Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data

Identifying and interrupting transmission chains is important for controlling infectious diseases. One way to identify transmission pairs - two hosts in which infection was transmitted from one to the other - is using the variation of the pathogen within each single host (within-host variation). However, the role of such variation in transmission is understudied due to a lack of experimental and clinical datasets that capture pathogen diversity in both donor and recipient hosts. In this work, we assess the utility of deep-sequenced genomic surveillance (where genomic regions are sequenced hundreds to thousands of times) using a mouse transmission model involving controlled spread of the pathogenic bacterium Citrobacter rodentium from infected to naïve female animals. We observe that within-host single nucleotide variants (iSNVs) are maintained over multiple transmission steps and present a model for inferring the likelihood that a given pair of sequenced samples are linked by transmission. In this work we show that, beyond the presence and absence of within-host variants, differences arising in the relative abundance of iSNVs (allelic frequency) can infer transmission pairs more precisely. Our approach further highlights the critical role bottlenecks play in reserving the within-host diversity during transmission.

The efficacy of commercial decontamination agents differs between standardised test settings and research laboratory usage for a variety of bacterial species

Decontamination of surfaces and items plays an important role in reducing the spread of infectious microorganisms in many settings including hospitals and research institutes. Regardless of the location, appropriate decontamination procedures are required for maintaining biosafety and biosecurity. For example, effective decontamination of microbial cultures is essential to ensure proper biocontainment and safety within microbiological laboratories. To this end, many commercial decontamination agents are available which have been tested to a prescribed standard to substantiate their efficacy. However, these standardised tests are unlikely to accurately reflect many conditions encountered in medical and biomedical research. Despite this, laboratory workers and other users of decontamination agents may assume that all decontamination agents will work in all situations. We tested commonly used commercial decontamination agents against a range of bacterial species to determine their efficacy under real-world research laboratory conditions. As each decontamination agent has a different recommended dilution for use, to compare their efficacy we calculated their 'effective ratio' which reflects the difference between the manufacturer-recommended dilution and the dilution needed to achieve decontamination under real-world research laboratory conditions. Effective ratios above one indicate that the agent was effective at a dilution more dilute than recommended whereas effective ratios lower than one indicate that the agent required a higher concentration than recommended. Our results show that the quaternary ammonium agents TriGene Advance and Chemgene HLD4L were the most effective out of the agents tested, with biocidal activity measured at up to 64 times the recommended dilution. In contrast, hypochlorite (bleach) and Prevail™ (stabilised hydrogen peroxide) had the lowest effective ratios amongst the tested agents. In conclusion, our data suggests that not all decontamination agents will work at the recommended dilutions under real-world research laboratory conditions. We recommend that the protocols for the use of decontamination agents are verified under the specific conditions required to ensure they are fit for purpose.

Preclinical confirmation of UVC efficacy in treating infectious keratitis

PURPOSE

Preclinical evaluation of the therapeutic potential of antimicrobial 265 nm UVC for infectious keratitis.

METHODS

Four experiments explored UVC: 1) impact on bacterial and fungal lawns on agar, in individual or mixed culture, 2) bacterial inactivation dose in an in vitro deep corneal infection model, 3) dose validation in an ex vivo porcine keratitis model and 4) efficacy in a masked, randomised, controlled murine keratitis trial using bioluminescent Pseudomonas aeruginosa.

RESULTS

Minimum effective UVC exposures ranged between 2 s and 5 s for lawn bacteria and fungi in individual or mixed culture. Significant P. aeruginosa growth inhibition in the in vitro infection model was achieved with 15 s UVC, that resulted in a >3.5 log10 reduction of bacteria in a subsequent ex vivo keratitis model (p < 0.05). Bioluminescence fell below baseline levels in all treated animals, within 8 h of treatment (p < 0.05), in the in vivo study. Re-epithelialisation with corneal clarity occurred within 24 h in 75% of UVC-treated cases, with no relapse at 48 h. On plating, bacteria were recovered only from untreated controls.

CONCLUSIONS

UVC inhibited all tested bacteria and fungi, including mixed culture and strains linked to antibiotic resistance, in vitro, with exposures of ≤ 5 s. In vitro and ex vivo testing confirmed therapeutic potential of 15 s UVC. In vivo, 15 s UVC administered in two doses, 4 h apart, proved effective in treating murine bacterial keratitis.

Effect of therapeutic UVC on corneal DNA: Safety assessment for potential keratitis treatment

PURPOSE

Antimicrobial ultraviolet C (UVC) has proven efficacy in vitro against keratitis isolates and has potential to treat corneal infection if safety can be confirmed.

