The current landscape of nucleic acid tests for filovirus detection.

Nucleic acid testing (NAT) for pathogenic filoviruses plays a key role in surveillance and to control the spread of infection. As they share clinical features with other pathogens, the initial spread of these viruses can be misdiagnosed. Tests that can identify a pathogen in the initial stages of infection are essential to control outbreaks. Since the Ebola virus disease (EVD) outbreak in 2014-2016 several tests have been developed that are faster than previous tests and more suited for field use. Furthermore, the ability to test for a range of pathogens simultaneously has been expanded to improve clinical pathway management of febrile syndromes. This review provides an overview of these novel diagnostic tests

Dental and microbiological risk factors for hospital-acquired pneumonia in non-ventilated older patients

We obtained a time series of tongue/throat swabs from 90 patients with lower limb fracture, aged 65-101 in a general hospital in the North East of England between April 2009-July 2010. We used novel real-time multiplex PCR assays to detect S. aureus, MRSA, E. coli, P. aeruginosa, S. pneumoniae, H. influenza and Acinetobacter spp. We collected data on dental/denture plaque (modified Quigley-Hein index) and outcomes of clinician-diagnosed HAP.The crude incidence of HAP was 10% (n = 90), with mortality of 80% at 90 days post discharge. 50% of cases occurred within the first 25 days. HAP was not associated with being dentate, tooth number, or heavy dental/denture plaque. HAP was associated with prior oral carriage with E. coli/S. aureus/P.aeruginosa/MRSA (p = 0.002, OR 9.48 95% CI 2.28-38.78). The incidence of HAP in those with carriage was 35% (4% without), with relative risk 6.44 (95% CI 2.04-20.34, p = 0.002). HAP was associated with increased length of stay (Fishers exact test, p=0.01), with mean 30 excess days (range -11.5-115). Target organisms were first detected within 72 hours of admission in 90% participants, but HAP was significantly associated with S. aureus/MRSA/P. aeruginosa/E. coli being detected at days 5 (OR 4.39, 95%CI1.73-11.16) or 14 (OR 6.69, 95%CI 2.40-18.60).Patients with lower limb fracture who were colonised orally with E. coli/ S. aureus/MRSA/P. aeruginosa after 5 days in hospital were at significantly greater risk of HAP (p = 0.002)

Utility of Multilocus Sequence Typing as an Epidemiological Tool for Investigation of Outbreaks of Gastroenteritis Caused by Campylobacter jejuni

Multilocus sequence typing (MLST) has been proven useful for the study of the global population structure of Campylobacter jejuni; however, its usefulness for the investigation of outbreaks of disease caused by C. jejuni has not been proven. In this study, MLST plus sequencing of the flaA short variable region (SVR) were applied to 47 isolates from 12 outbreaks of C. jejuni infection whose relatedness has been determined previously, and the results were compared to those of serotyping and pulsed-field gel electrophoresis (PFGE). Isolates implicated in an outbreak were indistinguishable by all four subtyping methods, with sporadic isolates being distinguished from outbreak isolates. Two sporadic isolates from one outbreak were resistant to SmaI digestion and therefore nontypeable by PFGE but were differentiated from the outbreak strain by the other methods. PFGE and flaA SVR typing were the most discriminatory methods, with discriminatory indices (DI) of 0.930 and 0.923, respectively. However, an epidemic strain from one outbreak was distinguished from the other outbreak isolates by flaA SVR typing; its flaA allele was different at five nucleotides, suggesting that this change was possibly mediated by recombination. MLST was less discriminatory than PFGE and flaA SVR typing (DI = 0.859), and many of the epidemic strains possessed common sequence types (STs) including ST-8, -21, -22, and -42. However, further discrimination within STs was achieved by flaA SVR typing or PFGE. The results from this study demonstrate that a combined approach of MLST plus flaA SVR typing provides a level of discrimination equivalent to PFGE for outbreak investigations

Relating HAP/LRTI and patient factors using univariate generalised linear modelling.

<p>Abbreviations: HAP = hospital acquired pneumonia, LRTI = lower respiratory tract infection, d.p. = decimal places, PQS = plaque quartile score, IMD = Index of multiple deprivation score, HABAM = Hierarchical Assessment of Balance and Mobility, PPI = proton pump inhibitor, ACE-I = Angiotensin converting enzyme inhibitor, Cef vs teic = Whether the patient received Cefuroxime or Teicoplanin perioperatively, COPD = Combined obstructive pulmonary disease, Any resp = Any respiratory comorbidity</p><p>¹: includes <i>S</i>. <i>aureus</i>, MRSA, <i>P</i>. <i>aeruginosa</i>, <i>E</i>. <i>coli</i></p><p>Relating HAP/LRTI and patient factors using univariate generalised linear modelling.</p

Baseline characteristics of study cohort, shown by patients with or without HAP (Fisher’s exact test).

<p>HAP = hospital acquired pneumonia, HABAM = Hierarchical Assessment of Balance and Mobility, PQS = Plaque quartile score, COPD = Combined obstructive pulmonary disease, d.p. = decimal places</p><p>*statistically significant p<0.01</p><p>^aincludes benzodiazepines, selective serotonin reuptake inhibitors, tricyclic antidepressants, opiates, gabapentin or anti-epileptic drugs.</p><p>¹Where mean and median were similar, only the mean is shown. Where there was large disparity between these values, mean, median and range are given.</p><p>Baseline characteristics of study cohort, shown by patients with or without HAP (Fisher’s exact test).</p

Association between HAP and presence of opportunistic organisms by day sampled.

<p>Association between HAP and presence of opportunistic organisms by day sampled.</p