Comparative transcriptomics of multidrug-resistant Acinetobacter baumannii in response to antibiotic treatments

Abstract Multidrug-resistant Acinetobacter baumannii, a major hospital-acquired pathogen, is a serious health threat and poses a great challenge to healthcare providers. Although there have been many genomic studies on the evolution and antibiotic resistance of this species, there have been very limited transcriptome studies on its responses to antibiotics. We conducted a comparative transcriptomic study on 12 strains with different growth rates and antibiotic resistance profiles, including 3 fast-growing pan-drug-resistant strains, under separate treatment with 3 antibiotics, namely amikacin, imipenem, and meropenem. We performed deep sequencing using a strand-specific RNA-sequencing protocol, and used de novo transcriptome assembly to analyze gene expression in the form of polycistronic transcripts. Our results indicated that genes associated with transposable elements generally showed higher levels of expression under antibiotic-treated conditions, and many of these transposon-associated genes have previously been linked to drug resistance. Using co-expressed transposon genes as markers, we further identified and experimentally validated two novel genes of which overexpression conferred significant increases in amikacin resistance. To the best of our knowledge, this study represents the first comparative transcriptomic analysis of multidrug-resistant A. baumannii under different antibiotic treatments, and revealed a new relationship between transposons and antibiotic resistance

Evaluation of hazardous airborne carbonyls in five urban roadside dwellings: A comprehensive indoor air assessment in Sri Lanka

Indoor hazardous airborne carbonyls were quantified in five natural-ventilated roadside dwellings in Colombo, Sri Lanka. The total concentrations of all targeted carbonyls ranged from 13.6 to 18.6 mu g/m(3). Formaldehyde (C1) was the most abundant carbonyl, followed by acetaldehyde (C2) and acetone (C3K). The concentrations of C1 and C2 ranged from 3.3 to 8.5 mu g/m(3) and 2.3 to 4.4 mu g/m(3), respectively, which accounted for 23 to 42% and 18 to 26% respectively, to the total quantified carbonyls. The highest carbonyls levels were obtained in the dwelling located in an urban district with a mixture of industrial, commercial and residential areas. Much lower concentrations of carbonyls were measured in a light local traffic value was counted. Moderate correlations between individual combustion markers from vehicular emissions suggest the strong impacts from traffics to the indoor airs. The concentrations of C1 and C2 were compared with international indoor guidelines established by different authorities. A health assessment was conducted by estimation of inhalation cancer risk, implementing the inhalation unit risk values provided by Integrated Risk Information System (IRIS), associated with C1 and C2, which were 6.2 x 10(-5) and 7.7 x 10(-6), respectively. Even though the risks did not reach the action level (1 x 10(-4)), their health impact should not be overlooked. This kick-off indoor monitoring study provides valuable scientific data to the environmental science community since only limit data is available in Sri Lanka

Effectiveness of BNT162b2 and CoronaVac vaccinations against SARS-CoV-2 omicron infection in people aged 60 years or above: a case–control study

BACKGROUND: In view of limited evidence that specifically addresses vaccine effectiveness (VE) in the older population, this study aims to evaluate the real-world effectiveness of BNT162b2 and CoronaVac in older adults during the Omicron BA.2 outbreak. METHODS: This case-control study analyzed data available between January and March 2022 from the electronic health databases in Hong Kong and enrolled individuals aged 60 or above. Each case was matched with up to 10 controls by age, sex, index date and Charlson Comorbidity Index for the four outcomes (COVID-19 infection, COVID-19-related hospitalization, severe complications, and all-cause mortality) independently. Conditional logistic regression was conducted to evaluate VE of BNT162b2 and CoronaVac against COVID-19-related outcomes within 28 days after COVID-19 infection among participants stratified by age groups (60-79, ≥80 years old). RESULTS: A dose-response relationship between the number of vaccine doses received and protection against severe or fatal disease was observed. Highest VE (95% CI) against COVID-19 infection was observed in individuals aged ≥80 who received three doses of BNT162b2 [75.5% (73.1-77.7%)] or three doses of CoronaVac [53.9% (51.0-56.5%)] compared to those in the younger age group who received three doses of BNT162b2 [51.1% (49.9-52.4%)] or three doses of CoronaVac [2.0% (-0.1-4.1%)]. VE (95% CI) was higher for other outcomes, reaching 91.9% (89.4-93.8%) and 86.7% (84.3-88.8%) against COVID-19-related hospitalization; 85.8% (61.2-94.8%) and 89.8% (72.4-96.3%) against COVID-19-related severe complications; and 96.4% (92.9-98.2%) and 95.0% (92.1-96.8%) against COVID-19-related mortality after three doses of BNT162b2 and CoronaVac in older vaccine recipients, respectively. A similar dose-response relationship was established in younger vaccine recipients and after stratification by sex and Charlson Comorbidity Index. CONCLUSION: Both BNT162b2 and CoronaVac vaccination were effective in protecting older adults against COVID-19 infection and COVID-19-related severe outcomes amidst the Omicron BA.2 pandemic, and VE increased further with the third dose

