Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide.This study aimed to determine the genomic diversity, virulence factor genes (VFGs), and antimicrobial resistance genes (ARGs) in the APEC MTR_BAU02 strain isolated from a layer chicken using whole-genome sequencing (WGS).Paired-end (2 × 250) WGS was performed using Illumina MiSeq sequencer (Illumina, San Diego, CA) and de novo assembly was performed using SPAdes. Core genome multilocus sequence typing (cgMLST) analysis between APEC MTR_BAU02 and all of the ST1196 E. coli strains retrieved from the National Center for Biotechnology Information (NCBI) GenBank database was performed using the BacWGSTdb 2.0 server. We utilized different databases to detect ARGs, VFGs, and genomic functional features of the APEC MTR_BAU02 strain.The complete genome of APEC MTR_BAU02 consists of 94 contigs comprising 4,924,680 bp (51.1% guanine-cytosine [GC] content), including 4681 protein-coding sequences, one chromosome, and one plasmid, and was assigned to ST1196. The closest relatives of APEC MTR_BAU02 were four isolates originating from human clinical specimens (diarrhetic stool) in Bangladesh and two clinical isolates originating from chicken in India, which differed by 694 core genome multilocus sequence typing (cgMLST) alleles. One hundred and twenty-two ARGs and 92 VFGs were identified in the APEC MTR_BAU02 genome. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups and pigments, respiration, membrane transport, stress response, motility and chemotaxis, and virulence, disease, and defense.This study reports the genome sequence of a multidrug-resistant APEC strain isolated from layer birds in Bangladesh. The ARGs and VFGs, widespread in APEC MTR_BAU02, are similar to those found in human isolates, and highlight the growing threat of antimicrobial resistance in both poultry and humans. 

Genomic characteristics, virulence, and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farm in Bangladesh

With the increasing efforts to utilize information and communication technologies (ICT) in disaster management, the massive amount of heterogeneous data that is generated through ubiquitous sensors paves the way for fast and informed decisions in the case of disasters. Utilization of the big “sensed” data leads to an effective and efficient management of disaster situations so as to prevent human and economic losses. The advancement of built-in sensing technologies in smart mobile devices enables crowdsourcing of sensed data, which is known as mobile crowdsensing (MCS). This systematic literature review investigates the use of mobile crowdsensing in disaster management on the basis of the built-in sensor types in smart mobile devices, disaster management categories, and the disaster management cycle phases (i.e., mitigation, preparedness, response, and recovery activities). Additionally, this work seeks to unveil the frameworks or models that can potentially guide disaster management authorities towards integrating crowd-sensed data with their existing decision-support systems. The vast majority of the existing studies are conceptual as they highlight a challenge in experimental testing of the disaster management solutions in real-life settings, and there is little emphasis on the use cases of crowdsensing through smartphone sensors in disaster incidents. In light of a thorough review, we provide and discuss future directions and open issues for mobile crowdsensing-aided disaster management.

/pdf/use-of-mobile-crowdsensing-in-disaster-management-a-3akfjstk.pdf

Use of Mobile Crowdsensing in Disaster Management: A Systematic Review, Challenges, and Open Issues

COVID-19 was officially declared a global pandemic disease on 11 March 2020, with severe implications for healthcare systems, economic activity, and human life worldwide. Fast and sensitive amplification of the severe acute respiratory syndrome virus 2 (SARS-CoV-2) nucleic acids is critical for controlling the spread of this disease. Here, a real-time reverse transcription recombinase-aided amplification (RT-RAA) assay, targeting conserved positions in the nucleocapsid protein gene (N gene) of SARS-CoV-2, was successfully established for SARS-CoV-2. The assay was specific to SARS-CoV-2, and there was no cross-reaction with other important viruses. The sensitivity of the real-time RT-RAA assay was 142 copies per reaction at 95% probability. Furthermore, 100% concordance between the real-time RT-RAA and RT-qPCR assays was achieved after testing 72 clinical specimens. Further linear regression analysis indicated a significant correlation between the real-time RT-RAA and RT-qPCR assays with an R2 value of 0.8149 (p < 0.0001). In addition, the amplicons of the real-time RT-RAA assay could be directly visualized by a portable blue light instrument, making it suitable for the rapid amplification of SARS-CoV-2 in resource-limited settings. Therefore, the real-time RT-RAA method allows the specific, sensitive, simple, rapid, and reliable detection of SARS-CoV-2.

/pdf/real-time-reverse-transcription-recombinase-aided-26ks3b5p.pdf

Real-Time Reverse Transcription Recombinase-Aided Amplification Assay for Rapid Amplification of the N Gene of SARS-CoV-2

