Retention of E. coli and water on the skin after liquid contact

The frequent contact people have with liquids containing pathogenic microorganisms provides opportunities for disease transmission. In this work, we quantified the transfer of bacteria-using E. coli as a model- from liquid to skin, estimated liquid retention on the skin after different contact activities (hand immersion, wet-cloth and wet-surface contact), and estimated liquid transfer following hand-to-mouth contacts. The results of our study show that the number of E. coli transferred to the skin per surface area (n [E. coli/cm2]) can be modeled using n = C (10-3.38+h), where C [E. coli/cm3] is the concentration of E. coli in the liquid, and h [cm] is the film thickness of the liquid retained on the skin. Findings from the E. coli transfer experiments reveal a significant difference between the transfer of E. coli from liquid to the skin and the previously reported transfer of viruses to the skin. Additionally, our results demonstrate that the time elapsed since the interaction significantly influences liquid retention, therefore modulating the risks associated with human interaction with contaminated liquids. The findings enhance our understanding of liquid-mediated disease transmission processes and provide quantitative estimates as inputs for microbial risk assessments

A systematic review of chlorine-based surface disinfection efficacy to inform recommendations for low-resource outbreak settings

BACKGROUND: Infectious diseases can be transmitted via fomites (contaminated surfaces/objects); disinfection can interrupt this transmission route. However, disinfection guidelines for low-resource outbreak settings are inconsistent and not evidence-based. METHODS: A systematic review of surface disinfection efficacy studies was conducted to inform low-resource outbreak guideline development. Due to variation in experimental procedures, outcomes were synthesized in a narrative summary focusing on chlorine-based disinfection against seven pathogens with potential to produce outbreaks in low-resource settings (Mycobacterium tuberculosis, Vibrio cholerae, Salmonella spp., hepatitis A virus, rotavirus, norovirus, Ebola virus). RESULTS: Data were extracted from 89 laboratory studies and made available, including 20 studies on relevant pathogens used in combination with surrogate data to determine minimum target concentrationxtime ("CT") factors. Stainless steel (68%) and chlorine-based disinfectants (56%) were most commonly tested. No consistent trend was seen in the influence of chlorine concentration and exposure time on disinfection efficacy. Disinfectant application mode; soil load; and surface type were frequently identified as influential factors in included studies. CONCLUSIONS: This review highlights that surface disinfection efficacy estimates are strongly influenced by each study's experimental conditions. We therefore recommend laboratory testing to be followed by field-based testing/monitoring to ensure effectiveness is achieved in situ

Prider: multiplexed primer design using linearly scaling approximation of set coverage

BackgroundDesigning oligonucleotide primers and probes is one of the key steps of various laboratory experiments such as multiplexed PCR or digital multiplexed ligation assays. When designing multiplexed primers and probes to complex, heterogeneous DNA data sets, an optimization problem can arise where the smallest number of oligonucleotides covering the largest diversity of the input dataset needs to be identified. Tools that provide this optimization in an efficient manner for large input data are currently lacking.ResultsHere we present Prider, an R package for designing primers and probes with a nearly optimal coverage for complex and large sequence sets. Prider initially prepares a full primer coverage of the input sequences, the complexity of which is subsequently reduced by removing components of high redundancy or narrow coverage. The primers from the resulting near-optimal coverage are easily accessible as data frames and their coverage across the input sequences can be visualised as heatmaps using Prider’s plotting function. Prider permits efficient design of primers to large DNA datasets by scaling linearly to increasing sequence data, regardless of the diversity of the dataset.ConclusionsPrider solves a recalcitrant problem in molecular diagnostics: how to cover a maximal sequence diversity with a minimal number of oligonucleotide primers or probes. The combination of Prider with highly scalable molecular quantification techniques will permit an unprecedented molecular screening capability with immediate applicability in fields such as clinical microbiology, epidemic virus surveillance or antimicrobial resistance surveillance.</p

Fecal Colonization With Multidrug-Resistant E. coli Among Healthy Infants in Rural Bangladesh

