A pinboard by
Kamila Kochan

Research Fellow, Centre for Biospectroscopy, Monash University


Rapid detection of pathogens in blood using their spectral fingerprint

I work on early detection of pathogen infection in blood using ATR-FTIR and Raman spectroscopy. Pathogen infection is caused mainly by bacteria or fungi. Their presence in body precedes and leads to a life threatening condition, known as sepsis (or more colloquially - blood poisoning). The risk of getting sepsis increases for people with weakened immune system (children, new born infants, people with chronic illness, etc.). In practice sepsis can affect anyone and develop even from a small wound.

At an initial stage, an infection does not present specific symptoms (flu-like) and is hard to recognise. However, without timely treatment pathogens multiply rapidly. Their overwhelming amount causes a strong immune response resulting in tissue damage, permanent organ failure and eventually death. This chain of events takes only few hours.

Sepsis has a tremendous mortality rate, affecting approx. 26 million people worldwide and leading to death in 1/3 of those. The mortality rate is much higher for cases diagnosed at advanced stage. It remains the largest killer of children and new born infants worldwide. Unlike any other disease and regardless of the medicine progress, the mortality rates of sepsis have not decreased since decades, and are actually predicted to increase (8-13% annually).

Several reasons are behind those statistics, with one having especially large impact: lack of appropriate diagnostic tool. The standard method involves incubating blood sample for 24h to grow pathogens. Meanwhile, the time between initial infection and severe sepsis (high risk of organ damage and death) is only few hours. Not surprisingly, the rate of survival drastically drops each hour within this time frame. Therefore, the ability to quickly diagnose an infection is critical for patients’ survival.

Vibrational spectroscopies offer advantages particularly suitable for rapid diagnostic, such as speed (1-2 min.), cost and lack of specific sample preparation. As each pathogen species has its own characteristic fingerprint, it is possible to identify their presence from blood spectra. My goal is to develop a spectroscopy-based method for direct detection of pathogen within the first hour from sample collection. Such test will allow to react immediately on pathogen infection, increasing the patients’ chance of survival. Furthermore, cost and portability makes it suitable for third world countries and possible to access in remote locations (villages, military action areas).


Mortality related to severe sepsis and septic shock among critically ill patients in Australia and New Zealand, 2000-2012.

Abstract: Severe sepsis and septic shock are major causes of mortality in intensive care unit (ICU) patients. It is unknown whether progress has been made in decreasing their mortality rate.To describe changes in mortality for severe sepsis with and without shock in ICU patients.Retrospective, observational study from 2000 to 2012 including 101,064 patients with severe sepsis from 171 ICUs with various patient case mix in Australia and New Zealand.Hospital outcome (mortality and discharge to home, to other hospital, or to rehabilitation).Absolute mortality in severe sepsis decreased from 35.0% (95% CI, 33.2%-36.8%; 949/2708) to 18.4% (95% CI, 17.8%-19.0%; 2300/12,512; P < .001), representing an overall decrease of 16.7% (95% CI, 14.8%-18.6%), an annual rate of absolute decrease of 1.3%, and a relative risk reduction of 47.5% (95% CI, 44.1%-50.8%). After adjusted analysis, mortality decreased throughout the study period with an odds ratio (OR) of 0.49 (95% CI, 0.46-0.52) in 2012, using the year 2000 as the reference (P < .001). The annual decline in mortality did not differ significantly between patients with severe sepsis and those with all other diagnoses (OR, 0.94 [95% CI, 0.94-0.95] vs 0.94 [95% CI, 0.94-0.94]; P = .37). The annual increase in rates of discharge to home was significantly greater in patients with severe sepsis compared with all other diagnoses (OR, 1.03 [95% CI, 1.02-1.03] vs 1.01 [95% CI, 1.01-1.01]; P < .001). Conversely, the annual increase in the rate of patients discharged to rehabilitation facilities was significantly less in severe sepsis compared with all other diagnoses (OR, 1.08 [95% CI, 1.07-1.09] vs 1.09 [95% CI, 1.09-1.10]; P < .001). In the absence of comorbidities and older age, mortality was less than 5%.In critically ill patients in Australia and New Zealand with severe sepsis with and without shock, there was a decrease in mortality from 2000 to 2012. These findings were accompanied by changes in the patterns of discharge to home, rehabilitation, and other hospitals.

Pub.: 19 Mar '14, Pinned: 21 Oct '17

Raman spectroscopy for medical diagnostics--From in-vitro biofluid assays to in-vivo cancer detection.