METHOD

Safety of 265 nm, 1.93 mW/cm² intensity UVC (15-300 s exposures) was investigated in vitro via cyclobutane pyrimidine dimer (CPD) formation in DNA of human cultured corneal epithelial cells; ex vivo, by evaluating UVC transmissibility as a function of porcine corneal thickness; and in vivo, by evaluating CPD induction in the mouse cornea following UVC exposure.

RESULTS

A single exposure of 15 s UVC did not induce significant CPD formation (0.92 ± 1.45%) in vitro relative to untreated control (p = 0.93) whereas 300 s exposure caused extensive CPD formation (86.8 ± 13.73%; p < 0.0001). Cumulative exposure to 15 s UVC daily for 3 days induced more CPD (14.6 ± 8.2%) than a single equivalent 45 s exposure (8.3 ± 4.0%) (p < 0.001) but levels returned to baseline within 72 h (p = 0.29), indicating highly efficient DNA repair. Ex vivo, UVC transmission decreased sharply with increasing corneal thickness, confirming UVC effects are limited to the superficial corneal layers. In vivo evaluations demonstrated no detectable CPD after three consecutive daily 15 s UVC exposures, whereas a single 300 s exposure induced extensive CPD formation in superficial corneal epithelium.

CONCLUSION

Up to three daily doses of 15 s UVC, in vivo, appear safe with respect to CPD formation. Ongoing research exploring UVC as a possible treatment for microbial keratitis is warranted.

A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity

Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.

Long-term safety of adalimumab in clinical trials in adult patients with Crohn's disease or ulcerative colitis

BACKGROUND

Adalimumab is used to treat moderate to severe Crohn's disease (CD) and ulcerative colitis (UC) when conventional therapies fail.

AIM

To update long-term adalimumab safety from CD and UC trials; the previous report was CD only, 3160 patients/3402 patient-years (PYs).

METHODS

Treatment-emergent adverse events (AEs; first dose to 70 days after last dose/December 31, 2015) in adults in phase 2/3 and 3/3b trials and open-label extensions were coded using Medical Dictionary for Regulatory Activities (MedDRA-v18.1). Rates were assessed as events/100 (E/100 PYs).

RESULTS

The database (16 trials; CD, N = 3606; UC, N = 1739) represented 4145 and 3397 PYs of exposure, respectively. For CD, incidences of any AEs with adalimumab were 60.8%-65.1%, depending on dose, and 71.5% with placebo; for UC, the incidences were 53.5%-54.8% and 56.1%, respectively. Rates of any AEs (CD, 605 E/100 PYs; UC, 361 E/100 PYs), serious AEs (CD, 36.1 E/100 PYs; UC, 18.9 E/100 PYs), and malignancies (CD, 1.2 E/100 PYs; UC, 1.0 E/100 PYs) were similar between current and prior analyses. Apparent rate of opportunistic infections was lowered to 0.3 and 0.2 E/100 PYs for CD and UC, respectively, by recent MedDRA changes excluding oral candidiasis and tuberculosis. Standardised incidence ratios for malignancies were similar to the general population (CD, 1.45 [95% CI, 0.90-2.22]; UC, 1.36 [95% CI, 0.84-2.07]). Demyelinating disorders were uncommon (CD, 0.1 E/100 PYs; UC, <0.1 E/100 PYs).

CONCLUSIONS

Patients with moderately to severely active Crohn's disease or ulcerative colitis continued to experience acceptable safety with adalimumab, without new safety signals.

Characterization of a mouse-adapted Staphylococcus aureus strain

More effective antibiotics and a protective vaccine are desperately needed to combat the ‘superbug’ Staphylococcus aureus. While in vivo pathogenicity studies routinely involve infection of mice with human S. aureus isolates, recent genetic studies have demonstrated that S. aureus lineages are largely host-specific. The use of such animal-adapted S. aureus strains may therefore be a promising approach for developing more clinically relevant animal infection models. We have isolated a mouse-adapted S. aureus strain (JSNZ) which caused a severe outbreak of preputial gland abscesses among male C57BL/6J mice. We aimed to extensively characterize this strain on a genomic level and determine its virulence potential in murine colonization and infection models. JSNZ belongs to the MLST type ST88, rare among human isolates, and lacks an hlb-converting phage encoding human-specific immune evasion factors. Naive mice were found to be more susceptible to nasal and gastrointestinal colonization with JSNZ than with the human-derived Newman strain. Furthermore, naïve mice required antibiotic pre-treatment to become colonized with Newman. In contrast, JSNZ was able to colonize mice in the absence of antibiotic treatment suggesting that this strain can compete with the natural flora for space and nutrients. In a renal abscess model, JSNZ caused more severe disease than Newman with greater weight loss and bacterial burden. In contrast to most other clinical isolates, JSNZ can also be readily genetically modified by phage transduction and electroporation. In conclusion, the mouse-adapted strain JSNZ may represent a valuable tool for studying aspects of mucosal colonization and for screening novel vaccines and therapies directed at preventing colonization.