Third generation cephalosporins (3GC) are one of the main choices for treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria. Due to their overuse, an increasing trend of resistance to 3GC has been observed in developing countries. Here, we describe fecal colonization of 3GC-resistant (3GCr) Escherichia coli in healthy infants (1–12 months old) living in rural areas of Bangladesh. We found that stool samples of 82% of infants (n = 100) were positive for 3GCr E. coli with a mean ± standard deviation of 6.21 ± 1.32 log10 CFU/g wet weight of stool. 3GCr E. coli encompasses an average one third (33%) of the total E. coli of stool. Almost 77% (n = 63) of these 3GCr E. coli were MDR (or resistant to ≥3 classes of antibiotics). Around 90% (n = 74) of 3GCr E. coli were extended spectrum beta-lactamase (ESBL)-producing in which blaCTX–M–group–1 was the predominant (96%, n = 71) ESBL-gene followed by blaTEM (41%, n = 30) and blaOXA–1 (11%, n = 8). A significant proportion (26.5%, n = 22) of 3GCr E. coli was pathogenic, comprising two types, enteroaggregative (EAEC, n = 19) and enteropathogenic (EPEC, n = 3). Colonization of 3GCr E. coli in infant guts was not associated with demographic characteristics such as age, sex, mode of delivery, maternal and infant antibiotic use, disease morbidity, and feeding practices. The high rate of colonization of 3GCr E. coli in infants’ guts is a serious public health concern which needs immediate attention and warrants further studies to explore the cause

Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously. Here, dMLA is used for simultaneous detection of 1187 β-lactamase-encoding genes, including extended spectrum β-lactamase (ESBL) genes, in 74 bacterial isolates. We demonstrate dMLA as a light-weight and cost-efficient workflow which provides a highly scalable tool for antimicrobial resistance surveillance and is also adaptable to genetic screening applications beyond antibiotic resistance

Radiation Therapy in Addition to Gross Total Resection of Retroperitoneal Sarcoma Results in Prolonged Survival: Results from a Single Institutional Study

Purpose. Typical treatment of retroperitoneal sarcomas (RPSs) is surgery with or without radiation therapy for localized disease. With surgery alone, local failure rates are as high as 90%; this led to radiation therapy playing an important role in the treatment of RPSs. Methods. Thirty-one patients with retroperitoneal sarcoma treated with gross total resection and radiation therapy make up this retrospective analysis. Nineteen were treated preoperatively and 12 postoperatively (median dose, 59.4 Gy)—sixteen also received intraoperative radiation therapy (IORT) (median dose, 11 Gy). Patients were followed with stringent regimens, including frequent CT scans of the chest, abdomen, and pelvis. Results. With a median follow-up of 19 months (range 1–66 months), the 2-year overall survival (OS) rate is 70% (median, 52 months). The 2-year locoregional control (LRC) rate is 77% (median, 61.6 months). The 2-year distant disease free survival (DDFS) rate is 70% (median not reached). There were no differences in radiation-related acute and late toxicities among patients treated pre- versus postoperatively, whether with or without IORT. Conclusions. Compared to surgery alone, neoadjuvant or adjuvant radiation therapy offers patients with RPS an excellent chance for long-term LRC, DDS, and OS. The integration of modern treatment planning for external beam radiation therapy and IORT allows for higher doses to be delivered with acceptable toxicities

ATR inhibition facilitates targeting of leukemia dependence on convergent nucleotide biosynthetic pathways.

Leukemia cells rely on two nucleotide biosynthetic pathways, de novo and salvage, to produce dNTPs for DNA replication. Here, using metabolomic, proteomic, and phosphoproteomic approaches, we show that inhibition of the replication stress sensing kinase ataxia telangiectasia and Rad3-related protein (ATR) reduces the output of both de novo and salvage pathways by regulating the activity of their respective rate-limiting enzymes, ribonucleotide reductase (RNR) and deoxycytidine kinase (dCK), via distinct molecular mechanisms. Quantification of nucleotide biosynthesis in ATR-inhibited acute lymphoblastic leukemia (ALL) cells reveals substantial remaining de novo and salvage activities, and could not eliminate the disease in vivo. However, targeting these remaining activities with RNR and dCK inhibitors triggers lethal replication stress in vitro and long-term disease-free survival in mice with B-ALL, without detectable toxicity. Thus the functional interplay between alternative nucleotide biosynthetic routes and ATR provides therapeutic opportunities in leukemia and potentially other cancers.Leukemic cells depend on the nucleotide synthesis pathway to proliferate. Here the authors use metabolomics and proteomics to show that inhibition of ATR reduced the activity of these pathways thus providing a valuable therapeutic target in leukemia