Abstract: Raman spectroscopy is an optical technique based on inelastic scattering of light by vibrating molecules and can provide chemical fingerprints of cells, tissues or biofluids. The high chemical specificity, minimal or lack of sample preparation and the ability to use advanced optical technologies in the visible or near-infrared spectral range (lasers, microscopes, fibre-optics) have recently led to an increase in medical diagnostic applications of Raman spectroscopy. The key hypothesis underpinning this field is that molecular changes in cells, tissues or biofluids, that are either the cause or the effect of diseases, can be detected and quantified by Raman spectroscopy. Furthermore, multivariate calibration and classification models based on Raman spectra can be developed on large "training" datasets and used subsequently on samples from new patients to obtain quantitative and objective diagnosis. Historically, spontaneous Raman spectroscopy has been known as a low signal technique requiring relatively long acquisition times. Nevertheless, new strategies have been developed recently to overcome these issues: non-linear optical effects and metallic nanoparticles can be used to enhance the Raman signals, optimised fibre-optic Raman probes can be used for real-time in-vivo single-point measurements, while multimodal integration with other optical techniques can guide the Raman measurements to increase the acquisition speed and spatial accuracy of diagnosis. These recent efforts have advanced Raman spectroscopy to the point where the diagnostic accuracy and speed are compatible with clinical use. This paper reviews the main Raman spectroscopy techniques used in medical diagnostics and provides an overview of various applications.

Pub.: 27 Mar '15, Pinned: 21 Oct '17

Impact of the Surviving Sepsis Campaign on the recognition and management of severe sepsis in the emergency department: are we failing?

Abstract: Severe sepsis/septic shock (SS/SS) has a high mortality. The past decade lays witness to a concerted international effort to tackle this problem through the Surviving Sepsis Campaign (SSC). However, bundle delivery remains problematic. In 2009, the College of Emergency Medicine (CEM) set out guidelines for the management of SS/SS. These set the standards for this audit.To assess the recognition and management of patients presenting with SS/SS across three emergency departments (EDs) within the West Midlands.Data were collected retrospectively over a 3-month period. Patients in the ED with a diagnostic code of, or presenting complaint suggestive of, sepsis, had their scanned notes assessed for evidence of SS/SS. Compliance with the CEM guidelines, and evidence of referral to the intensive care staff was evaluated.255 patients with SS/SS were identified. Of these, 17% (44/255) were documented as septic by ED staff. The CEM standard of care was received in 41% of those with a documented diagnosis of severe sepsis in the ED, and 23% of patients with SS/SS overall. 89% of patients received the 'treatment' aspects of care: oxygen, IV antibiotics and IV fluids. Twelve patients with a raised lactate level and normal blood pressure (cryptic shock) failed to receive fluid resuscitation. 71% of patients with SS/SS had no documented discussion or consideration of referral to the intensive care unit.The SSC has had some impact; however, there is still a long way to go. It is assumed that the picture is similar in EDs across the UK and recommendations are made based on these local findings.

Pub.: 28 Jul '10, Pinned: 21 Oct '17

Comparison of FTIR transmission and transfection substrates for canine liver cancer detection.

Abstract: FTIR spectroscopy is a widely used technique that provides insights into disease processes at the molecular level. Due to its numerous advantages it is becoming an increasingly powerful tool for the study of biological materials and has the potential to become an excellent diagnostic method, especially considering the low cost of transflection substrates. However, questions about the usefulness of the transflection measurement mode due to the complicated nature of physical processes occurring during the measurement and in particular the Electric Field Standing Wave (EFSW) effect have been raised. In this paper we present a comparison of the two most common FT-IR measurement modes: transmission and transfection using healthy and pathologically altered tissue (histiocytic sarcoma). We found that the major differences between normal and cancerous tissue were associated with changes DNA and carbohydrate content. In particular we identified a band at 964 cm(-1) assigned to a nucleic acid phosphodiester backbone mode, which appeared more pronounced in cancerous tissue irrespective of the substrate. We applied Principal Component Analysis, Unsupervised Hierarchical Cluster Analysis and k-means clustering to transmission and transflection substrates and found that both measurement modes were equally capable of discrimination normal form cancerous tissue. Moreover, the differences between spectra from cancerous and normal tissue were significantly more important than the ones arising from the measurement modes.

Pub.: 17 Dec '14, Pinned: 21 Oct '17