Comparing hybrid and regular COVID-19 vaccine-induced immunity against the Omicron epidemic

Evidence on the effectiveness of COVID-19 vaccines among people who recovered from a previous SARS-CoV-2 infection is warranted to inform vaccination recommendations. Using the territory-wide public healthcare and vaccination records of over 2.5 million individuals in Hong Kong, we examined the potentially differential risk of SARS-CoV-2 infection, hospitalization, and mortality between those receiving two homologous doses of BNT162b2 or CoronaVac versus those with a previous infection receiving only one dose amid the Omicron epidemic. Results show a single dose after a SARS-CoV-2 infection is associated with a lower risk of infection (BNT162b2: adjusted incidence rate ratio [IRR] = 0.475, 95% CI: 0.410–0.550; CoronaVac: adjusted IRR = 0.397, 95% CI: 0.309–0.511) and no significant difference was detected in the risk of COVID-19-related hospitalization or mortality compared with a two-dose vaccination regimen. Findings support clinical recommendations that those with a previous infection could receive a single dose to gain at least similar protection as those who received two doses without a previous infection

Waning effectiveness against COVID-19-related hospitalisation, severe complications, and mortality with two to three doses of CoronaVac and BNT162b2: a case-control study

BACKGROUND: This study aims to evaluate waning effectiveness against severe and fatal COVID-19 with 2-3 doses of CoronaVac/BNT162b2, where data is limited. METHODS: A case-control study included individuals aged ≥18 years, unvaccinated or received 2-3 doses of CoronaVac/BNT162b2, using electronic healthcare databases in Hong Kong. Those with first COVID-19-related hospitalisation, severe complications, or mortality between 1 January and 15 August 2022 were defined as cases and matched with up-to-10 controls by age, sex, index date, and Charlson Comorbidity Index. Vaccine effectiveness (VE) against COVID-19-related outcomes was estimated at different time intervals from second and third dose vaccination (0-13 up-to 210-240 days) using conditional logistic regression adjusted for comorbidities and medications. RESULTS: By 211-240 days after second dose, VE against COVID-19-related hospitalisation reduced to 46.6% (40.7%-51.8%) for BNT162b2 and 36.2% (28.0%-43.4%) for CoronaVac, and VE against COVID-19-related mortality were 73.8% (55.9%-84.4%) and 76.6% (60.8%-86.0%). After third dose, VE against COVID-19-related hospitalisation decreased from 91.2% (89.5%-92.6%) for BNT162b2 and 76.7% (73.7%-79.4%) for CoronaVac at 0-13 days, to 67.1% (60.4%-72.6%) and 51.3% (44.2%-57.5%) at 91-120 days. VE against COVID-19-related mortality for BNT162b2 remained high from 0-13 days [98.2% (95.0%-99.3%)] to 91-120 days [94.6% (77.7%-98.7%)], and for CoronaVac reduced from 0-13 days [96.7% (93.2%-98.4%)] to 91-120 days [86.4% (73.3%-93.1%)]. CONCLUSIONS: Significant risk reduction against COVID-19-related hospitalisation and mortality after CoronaVac or BNT162b2 vaccination was observed for >240 and >120 days after second and third dose compared to unvaccinated, despite significant waning over time. Timely administration of booster doses could provide higher levels of protection

IRAK2, an IL1R/TLR Immune Mediator, Enhances Radiosensitivity via Modulating Caspase 8/3-Mediated Apoptosis in Oral Squamous Cell Carcinoma

