PediCXR: An open, large-scale chest radiograph dataset for interpretation of common thoracic diseases in children.

Computer-aided diagnosis systems in adult chest radiography (CXR) have recently achieved great success thanks to the availability of large-scale, annotated datasets and the advent of high-performance supervised learning algorithms. However, the development of diagnostic models for detecting and diagnosing pediatric diseases in CXR scans is undertaken due to the lack of high-quality physician-annotated datasets. To overcome this challenge, we introduce and release PediCXR, a new pediatric CXR dataset of 9,125 studies retrospectively collected from a major pediatric hospital in Vietnam between 2020 and 2021. Each scan was manually annotated by a pediatric radiologist with more than ten years of experience. The dataset was labeled for the presence of 36 critical findings and 15 diseases. In particular, each abnormal finding was identified via a rectangle bounding box on the image. To the best of our knowledge, this is the first and largest pediatric CXR dataset containing lesion-level annotations and image-level labels for the detection of multiple findings and diseases. For algorithm development, the dataset was divided into a training set of 7,728 and a test set of 1,397. To encourage new advances in pediatric CXR interpretation using data-driven approaches, we provide a detailed description of the PediCXR data sample and make the dataset publicly available on https://physionet.org/content/vindr-pcxr/1.0.0/ .

WGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia.

Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3")-IIa, armA, aph(6)-Id and aph(3") genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains. A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3")-IIa, aph(3")-Ib, aph(6)-Id, armA and aph(3')-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.

Phenotypic and WGS-derived antimicrobial resistance profiles of clinical and non-clinical Acinetobacter baumannii isolates from Germany and Vietnam.

OBJECTIVES: This study aimed to combine in vitro phenotyping analysis and whole-genome-sequencing (WGS) to characterise the phenotype and genetic determinants associated with intrinsic resistance in 100 clinical and non-clinical Acinetobacter baumannii strains originating from Germany and Vietnam. Moreover, it aimed to assess whether powdered milk as a food source functions as a potential reservoir of antibiotic resistance and possesses similar antimicrobial resistance (AMR) genes as in clinical strains isolated from Germany. METHODS: Antimicrobial susceptibility testing was performed using the broth microdilution method and the minimum inhibitory concentration (MIC) was determined for 18 antibiotics. The WGS data from all isolates were mapped to intrinsic genes known to be associated with phenotypic AMR. RESULTS: The highest resistance frequency was observed for chloramphenicol (100%), followed by fosfomycin (96%) and cefotaxime (95%). The lowest resistant rates were observed for colistin (3%), trimethoprim/sulfamethoxazole (17%), tigecycline (19%), and amikacin (19%). Thirty-five percent of tested strains displayed resistance to at least one of the carbapenems. Resistance to fluoroquinolones, aminoglycosides, tigecycline, penicillins, trimethoprim/sulfamethoxazole, and fourth-generation cephalosporins was determined only in human strains. About one-quarter of isolates (24%) was multidrug-resistant (MDR) and all were of human origin. Among them, 16 isolates were extensively drug resistant (XDR) and 10 from those 16 isolates showed resistance to all tested antibiotics except colistin. In silico detection of intrinsic AMR genes revealed the presence of 36 ß-lactamases and 24 non-ß-lactamase resistance genes. Two colistin-resistant and 10 ertapenem-resistant strains were isolated from powdered milk produced in Germany. Thirty-eight AMR genes associated with resistance to antibiotics were found in isolates recovered from milk powder. Several resistance mechanisms towards many classes of antibiotics existed in A. baumannii including ß-lactamases, multidrug efflux pumps and aminoglycoside-modifying enzymes. CONCLUSION: The use of WGS for routine public health surveillance is a reliable method for the rapid detection of emerging AMR in A. baumannii isolates. Milk powder poses a risk to contain MDR Acinetobacter strains or resistance genes in Germany.