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Background In 2012, we identified the dissemination of methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)45 strain in 14 nursing homes in Taiwan and foreign nurse workers, a significant risk factor for MRSA carriage. We conducted this study to understand MRSA carriage and molecular characteristics among foreign workers recruited from Southeastern Asian countries. Methods A cross-sectional study involving a total of 1935 foreign workers—929 (arrival group) and 1006 (staying group)—from Vietnam (n = 843), Indonesia (n = 780), the Philippines (n = 239), and Thailand (n = 70) were conveniently recruited during upon-arrival and regular health examination in a regional hospital. A nasal swab was obtained from each participant for detection of MRSA. Results Overall, MRSA carriage rate was 2.72%, with 2.26% for arrival group and 3.18% for staying group, and 4.74% for Vietnamese, 1.28% for Indonesians, 1.26% for Filipino, and none for Thai workers. Pulsotype AK/ST45 (57%) and pulsotype AX/ST188 (14%) were the top 2 dominant clones for the arrival group, whereas pulsotype D/ST59 (41%) (an endemic community clone in Taiwan) and pulsotype AK/ST45 (19%) were predominant for the staying group. A significant decrease of pulsotype AK/ST45 from 57% to 19% (P = .007) and increase of pulsotype D/ST59 from 4.8% to 41% (P = .004) were found between the arrival and the staying groups. Conclusions Approximately 3% of foreign workers recruited from Southeastern Asian countries to Taiwan were colonized with MRSA, including the ST45 strain. However, the MRSA isolates from workers staying in Taiwan were mostly a locally endemic clone and genetically different from those identified from workers on arrival.

Background In 2012, we identified the dissemination of methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)45 strain in 14 nursing homes in Taiwan and foreign nurse workers, a significant risk factor for MRSA carriage. We conducted this study to understand MRSA carriage and molecular characteristics among foreign workers recruited from Southeastern Asian countries. Methods A cross-sectional study involving a total of 1935 foreign workers—929 (arrival group) and 1006 (staying group)—from Vietnam (n = 843), Indonesia (n = 780), the Philippines (n = 239), and Thailand (n = 70) were conveniently recruited during upon-arrival and regular health examination in a regional hospital. A nasal swab was obtained from each participant for detection of MRSA. Results Overall, MRSA carriage rate was 2.72%, with 2.26% for arrival group and 3.18% for staying group, and 4.74% for Vietnamese, 1.28% for Indonesians, 1.26% for Filipino, and none for Thai workers. Pulsotype AK/ST45 (57%) and pulsotype AX/ST188 (14%) were the top 2 dominant clones for the arrival group, whereas pulsotype D/ST59 (41%) (an endemic community clone in Taiwan) and pulsotype AK/ST45 (19%) were predominant for the staying group. A significant decrease of pulsotype AK/ST45 from 57% to 19% (P = .007) and increase of pulsotype D/ST59 from 4.8% to 41% (P = .004) were found between the arrival and the staying groups. Conclusions Approximately 3% of foreign workers recruited from Southeastern Asian countries to Taiwan were colonized with MRSA, including the ST45 strain. However, the MRSA isolates from workers staying in Taiwan were mostly a locally endemic clone and genetically different from those identified from workers on arrival.