The multi-element content of the lichen Parmelia sulcata, soil, and oak bark in relation to acidification and climate

Understanding how biodiversity is influenced by changing atmospheric conditions is important for conservation, public policy and environmental health. In a recent study, an impact on two of the most abundant lichens in Europe (Parmelia sulcata and Hypogymnia physodes) was recorded at Burnham Beeches lying 40 km west of London (UK) during unusual atmospheric conditions whilst other species remained unaffected. Bark and soil chemistry also influence lichen vitality and community composition. Correlations between element concentrations and element ratios in different samples help understand element cycling. To study this further, the multi-element content of the lichen P. sulcata and bark sampled in 2000 from 16 oak (Quercus robur) trees at Burnham Beeches was compared with the same elements determined in 24 surface soils sampled in 2005 from beneath the same trees. Soil pH ranged from 4.1 to 6.7. Highly significant correlations (p<0.001) for Mn/Ca ratios in lichen versus bark, soil versus bark and soil versus lichen samples confirmed cycling via the soil-tree-lichen system. Similar Mn/Ca ratios were reported in coniferous forests where high Mn concentrations were shown to limit epiphytic lichen abundance. Soil acidification influences element bioavailability and bark chemistry in Burnham Beeches with implications for lichen diversity and health. Recovery was recorded in P. sulcata, including regeneration within monitoring quadrats. Biological systems are well known to be influenced by pollution episodes.

The impact of a supplementary medication review and counselling service within the oncology outpatient setting

The impact on the care of breast cancer patients, of a pharmacy technician-led medication review and counselling clinic, provided in an outpatient setting, was investigated using a controlled randomised study. Compared to the controls, clinic patients showed a significantly improved level of understanding of their chemotherapy support medication (95% CI for difference in mean knowledge rating scores=2.165-2.826, P<0.001) and a significant reduction in the median number of support items required (two compared to five in the control, P<0.001). This resulted in a significant reduction in mean medication expenditure per patient (26.70 vs 10.20 British Pound, 95% CI for the mean difference in cost 6.72 - 26.26 British Pound, P<0.001). The clinic was also associated with significant reductions in chemotherapy delays (P<0.001) and dose reductions due to side effects (P=0.003). Other benefits from the clinic were a reduction in pharmacy dispensing time and a highly significant reduction in pharmacy time spent resolving post-clinic prescription queries (P<0.001). Taking into account the initial technician training cost, the scheme represented an annual saving to the Trust of over 15,000 British Pound. The clinic serves as a model for those wishing to improve outpatient services to breast cancer patients.

Which factors are responsible for the changing lichen floras of London?

SO(2) is no longer the principal factor influencing the vitality and composition of lichen assemblages in London. We provide direct evidence for an impact on lichen growth during episodic high exhaust emissions coupled with unusual climatic conditions. This suggests a combination of particles and nitrogen plays a major role in influencing lichen growth. Nitrogen from traffic emissions may be at least as important as agriculture in influencing the composition of lichen assemblages.

Protein-bound cobalamin absorption declines in the elderly

A modified protein-bound cobalamin absorption test was used to study dietary cobalamin absorption in healthy adults of different age groups and patients with isolated low serum concentrations of cobalamin. Dietary cobalamin absorption was significantly reduced in healthy adults aged 55-75 years compared with young adults, with a further reduction in those older than 75 years. No difference was detected between dietary cobalamin absorption in patients with isolated low serum cobalamin and controls of a similar age group. Cobalamin malabsorption was associated with elevated serum gastrin. The diagnostic value of this protein-bound cobalamin absorption test in the elderly was limited by the frequent finding of reduced absorption in healthy elderly people with normal serum cobalamin concentrations. The performance of such tests should be evaluated in different age groups before application in diagnosis.

Prophylaxis of cyanobacterial and mushroom cyclic peptide toxins

The pathogenicity of virulent cyclic peptide toxins of the cyanobacterium, Microcystis aeruginosa, and the mushroom, Amanita phalloides, was prevented in mice by pretreatment with a variety of chemically unrelated agents including hydrocortisone, shellac, certain diazo and triazine dyes and cyclosporine. A. Despite the diverse nature of the protective agents, a feature commonly associated with protection was the ability to impair hepatic uptake of 51Cr-labeled sheep erythrocytes, a function of hepatic macrophages (Kupffer cells). In addition, several of the protective agents are known to affect other aspects of reticuloendothelial cell function. Therefore it seems likely that the hepatic macrophage is involved in the observed protection, although by what mechanism(s) is unknown. The most remarkable prophylaxis was seen with a single injection of Trypan red, which provided nonimmunologic protection against a lethal dose of a cyanobacterial toxin, cyanoginosin-LR, for periods up to 3 months.