Table_1.xlsx

<p>Mycobacterium avium subsp. hominissuis (MAH) is an important zoonotic pathogen with raising global health concerns. In humans, MAH is one of the most widespread non-tuberculous mycobacterial species responsible for lung disease. In animals, MAH is frequently isolated from pigs; however, it is also an opportunistic pathogen for other mammals including cattle. To elucidate the genetic diversity of MAH in cattle, a molecular characterization of isolates (n = 26) derived from lymph nodes was performed. Fourteen isolates originated from slaughtered cattle with visible altered lymph nodes at meat inspection, whereas 12 isolates were from lymph nodes without any gross pathological changes of healthy slaughtered cattle. Variable number of tandem repeat (VNTR) analysis was performed at 20 loci to examine genetic differences of isolates and to compare to previously reported VNTR data of human isolates from different countries. Genetic elements IS901, IS1245, IS1311, LSPA17, ITS1 sequevar, and hsp65 code were determined. Interestingly, two bovine MAH isolates harbored ISMav6 and hsp65 code 15, which so far has only been observed in human isolates. We supposed that VNTR data of Swiss samples would show clustering with European samples. Minimum spanning tree and unweighted pair group method using arithmetic averages analyses based on the VNTR data indicated a specific cluster of MAH isolates obtained from lymph nodes without any gross pathological changes of healthy slaughtered cattle. Comparing Swiss isolates with isolates from different other countries, no geographical clustering was observed; however, four Swiss isolates had an identical VNTR profile as human isolates from the Netherlands, the United States, and Japan. These findings indicate a possible public health issue.</p

Characteristics and antimicrobial susceptibility profiles of ESBL-producing <i>Enterobacteriaceae</i> isolated from cattle younger than 2

<p><b>years.</b> Symbols: black square, positive result or resistant to a specific antimicrobial agent; white square, negative result or susceptible to a specific antimicrobial. Abbreviations: AM, ampicillin (resistant ≤13 mm); AMC, amoxicillin-clavulanic acid (resistant ≤13 mm); CF, cephalothin (resistant ≤14 mm); CXM, cefuroxime (resistant ≤14 mm); FOX, cefoxitin (resistant ≤14 mm); CPD, cefpodoxime (resistant ≤17 mm); CTX, cefotaxime (resistant ≤14 mm); CAZ, ceftazidime (resistant ≤14 mm); FEP, cefepime (resistant ≤14 mm); GM, gentamicin (resistant ≤10 mm); S, streptomycin (resistant ≤11 mm); SXT, trimethoprim-sulfamethoxazole (resistant ≤10 mm); TE, tetracycline (resistant ≤11 mm); NA, nalidixic acid (resistant ≤13 mm); CIP, ciprofloxacin (resistant ≤15 mm); C, chloramphenicol (resistant ≤12 mm). Discrimination between “susceptible” and “resistant” was strictly according to CLSI interpretive criteria. It should be noted, however, that for clinical and therapeutic purposes, ESBL producers should generally be reported resistant to cephalosporins of all 4 generations and monobactams.</p

Table_1_Strain diversity in Mycobacterium avium subsp. paratuberculosis-positive bovine fecal samples collected in Switzerland.XLSX

Paratuberculosis or Johne’s disease is a chronic intestinal disease in domestic and wild ruminants. It affects global dairy economy and is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The objective of this study was to analyze strain diversity in MAP-positive fecal samples by using a particular single nucleotide polymorphism (SNP) distinguishing between cattle (C-) and sheep (S-) type MAP and analysis of SNPs within gyrA and gyrB genes differentiating between Types I, II, and III. Moreover, mycobacterial interspersed repetitive unit and variable-number tandem repeat (MIRU-VNTR) analysis using eight established loci was performed. A total of 90 fecal samples from diseased animals presenting diarrhea and/or weight loss, originating from 59 bovine herds across 16 cantons of Switzerland were screened by PCR for the MAP-specific F57 and IS900 genes and were further subtyped. 96.7% and 3.3% of the samples contained C- and S-type MAP, respectively. Ten INRA Nouzilly MIRU-VNTR (INMV) profiles, with a discriminatory index of 0.802, calculated based on 65 epidemiological independent genotypes, were detected: INMV 1 (33.8%), INMV 2 (23.1%), INMV 6 (16.9%), INMV 9 (9.2%), INMV 116 (4.6%), INMV 3 (3.1%), INMV 5 (3.1%) and INMV 72 (1.5%), including two novel INMV profiles, namely INMV 253 (3.1%; S-type III) and INMV 252 (1.5%; C-type). INMV 1, INMV 2, and INMV 6 comprised almost 75% of the F57- and IS900-positive samples. Typing data from 11 herds suggest that there are some herds with intra-herd diversity of genotypes. The results of this study indicate a heterogeneity of MAP in Switzerland.</p

Description of risk factors studied in univariate and multivariate logistic regression models.

<p>Description of risk factors studied in univariate and multivariate logistic regression models.</p

Prevalences of animals with ESBL positive isolates.

*<p>95% confidence interval with Yates' continuity correction.</p

Quinolone resistance, amino acid substitutions in the QRDR of GyrA, ParC and ParE proteins in terms of amino acid positions and PMQR determinants in extended-spectrum β-lactamase (ESBL) producing <i>Escherichia coli</i> isolated from rivers and lakes in Switzerland.

a<p>) see Zurfluh et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095864#pone.0095864-Zurfluh1" target="_blank">[10]</a> for comparison.</p><p>AM, ampicillin; AMC, amoxicillin-clavulanic acid; CF, cephalothin; CTX, cefotaxime; CIP, ciprofloxacin; GM, gentamicin; TE, tetracycline; S, streptomycin; C, chloramphenicol; K, kanamycin; NA, nalidixic acid; SMZ, sulfamethoxazole; TMP, trimethoprim.</p><p>QRDR: quinolone resistance-determining regions; PMQR: plasmid-mediated quinolone resistance mechanisms.</p

MIC values of nalidixic acid in the presence and absence of Phe-Arg-β-naphthylamide in selected <i>E. coli</i> isolates.

<p>MIC values of nalidixic acid in the presence and absence of Phe-Arg-β-naphthylamide in selected <i>E. coli</i> isolates.</p

Animal level risk factors for ESBL shedding.

<p>Logistic regression model.</p

Farm level risk factors for ESBL shedding.

<p>Multivariate logistic regression model.</p

Plasmid-mediated quinolone resistance mechanisms, replicon types of transferred plasmids and quinolone resistance levels of the transconjugants of selected <i>E. coli</i> isolates.

<p><i>E. coli</i> HK225 Strep^RRif^R, recipient strain resistant to streptomycin and rifamycin.</p><p>TC_OW54E2, transconjugant receiving the plasmid from the donor strain OW54E2.</p