The most distinctive clusters for all other cases were seen in WNR (SFL-SSC) and WNR (SSC-FSC) scattergrams. FCS data for the same were analysed to gate for those events. The gated events correlated (Spearman ρ = 0.77, p < 0.01) with the parasite load of the patients. By observing the scattergrams and different parameters in the Sysmex XN-series analyser, malaria can be detected from the analyser itself.

Lupus erythematosus cell in body fluids: A case report and review of literature

The diagnosis of systemic lupus erythematosus (SLE) has undergone radical change after the development of serological techniques. The in vitro demonstration of lupus erythematosus (LE) cell has less significance for the diagnosis of SLE in the present scenario. Although over the years, the spontaneous in vivo occurrence of LE cell in numerous body fluids as an initial presentation of SLE has been documented. The report of the presence of the LE cell can not only aid in the further workup of the patient but also suggest the involvement of a particular organ or body cavities by SLE. The morphology and mimickers of the LE cell should be cogitated and meticulous search of such cells should play an important role in the evaluation of body fluids. In our case, the patient presented at emergency with pericardial tamponade and cytological evaluation of the pericardial fluid demonstrated in vivo presence of LE cells. The serological work-up then confirmed the case to be SLE. This report and review of literature wish to highlight the fact that this cell still plays a significant role even in the era of immunoassays.