Variation in the genome of Pseudomonas aeruginosa, an important pathogen, can have dramatic impacts on the bacterium's ability to cause disease. We therefore asked whether it was possible to predict the virulence of P. aeruginosa isolates based on their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinical P. aeruginosa isolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithm's performance, suggesting instead that virulence predictions are derived from a diffuse genomic signature. These results were validated with an independent test set of 25 P. aeruginosa isolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single-nucleotide variants and whole-genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity in P. aeruginosa and highlight the potential of this approach for predicting patient outcomes. IMPORTANCE Pseudomonas aeruginosa is a clinically important Gram-negative opportunistic pathogen. P. aeruginosa shows a large degree of genomic heterogeneity both through variation in sequences found throughout the species (core genome) and through the presence or absence of sequences in different isolates (accessory genome). P. aeruginosa isolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level of P. aeruginose isolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genomes are predictive of virulence. This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence., This work was supported by the National Institute of General Medical Sciences (grants T32 GM008061 and T32 GM008152 [N.B.P.]), by the American Cancer Society (grant MRSG-13-220-01-MPC [E.A.O.]), and by the National Institute of Allergy and Infectious Diseases (grants R01 AI118257, R21 129167, K24 AI104831, and U19 AI135964 [A.R.H.]). J.J.D. and M.N. are supported by the United States Defense Advanced Research Projects Agency Friend or Foe program iSENTRY award (contract HR0011937807 [J.J.D.]) and by the U.S. National Institute of Allergy and Infectious Diseases Bacterial and Viral Bioinformatics Resource Center award (contract 75N93019C00076 [principal investigator Rick Stevens]). A.O. is supported by Instituto de Salud Carlos III, Subdireccion General de Redes y Centros de Investigacion Cooperativa, Ministerio de Economia y Competitividad, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016/0004), cofinanced by the European Development Regional Fund A way to achieve Europe and operative program Intelligent Growth 2014-2020.; This research was supported in part through the computational resources and staff contributions provided by the Genomics Compute Cluster, which is jointly supported by the Feinberg School of Medicine, the Center for Genetic Medicine, and Feinberg's Department of Biochemistry and Molecular Genetics, the Office of the Provost, the Office for Research, and Northwestern Information Technology. The Genomics Compute Cluster is part of Quest, Northwestern University's high-performance computing facility, with the purpose of advancing research in genomics. We acknowledge the University of Maryland School of Medicine Institute for Genome Sciences for performance of PacBio whole-genome sequencing.

FliA is known to be a sigma factor that regulates bacterial flagella gene expression. Accumulating evidence suggests that FliA is involved in bacterial behavior other than motility. To elucidate the contribution of FliA to Pseudomonas aeruginosa pathophysiology, we analyzed the biological properties and gene expression profiles of a ΔfliA mutant. Transcriptome analysis results demonstrated that the expression levels of flagella biogenesis genes decreased dramatically in the mutant; consequently, the Δ fliA mutant failed to synthesize flagella and exhibited reduced motility. The ΔfliA mutant displayed stronger hemolytic and caseinolytic activities, as well as pyocyanin production. The expression of type 6 secretion system-II genes and interbacterial competition activity was decreased in the ΔfliA mutant. Direct evidence of fliA participation in virulence was obtained from analysis of hypervirulent strain B136-33. Adhesion to and cytotoxicity toward mammalian cells and penetration through cell layers were noted; furthermore, the colonization ability of the fliA::Tn5 mutant in the intestines of laboratory mice was compromised. Notably, the fliA-overexpressing strain displayed phenotypes similar to that of the fliA -defective strain, indicating that optimal FliA levels are critical to bacterial physiology . Our findings indicate that FliA plays diverse roles in P. aeruginosa , not only in flagella biosynthesis, but also in pathophysiology.

Objectives Mycoplasma pneumoniae is currently the most commonly detected bacterial cause of childhood community-acquired pneumonia in several countries. Of note, clonal expansion of macrolide-resistant ST3 occurred in Japan and South Korea. An alarming surge in macrolide resistance complicates the treatment of pneumonia. We aimed to evaluate the clinical manifestation and clonal relatedness of M. pneumoniae circulating among children in Taiwan. Methods We prospectively enrolled 626 children with radiologically confirmed pneumonia between 2017 and 2019. An M. pneumoniae infection was suspected on clinical grounds, and tested by real-time PCR and oropharyngeal swab cultures. We used multilocus sequence typing and whole-genome sequencing to characterize the genetic features of M. pneumoniae. Results A total of 226 children with M. pneumoniae pneumonia were enrolled. Macrolide resistance was found in 77% (174/226) of patients. Multi-locus sequence typing revealed that ST3 (n = 93) and its single-locus variant ST17 (n = 84) were the predominant clones among macrolide-resistant strains. ST17 presented clinical characteristics comparable to its ancestor ST3. On multivariate analysis, macrolide resistance (OR 3.5; 95% CI 1.4–8.5; p 0.007) was independently associated with fever >72 hours after macrolide treatment. By whole-genome sequencing, prediction analysis of recombination sites revealed one recombination site in ST3 and ST17 compared with M29 (a macrolide-sensitive ST3 strain isolated from China in 2005) containing cytadhesin MgpC-like protein, RepMP4 and RepMP5. ST17 had another recombination site containing an adhesin and RepMP2/3. Conclusions In addition to macrolide resistance, ST3 and its ST17 variant might evolve through recombination between repetitive sequences and non-P1 cytadhesins for persistent circulation in Taiwan.