Predicting and overcoming radioresistance are crucial in radiation oncology, including in managing oral squamous cell carcinoma (OSCC). First, we used RNA-sequence to compare expression profiles of parent OML1 and radioresistant OML1-R OSCC cells in order to select candidate genes responsible for radiation sensitivity. We identified IRAK2, a key immune mediator of the IL-1R/TLR signaling, as a potential target in investigating radiosensitivity. In four OSCC cell lines, we observed that intrinsically low IRAK2 expression demonstrated a radioresistant phenotype (i.e., OML1-R and SCC4), and vice versa (i.e., OML1 and SCC25). Next, we overexpressed IRAK2 in low IRAK2-expression OSCC cells and knocked it down in high IRAK2-expression cells to examine changes of irradiation response. After ionizing radiation (IR) exposure, IRAK2 overexpression enhanced the radiosensitivity of radioresistant cells and synergistically suppressed OSCC cell growth both in vitro and in vivo, and vice versa. We found that IRAK2 overexpression restored and enhanced radiosensitivity by enhancing IR-induced cell killing via caspase-8/3-dependent apoptosis. OSCC patients with high IRAK2 expression had better post-irradiation local control than those with low expression (i.e., 87.4% vs. 60.0% at five years, P = 0.055), showing that IRAK2 expression was associated with post-radiation recurrence. Multivariate analysis confirmed high IRAK2 expression as an independent predictor for local control (HR, 0.11; 95% CI, 0.016 – 0.760; P = 0.025). In conclusion, IRAK2 enhances radiosensitivity, via modulating caspase 8/3-medicated apoptosis, potentially playing double roles as a predictive biomarker and a novel therapeutic target in OSCC

Effectiveness of BNT162b2 and CoronaVac vaccinations against mortality and severe complications after SARS-CoV-2 Omicron BA.2 infection: a case–control study

Data regarding protection against mortality and severe complications after Omicron BA.2 infection with CoronaVac and BNT162b2 vaccines remains limited. We conducted a case–control study to evaluate the risk of severe complications and mortality following 1–3 doses of CoronaVac and BNT162b2 using electronic health records database. Cases were adults with their first COVID-19-related mortality or severe complications between 1 January and 31 March 2022, matched with up-to 10 controls by age, sex, index date, and Charlson Comorbidity Index. Vaccine effectiveness against COVID-19-related mortality and severe complications by type and number of doses was estimated using conditional logistic regression adjusted for comorbidities and medications. Vaccine effectiveness (95% CI) against COVID-19-related mortality after two doses of BNT162b2 and CoronaVac were 90.7% (88.6–92.3) and 74.8% (72.5–76.9) in those aged ≥65, 87.6% (81.4–91.8) and 80.7% (72.8–86.3) in those aged 50–64, 86.6% (71.0–93.8) and 82.7% (56.5–93.1) in those aged 18–50. Vaccine effectiveness against severe complications after two doses of BNT162b2 and CoronaVac were 82.1% (74.6–87.3) and 58.9% (50.3–66.1) in those aged ≥65, 83.0% (69.6–90.5) and 67.1% (47.1–79.6) in those aged 50–64, 78.3% (60.8–88.0) and 77.8% (49.6–90.2) in those aged 18–50. Further risk reduction with the third dose was observed especially in those aged ≥65 years, with vaccine effectiveness of 98.0% (96.5–98.9) for BNT162b2 and 95.5% (93.7–96.8) for CoronaVac against mortality, 90.8% (83.4–94.9) and 88.0% (80.8–92.5) against severe complications. Both CoronaVac and BNT162b2 vaccination were effective against COVID-19-related mortality and severe complications amidst the Omicron BA.2 pandemic, and risks decreased further with the third dose

Spatial analysis of the impact of urban geometry and socio-demographic characteristics on COVID-19, a study in Hong Kong

The World Health Organization considered the widespread of COVID-19 over the world as a pandemic. There is still a lack of understanding of its origin, transmission, and treatment methods. Understanding the influencing factors of the COVID-19 can help mitigate its spread, but little research on the spatial factors has been conducted. Therefore, this study explores the effects of urban geometry and socio-demographic factors on the COVID-19 cases in Hong Kong. For each patient, the places they visited during the incubation period before going to hospital were identified, and matched with corresponding attributes of urban geometry (i.e., building geometry, road network, greenspace) and socio-demographic factors (i.e., demographic, educational, economic, household and housing characteristics) based on the coordinates. The local cases were then compared with the imported cases using the stepwise logistic regression, the logistic regression with case-control of time, and the least absolute shrinkage and selection operator regression to identify factors influencing local disease transmission. Results show that the building geometry, road network and certain socio-economic characteristics are significantly associated with COVID-19 cases. In addition, the results indicate that urban geometry is playing a more important role than the socio-demographic characteristics in affecting the COVID-19 incidences. These findings provide a useful reference to the government and the general public as to the spatial vulnerability of the COVID-19 transmission and to take appropriate preventive measures in high-risk areas