Introduction The global emergence of plasmid-mediated colistin resistance is threatening the efficacy of colistin as one of the last treatment options against multi-drug resistant Gram-negative bacteria. To date, ten mcr-genes (mcr-1 to mcr-10) were reported. While mcr-1 has disseminated globally, the occurrence of mcr-2 was reported scarcely. Methods and results We determined the occurrence of mcr-1 and mcr-2 genes among Escherichia coli isolates from swine and performed detailed genomic characterization of mcr-2-positive strains. In the years 2010-2017, 7,614 porcine E. coli isolates were obtained from fecal swine samples in Europe and isolates carrying at least one of the virulence associated genes predicting Shiga toxin producing E. coli (STEC), enterotoxigenic E. coli (ETEC) or enteropathogenic E. coli (EPEC) were stored. 793 (10.4%) of these isolates carried the mcr-1 gene. Of 1,477 additional E. coli isolates obtained from sheep blood agar containing 4 mg/L colistin between 2018 and 2020, 36 (2.4%) isolates were mcr-1-positive. In contrast to mcr-1, the mcr-2 gene occurred at a very low frequency (0.13%) among the overall 9,091 isolates. Most mcr-2-positive isolates originated from Belgium (n = 9), one from Spain and two from Germany. They were obtained from six different farms and revealed multilocus sequence types ST10, ST29, ST93, ST100, ST3057 and ST5786. While the originally described mcr-2.1 was predominant, we also detected a new mcr-2 variant in two isolates from Belgium, which was termed mcr-2.8. MCR-2 isolates were mostly classified as ETEC or ETEC-like, while one isolate from Spain represented an atypical enteropathogenic E. coli (aEPEC; eae+). The ST29-aEPEC isolate carried mcr-2 on the chromosome. Another eight isolates carried their mcr-2 gene on IncX4 plasmids that resembled the pKP37-BE MCR-2 plasmid originally described in Belgium in 2015. Three ST100 E. coli isolates from a single farm in Belgium carried the mcr-2.1 gene on a 47-kb self-transmissible IncP type plasmid of a new IncP-1 clade. Discussion This is the first report of mcr-2 genes in E. coli isolates from Germany. The detection of a new mcr-2 allele and a novel plasmid backbone suggests the presence of so far undetected mcr-2 variants and mobilizable vehicles.

https://www.frontiersin.org/articles/10.3389/fmicb.2022.1076315/pdf

Occurrence of mcr-1 and mcr-2 colistin resistance genes in porcine Escherichia coli isolates (2010–2020) and genomic characterization of mcr-2-positive E. coli

In this paper, an innovative strengthening system for masonry walls made of externally bonded Fabric-Reinforced Cementitious Matrix (FRCM) is presented. Due to the good mechanical properties and the compatibility with the architectural heritage, the FRCM is an adequate alternative to the use of Fiber-Reinforced Polymer (FRP) composites and other traditional techniques. The proposed system is applied to the strengthening of a classical architectural typology in cultural heritage architecture, which is the “in falso” masonry: a load-bearing wall built over a masonry vault, and hence without a direct load path to the ground. A research program, characterized by an experimental campaign, has been started in order to devise and verify an optimal strengthening system that assures for the masonry wall a structural behavior similar to a “wall beam”, so to prevent progressive collapses when the underlying masonry vault loses its carrier function. In particular, rather than the canonical application, consisting in widespread application to the whole surface of the masonry wall, an innovative intervention made of “Green Tape” of composites has been designed and verified by a specifically designed experimental set-up. The main objective of the research is to propose a reinforcement strategy not detrimental to unmovable artistic assets and tied to the safety and robustness of the architectural heritage.

/pdf/natural-frcm-and-heritage-buildings-experimental-approach-to-26uw6gb9.pdf

Natural FRCM and Heritage Buildings: Experimental Approach to Innovative Interventions on “Wall Beams”

Structural health monitoring (SHM) is of great significance for post-earthquake damage assessment. Smartphone-based monitoring techniques provide the possibility to perform crowdsensing for all buildings in urban regions after an earthquake. However, this idea still faces many difficulties and is hard to realize. Fortunately, the development of game engines provides the opportunity for simulating this kind of experiment. The main objective of this study was to use Unity to simulate the whole process when a city is struck by an earthquake that consists of one main shock and one aftershock. During the emergency response, the citizens and the “city brain” in Unity, named Ground Eye, cooperate to finish the task of taking refuge and collecting data for regional damage assessment. Some basic assumptions were made first. Then the city model was established in Unity, and the behaviors of the citizens were directed by the behavior tree artificial intelligence (AI). OpenSees was utilized to determine the monitoring demand and simulate the monitoring results. A GUI was built to exhibit the data during the whole process. The results show that the evacuation and monitoring plan is feasible. The simulation framework presented in this paper can be used in other SHM application scenarios.

/pdf/simulation-of-smartphone-based-public-participation-in-2l2c0jrr.pdf

Simulation of Smartphone-Based Public Participation in Earthquake Structural Response Emergency Monitoring Using a Virtual Experiment and AI

A CRISPR-based nucleic acid detection method for severe fever with thrombocytopenia syndrome virus.

https://doi.org/10.1016/j.virusres.2022.199038

Murine models of neonatal susceptibility to a clinical strain of enterovirus A71

A cluster of Chlamydia psittaci (C. psittaci) cases was reported in Zhejiang Province, China, 2019. This study evaluates the extent of the outbreak and determines the source of infection. Real‐time PCR and sequencing of the ompA gene of C. psittaci were performed to identify the cases, the domesticated poultry and close contacts. The index patient was a 76‐year‐old woman with chronic vertigo, and Case 2 was a 64‐year‐old female farmer with herpes zoster. Both women bought psittaci‐infected chickens or ducks from the same mobile street vendor and raised them for 10 days and 23 days before fever onset. There were no direct contact between the two women. C. psittaci test was positive for the two patients, one sick chicken, three healthy ducks and the vendor's chicken cage. Phylogenetic analysis showed that all seven C. psittaci positive samples carried identical ompA genotype A of C. psittaci. Of all of the patients' 148 close contacts, none tested positive for C. psittaci, or developed acute respiratory symptoms. Both patients were discharged after a 4‐week hospital stay. In conclusion, the source of this cluster was the poultry infected with C. psittaci, which occasionally cause infections in farmers, but inter‐human transmission seems unlikely.

A cluster of two psittacosis cases among women farmers exposed to Chlamydia psittaci‐infected domestic poultry in Zhejiang Province, China

Correction: Isolation, genetic, and biological characterization of human adenovirus type 55 positive isolates from Wuhan, China

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