Scientific Literature Review: Infectious diseases

Identifying volatile metabolite signatures for the diagnosis of bacterial respiratory tract infection using electronic nose technology: a pilot study
^{Lewis JM, Savage RS, Beeching NJ, Beadsworth MBJ, Feasey N, Covington JA. PLoS One 2017; 12(12): e0188879}

OBJECTIVES: New point of care diagnostics are urgently needed to reduce the over-prescription of antimicrobials for bacterial respiratory tract infection (RTI). A pilot cross-sectional study was performed to assess the feasibility of gas-capillary column ion mobility spectrometer (GC-IMS), for the analysis of volatile organic compounds (VOC) in exhaled breath to diagnose bacterial RTI in hospital inpatients.

METHODS: 71 patients were prospectively recruited from the Acute Medical Unit of the Royal Liverpool University Hospital between March and May 2016 and classified as confirmed or probable bacterial or viral RTI on the basis of microbiologic, biochemical and radiologic testing. Breath samples were collected at the patient’s bedside directly into the electronic nose device, which recorded a VOC spectrum for each sample. Sparse principal component analysis and sparse logistic regression were used to develop a diagnostic model to classify VOC spectra as being caused by bacterial or non-bacterial RTI.

RESULTS: Summary area under the receiver operator characteristic curve was 0.73 (95% CI 0.61–0.86), summary sensitivity and specificity were 62% (95% CI 41–80%) and 80% (95% CI 64–91%) respectively (p=0.00147).

CONCLUSIONS: GC-IMS analysis of exhaled VOC for the diagnosis of bacterial RTI shows promise in this pilot study and further trials are warranted to assess this technique.

Cerebrospinal fluid B-lymphocyte chemoattractant CXCL13 in the diagnosis of acute Lyme neuroborreliosis in children
_{Barstad B, Tveitnes D, Noraas S, Selvik Ask I, Saeed M, Bosse F, et al. Pediatr Infect Dis J 2017; 36(12): e286–e292}

BACKGROUND: Current markers of Lyme neuroborreliosis (LNB) in children have insufficient sensitivity in the early stage of disease. The B-lymphocyte chemoattractant CXCL13 in the cerebrospinal fluid (CSF) may be useful in diagnosing LNB, but its specificity has not been evaluated in studies including children with clinically relevant differential diagnoses. The aim of this study was to elucidate the diagnostic value of CSF CXCL13 in children with symptoms suggestive of LNB.

METHODS: Children with symptoms suggestive of LNB were included prospectively into predefined groups with a high or low likelihood of LNB based on CSF pleocytosis and the detection of Borrelia antibodies or other causative agents. CSF CXCL13 levels were compared between the groups, and receiver-operating characteristic analyses were performed to indicate optimal cutoff levels to discriminate LNB from non-LNB conditions.

RESULTS: Two hundred and ten children were included. Children with confirmed LNB (n=59) and probable LNB (n=18) had higher CSF CXCL13 levels than children with possible LNB (n=7), possible peripheral LNB (n=7), non-Lyme aseptic meningitis (n=12), non-meningitis (n=91) and negative controls (n=16). Using 18 pg/mL as a cutoff level, both the sensitivity and specificity of CSF CXCL13 for LNB (confirmed and probable) were 97%. Comparing only children with LNB and non-Lyme aseptic meningitis, the sensitivity and specificity with the same cutoff level were 97% and 83%, respectively.

CONCLUSION: CSF CXCL13 is a sensitive marker of LNB in children. The specificity to discriminate LNB from non-Lyme aseptic meningitis may be more moderate, suggesting that CSF CXCL13 should be used together with other variables in diagnosing LNB in children.