Objectives Clostridium innocuum can cause extraintestinal infection in patients with underlying diseases. The role of C. innocuum in antibiotic-associated diarrhoea (AAD) remains unknown. Methods Clinical information of 103 patients from whom C. innocuum was isolated was reviewed. We carried out cellular and animal experiments to examine the pathogenic potential of C. innocuum in AAD. Results Eighty-eight per cent (91/103) of the 103 patients received antibiotics within 2 weeks of diarrhoea onset. Patients were further classified into two groups, severe colitis and diarrhoea, according to clinical severity level. The mortality rate was 13.6% (14/103) among the patients from whom C. innocuum was isolated. The lowest concentrations at which 90% of the isolates were inhibited for metronidazole and vancomycin were 0.5 and 16 mg/L, respectively. All isolates tested were susceptible to metronidazole but resistant to vancomycin. Nineteen randomly selected isolates (ten from severe colitis group, nine from diarrhoea group) were subjected to further in vitro cellular examinations. The level of cytotoxicity to Vero cells was significantly higher in isolates from the severe colitis group at both 24 and 48 hours after inoculation (24 and 48 hours, p 0.042 and 0.033, respectively). We observed apoptotic changes that subsequently led to cell death in C. innocuum –infected Vero cells. Tissue damages, necrotic changes and oedema were observed in the mouse ileal loop infected by C. innocuum. Conclusions Vancomycin-resistant C. innocuum may play a potential role as a causative agent of AAD. The clinical manifestations of AAD caused by C. innocuum were diarrhoea or severe colitis, including pseudomembranous colitis.

Background Shanghai fever, a community-acquired enteric illness associated with sepsis caused by Pseudomonas aeruginosa, was first described in 1918. The understanding of Shanghai fever is incomplete. Objective To delineate the clinical features and to examine the host and microbial factors associated with Shanghai fever. Methods We prospectively enrolled 27 consecutive previously healthy children with community-acquired P aeruginosa enteritis and sepsis between July 2003 and June 2012. An immunological investigation, including measurement of serum immunoglobulin levels and lymphocyte subpopulations, was performed. The clonal relationship of bacterial isolates was determined by multilocus sequence typing (MLST) and the virulence of isolates was measured using cellular and animal models. Results The median age of the patients was 7 months; 24 (89%) were aged

Kawasaki disease (KD) is rare in infantsor =3 months of age. This study analyzed the features of KD in 25 infantsor =3 months of age treated from February 1994 to December 2004.Basic characteristics, clinical, laboratory, echocardiographic, therapeutic, and follow-up data of the infants were obtained from chart records.There were 19 male and 6 female infants in this cohort. The frequency of the 5 principal clinical features was as follows: changes in lips and oral cavity, 84%; bilateral bulbar conjunctival injection without exudates, 80%; polymorphous exanthem, 68%; cervical lymphadenopathy, 28%; and changes in extremities, 24%. Six infants (24%) fulfilled criteria for KD including fever which persists for 5 or more days with at least 4 of the principal clinical criteria, and the remaining infants were classified as having incomplete KD (all of whom showed coronary involvement). Coronary artery dilatation was found in 20 infants (80%). One infant developed a medium-size aneurysm (5.2 mm), while the others had only coronary arterial ectasia or small aneurysms. Coronary artery aneurysms regressed within 1-year follow-up in all but one infant. No fatal or recurrent case was observed during the study period.Infantsor =3 months of age with KD usually presented with incomplete clinical features. A high proportion of coronary artery involvement was observed in this series. Echocardiography should be considered in very young infants with unexplained prolonged fever who do not present all of the principal clinical features of KD.

1Division of Pediatric Gastroenterology, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan 2Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan 3St Paul’s Hospital, Taoyuan, Taiwan 4Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Children’s Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan