Distribution and combinations of β-lactamase genes in 106 <i>E</i>. <i>coli</i> identified from 47 German pig farms.

<p>Distribution and combinations of β-lactamase genes in 106 <i>E</i>. <i>coli</i> identified from 47 German pig farms.</p

Antibiotic susceptibility data of 106 <i>E</i>. <i>coli</i> isolates from 47 German pig farms.

<p>Antibiotic susceptibility data of 106 <i>E</i>. <i>coli</i> isolates from 47 German pig farms.</p

Antibiotic susceptibility data of 106 <i>E</i>. <i>coli</i> isolates from 47 German pig farms.

<p>Antibiotic susceptibility data of 106 <i>E</i>. <i>coli</i> isolates from 47 German pig farms.</p

DataSheet1.xlsx

<p>Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.</p

Demographic characteristics of the subjects.

*<p>Not known.</p

Distribution and adjusted odds ratios^a,b for nasopharyngeal bacterial colonization, co-occurrence with each of the other bacteria, respiratory viruses and risk factors.

<p>Abbreviations: aOR, adjusted odds ratio; CI, confidence interval; NA, not applicable (i.e., not included in the model for that particular bacterial pathogen), RSV, respiratory syncytial virus.</p>a<p>Adjusted for age and all variables with a P value of <0.1 in univariate analysis.</p>b<p>Statistically significant associations are shown in bold.</p

Distribution and adjusted odds ratios^a,b for nasopharyngeal presence of the most common viruses, co-occurrence with each of the other respiratory viruses, bacteria and risk factors.

<p>Abbreviations: aOR, adjusted odds ratio; CI, confidence interval; NA, not applicable (i.e., not included in the model for that particular virus or pooled group of viruses), RSV, respiratory syncytial virus.</p>a<p>Adjusted for age and all variables with a P value of <0.1 in univariate analysis.</p>b<p>Statistically significant associations are shown in bold.</p

Characteristics of the children, nasopharyngeal bacterial colonization and viral detection rates.

<p>Abbreviations: SD, standard deviation; NA, not applicable; PCV-7, 7-valent pneumococcal conjugate vaccine; URTI, upper respiratory tract infection.</p>a<p>Defined as more than 4 hours per week with at least one child from another family (yes/no).</p>b<p>Defined as use of an antibiotic, orally or intravenously administered with start date within 2 months before sampling date (yes/no). Of those, the prescribed antibiotic was amoxicillin (n = 69), penicillin (n = 1), amoxicillin/clavulanic acid (n = 3), a macrolide (n = 14; claritromycin (n = 8), azitromycin (n = 5), erythromycin (n = 1), a cephalosporin (n = 1, unknown type), and 3 unknowns.</p>c<p>Parent-reported presence of mild symptoms of an upper respiratory tract infection (eg, a runny nose) at the time of sampling (yes/no).</p>d<p>Presence of enteroviruses and human parechovirus was determined in a subgroup of samples (N = 831) due to insufficient amounts of remaining nasopharyngeal swab material or nucleic acids to run these tests. Missing values were imputed by the single imputation procedure in multivariate analysis models in which these viruses were included to retain statistical power.</p

HA1 antigens used for the microarray.

<p>HA1 antigens used for the microarray.</p

Graphical representation of interaction patterns.

<p>Visualization of the partial correlations between bacteria and viruses (A) and epidemiologic drivers (risk factors) of those interactions (B). The patterns depicted here result from partial correlation network analysis and are visualized by Cytoscape. Bacteria are shown in blue, respiratory viruses in orange and risk factors in grey boxes. The solid lines represent associations with a p-value less than 0.01, the dashed lines represent associations with a p-value between 0.01 and 0.05. Green lines indicate positively correlated variables; red lines indicate negative correlations. The thickness of the line indicates the magnitude of the correlation. Abbreviations: SP, <i>S. pneumoniae</i>; HI, <i>H. influenzae</i>; MC, <i>M. catarrhalis</i>; SA, <i>S. aureus</i>; HRV, human rhinovirus, EV, enterovirus; HBoV, human bocavirus; WUPyV, WU polyomavirus; HCoV, human coronavirus; PIV, parainfluenza virus; HAdV, human adenovirus; IV, influenza virus; HPeV, human parechovirus; RSV, respiratory syncytial virus; AB, antibiotic use within 2 months before sampling; ‘crowding’ was entered into the model as a variable combining the presence of siblings (yes/no) and day care attendance (yes/no); 0 = no siblings and no day care attendance, 1 = siblings present, but not attending day care, or vice versa, and 2 = siblings present and attending day care.</p