Neutrophil CD64 – A potential biomarker in patients with complicated intra-abdominal infections? A literature review
^{Dimitrov E, Enchev E, Halacheva K, Minkov G, Yovtchev Y. Acta Microbiol Immunol Hung 2018; doi: 10.1556/030.65.2018.011}

Complicated intra-abdominal infections (cIaIs) represent a serious cause of morbidity and mortality. Early diagnosis and well-timed treatment can improve patients’ outcome, whereas the delay in management often result in rapid progression to circulatory collapse, multiple organ failure, and death. Neutrophil CD64 antigen expression has been studied for several years as infectious and sepsis biomarker and has several characteristics that make it good for clinical employment. It has been suggested to be predictive of positive bacterial cultures and a useful test for management of sepsis and other significant bacterial infections. Our review concluded that the neutrophil CD64 expression could be a promising and meaningful biomarker in patients with cIaIs. It shows good potential for evaluating the severity of the disease and could give information about the outcome. However, more large studies should be performed before using it in clinical practice.

Mycoplasma genitalium: accurate diagnosis is necessary for adequate treatment
^{Gaydos CA. J Infect Dis 2017; 216(suppl_2): S406–S411}

BACKGROUND: Mycoplasma genitalium is very difficult to grow in culture but has been more able to be studied for disease associations since the advent of research molecular amplification assays. Polymerase chain reaction (PCR) and other molecular assays have demonstrated an association with adverse disease outcomes, such as urethritis or nongonococcal urethritis in men and adverse reproductive sequelae in women-for example, cervicitis, endometritis, and pelvic inflammatory disease, including an association with risk for human immunodeficiency virus. The lack of commercially available diagnostic assays has limited widespread routine testing. Increasing reports of high rates of resistance to azithromycin detected in research studies have heightened the need available commercial diagnostic assays as well as standardized methods for detecting resistance markers. This review covers available molecular methods for the diagnosis of M. genitalium and assays to predict the antibiotic susceptibility to azithromycin.

METHODS: A PubMed (US National Library of Medicine and National Institutes of Health) search was conducted for literature published between 2000 and 2016, using the search terms ‘Mycoplasma genitalium’, ‘M. genitalium’, ‘diagnosis’, and ‘detection’.

RESULTS: Early PCR diagnostic tests focused on the MPa adhesion gene and the 16S ribosomal RNA gene. Subsequently, a transcription-mediated amplification assay targeting ribosomes was developed and widely used to study the epidemiology of M. genitalium. Newer methods have proliferated and include quantitative PCR for organism load, AmpliSens PCR, PCR for the pdhD gene, a PCR-based microarray for multiple sexually transmitted infections, and multiplex PCRs. None yet are cleared by the Food and Drug Administration in the United States, although several assays are CE marked in Europe. As well, many research assays, including PCR, gene sequencing, and melt curve analysis, have been developed to detect the 23S ribosomal RNA gene mutations that confer resistance to azithromycin. One recently developed assay can test for both M. genitalium and azithromycin resistance mutations at the same time.

CONCLUSIONS: It is recommended that more commercial assays to both diagnose this organism and guide treatment choices should be developed and made available through regulatory approval. Research is needed to establish the cost-effectiveness of routine M. genitalium testing in symptomatic patients and screening in all individuals at high risk of acquiring and transmitting sexually transmitted infections.

Prognostic value of secretoneurin in patients with severe sepsis and septic shock: data from the Albumin Italian Outcome Sepsis Study
_{Røsjø H, Masson S, Caironi P3,4, Stridsberg M, Magnoli M, et al. Crit Care Med 2018; doi: 10.1097/CCM.0000000000003050}

OBJECTIVES: Secretoneurin directly influences cardiomyocyte calcium handling, and circulating secretoneurin levels seem to improve risk prediction in patients with myocardial dysfunction by integrating information on systemic stress, myocardial function, and renal function. Accordingly, in this study, we hypothesized that secretoneurin would improve risk prediction in patients with sepsis and especially in patients with septic shock as these patients are more hemodynamically unstable.

DESIGN: Multicentre, interventional randomized clinical trial.

SETTING: Multicentre, pragmatic, open-label, randomized, prospective clinical trial testing fluid administration with either 20% human albumin and crystalloids or crystalloid solutions alone in patients with severe sepsis or septic shock (The Albumin Italian Outcome Sepsis).
PATIENTS OR SUBJECTS: In total, 540 patients with septic shock and 418 patients with severe sepsis.

INTERVENTIONS: Either 20% human albumin and crystalloids or crystalloid solutions alone.

MEASUREMENTS AND MAIN RESULTS: We measured secretoneurin on days 1, 2, and 7 after randomization and compared the prognostic value of secretoneurin for ICU and 90-day mortality with established risk indices and cardiac biomarkers in septic shock and severe sepsis. High secretoneurin levels on day 1 were associated with age and serum concentrations of lactate, bilirubin, creatinine, and N-terminal pro-B-type natriuretic peptide. Adjusting for established risk factors and cardiovascular biomarkers, secretoneurin levels on day 1 were associated with ICU (odds ratio, 2.27 [95% CI, 1.05–4.93]; p=0.04) and 90-day mortality (2.04 [1.02–4.10]; p=0.04) in patients with septic shock, but not severe sepsis without shock. Secretoneurin levels on day 2 were also associated with ICU (3.11 [1.34–7.20]; p=0.008) and 90-day mortality (2.69 [1.26–5.78]; p=0.01) in multivariate regression analyses and improved reclassification in patients with septic shock, as assessed by the net reclassification index. Randomized albumin administration did not influence the associations between secretoneurin and outcomes.

CONCLUSIONS: Secretoneurin provides early and potent prognostic information in septic patients with cardiovascular instability.

Adaptation of the Amoebae Plate Test to recover Legionella strains from clinical samples
_{Descours G, Hannetel H, Reynaud JV, Ranc AG, Beraud L, Kolenda C, et al. J Clin Microbiol 2018; doi: 10.1128/JCM.01361-17}

The isolation of Legionella from respiratory samples is the gold standard for Legionnaires’ disease (LD) diagnosis and enables epidemiological studies and outbreak investigations. The purpose of this work was to adapt and evaluate the performance of an amoebic co-culture procedure (the amoebae plate test, APT) to the recovery of Legionella strains from respiratory samples, in comparison with axenic culture and a liquid-based amoebic co-culture (LAC). Axenic culture, LAC, and APT were prospectively performed on 133 respiratory samples from patients with LD. The sensitivities and times-to-result of the three techniques were compared. Using the three techniques, Legionella strains were isolated in 46.6% (n=62) of the 133 respiratory samples. The sensitivity of axenic culture was 42.9% (n=57), that of LAC was 30.1% (n=40), and that of APT 36.1% (n=48). Seven samples were positive by axenic culture only; for these there were less than 10 colonies in total. Five samples, all sputa, were positive by an amoebic procedure only (5/5 by APT, 2/5 by LAC); all had overgrowth by oropharyngeal flora with axenic culture. The combination of axenic culture with APT yielded a maximal isolation rate (i.e. 46.6%). Overall, the APT significantly reduced the median time for Legionella identification to 4 days, versus 7 days for LAC (p<0.0001). The results of this study promote the substitution of LAC by APT, which could be implemented as a second-line technique on culture-negative and microbial overgrown samples, especially sputa. They provide a logical basis for further studies in both clinical and environmental settings.

Design, implementation, and interpretation of amplification studies for prion detection
_{Haley NJ, Richt JA, Davenport KA, Henderson DM, Hoover EA, Manca M, et al. Prion 2018;  doi: 10.1080/19336896.2018.1443000}

Amplification assays for transmissible spongiform encephalopathies (TSEs) have been in development for close to 15 years, with critical implications for the post-mortem and ante-mortem diagnosis of human and animal prion diseases. Little has been published regarding the structured development, implementation and interpretation of experiments making use of protein misfolding cyclic amplification (PMCA) and real-time quaking-induced conversion (RT-QuIC), and the goal with this Perspectives manuscript is to offer a framework which might allow for more efficient expansion of pilot studies into diagnostic trials in both human and animal subjects. This framework is made up of approaches common to diagnostic medicine, including a thorough understanding of analytical and diagnostic sensitivity and specificity, an a priori development of amplification strategy, and an effective experimental design. It is our hope that a structured framework for prion amplification assays will benefit not only experiments seeking to sensitively detect naturally-occurring cases of prion diseases and describe the pathogenesis of TSEs, but ultimately assist with future endeavours seeking to use these methods more broadly for other protein misfolding disorders, including Alzheimer’s and Parkinson’s disease.

A microfluidic enrichment platform with a recombinase polymerase amplification sensor for pathogen diagnosis
_{Dao TNT, Lee EY, Koo B, Jin CE, Lee TY, Shin Y. Anal Biochem 2017; 544: 87–92}

Rapid and sensitive detection of low amounts of pathogen in large samples is needed for early diagnosis and treatment of patients and surveillance of pathogen. In this study, we report a microfluidic platform for detection of low pathogen levels in a large sample volume that couples an Magainin 1 based microfluidic platform for pathogen enrichment and a recombinase polymerase amplification (RPA) sensor for simultaneous pathogenic DNA amplification and detection in a label-free and real-time manner. Magainin 1 is used as a pathogen enrichment agent with a herringbone microfluidic chip. Using this enrichment platform, the detection limit was found to be 20 times more sensitive in 10 ml urine with Salmonella and 10 times more sensitive in 10 ml urine with Brucella than that of real-time PCR without the enrichment process. Furthermore, the combination system of the enrichment platform and an RPA sensor that based on an isothermal DNA amplification method with rapidity and sensitivity for detection can detect a pathogen at down to 50 CFU in 10 ml urine for Salmonella and 102 CFU in 10 ml urine for Brucella within 60 min. This system will be useful as it has the potential for better diagnosis of pathogens by increasing the capture efficiency of the pathogen in large samples, subsequently enhancing the detection limit of pathogenic DNA.

Long-term follow-up and quantitative hepatitis B surface antigen monitoring in North American chronic HBV carriers
_{O’Neil CR, Congly SE, Rose MS, Lee SS, Borman MA, Charlton CL, et al. Ann Hepatol 2018; 17(2): 232–241}

INTRODUCTION: Quantitative hepatitis B surface antigen (qHBsAg) combined with HBV DNA may be useful for predicting chronic hepatitis B (CHB) activity and nucleoside analogue (NA) response.

MATERIAL AND METHODS: In this retrospective cohort study qHBsAg levels were evaluated according to CHB disease phase and among patients on treatment. Random effect logistic regression analysis was used to analyse qHBsAg change with time in the NA-treated cohort.

RESULTS: 545 CHB carriers [56% M, median age 48 y (IQR 38–59), 73% Asian] had qHBsAg testing. In the untreated group (44%), 8% were classified as immune tolerant, 10% immune clearance, 40% inactive, and 43% had HBeAg-CHB and the median HBsAg levels were 4.6 (IQR 3.4–4.9), 4.0 (IQR 3.4–4.5), 2.9 (IQR 1.4–3.8), and 3.2 log IU/mL (IQR 2.6–4.0), respectively; p<0.001. In the NA-treated group (28% entecavir, 68% tenofovir, 4% lamivudine), no significant change in qHBsAg levels occurred with time, 19% of patients on long-term NA had sustained qHBsAg <2 log₁₀ IU/mL.

CONCLUSION: qHBsAg titres were associated with CHB phase and remained stable in those on long-term NA. A significant number of treated patients had low-level qHBsAg, of which some may be eligible for treatment discontinuation without risk
of flare.