Minimum depth, mean depth or something in between?

Reliable information about the seafloor and river-bed bathymetry is of high interest for a large number of applications. A Multi-Beam echo sounder (MBES) system is able to produce high-resolution bathymetry data at relatively small cost. These measurements, providing a depth for each beam and every ping, are processed to obtain a more ordered structure, such as a grid. Most approaches for assigning a depth to the centre of a cell (in a grid) use the shallowest or the mean depth in each cell. However, while the grid derived from the mean depth might be too deep compared to the shallowest depth, using the shallowest depth approach can result in an artificially shallow grid, affected by outliers. This paper introduces a number of alternatives to the current methods by combining the mean depth with statistical properties derived from the point cloud of the MBES data. In addition, the possibility of assigning a depth based on the regression coefficients of each cell is considered. The methods introduced have been tested on data acquired in different survey areas. The resulting grids have been compared to their shallowest and mean counterparts to obtain a better understanding of their advantages and limitations.La información fidedigna sobre la batimetría del fondo marino y del fondo fluvial es de gran interés para un gran número de aplicaciones. Un sistema de ecosonda multihaz (MBES) puede producir datos de batimetría de alta resolución a un coste relativamente pequeño. Estas mediciones, que proporcionan una profundidad para cada haz y cada pulso, son procesadas para obtener una estructura más ordenada, como una retícula. La mayoría de los enfoques para atribuir una profundidad al centro de una celda (en una retícula) utilizan la profundidad menos profunda o la profundidad media en cada celda. Sin embargo, mientras que la retícula derivada de la profundidad media podría ser demasiado profunda comparada con la profundidad menor, el uso del enfoque de la profundidad menor puede resultar en una retícula artificialmente poco profunda, afectada por valores anómalos. Este artículo introduce un número de alternativas a los métodos actuales mediante la combinación de la profundidad media con propiedades estadísticas derivadas del punto de la nube de los datos MBES. Además, se considera la posibilidad de atribuir una profundidad basada en los coeficientes de regresión de cada celda. Los métodos introducidos han sido probados en datos adquiridos en diferentes áreas de levantamien-tos. Las retículas resultantes han sido comparadas a sus contrapartidas menos profundas y medias para lograr una mayor comprensión de sus ventajas y limitaciones.Des informations fiables sur la bathymétrie des fonds marins et des lits fluviaux présentent un grand intérêt pour de nombreuses applications. Les systèmes de sondeurs acoustiques multifaisceaux (SMF) sont à même de produire des données bathymétriques à haute résolution à un coût relativement faible. Ces mesurages, qui fournissent une profondeur pour chaque faisceau et pour chaque ping, sont traités afin d’obtenir une structure plus ordonnée, une grille par exemple. La plupart des approches permettant d’attribuer une profondeur au centre d’une cellule (dans une grille) utilisent la profondeur la plus petite ou la profondeur moyenne au sein de chaque cellule. Néanmoins, si la grille dérivée de la profondeur moyenne peut être trop profonde par comparaison à la profondeur minimale, l’utilisation de l’approche de la profondeur la plus petite peut aboutir à une grille artificielle-ment peu profonde, affectée par des valeurs anormales. Cet article présente plusieurs alternatives aux méthodes actuelles en combinant la profondeur moyenne avec des propriétés statistiques dérivées du nuage de points des données issues de SMF. En outre, la possibilité d’attribuer une profondeur basée sur les coefficients de régression de chaque cellule est envisagée. Les méthodes présentées ont été testées sur des données acquises dans différentes zones hydrographiées. Les grilles qui en ont résulté ont été comparées à leurs équivalents en eaux peu profondes et de profondeur moyenne afin de parvenir à une meilleure compréhension de leurs avantages et de leurs limites

Salmonella enterica serotype Virchow associated with human infections in Switzerland: 2004-2009

BACKGROUND: Salmonellosis is one of the most important foodborne diseases and a major threat to public health. Salmonella serotype Virchow ranks among the top five serovars in Europe. METHOD: A total of 153 strains isolated from different patients from 2004 through 2009 in Switzerland were further characterized by (i) assessing phenotypic antibiotic resistance profiles using the disk diffusion method and (ii) by genotyping using pulsed-field gel electrophoresis (PFGE) after macrorestriction with XbaI in order to evaluate strain relationship. RESULTS: The relative frequency of S. Virchow among other Salmonella serovars varied between 4th to 8th rank. The annual incidence ranged from 0.45/100'000 in 2004 to 0.40/100'000 in 2009. A total of 48 strains (32%) were resistant to one to 3 antimicrobials, 54 strains (36%) displayed resistance patterns to more than three antibiotics. No trend was identifiable over the years 2004 to 2009. We found a high prevalence (62%) of nalidixic acid resistant strains, suggesting an equally high rate of decreased fluoroqionolone susceptibility, whereas intermediate resistance to ciprofloxacin was negligible. Two strains were extended spectrum β-lactamase (ESBL) producers. Analysis of PFGE patterns uncovered a predominant cluster (similarity coefficient above 80%) consisting of 104 of the 153 strains. CONCLUSION: The worldwide increase of antibiotic resistances in Salmonella is an emerging public health problem. For Switzerland, no clear trend is identifiable over the years 2004 to 2009 for S. Virchow. Antimicrobial susceptibility and resistance profiles varied considerably within this period. Nevertheless, the situation in Switzerland coincided with findings in other European countries. Genotyping results of this strain collection revealed no evidence for an undetected outbreak within this time period

Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages

Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids

Enterobacteriaceae rsistant to third-generation cephalosporins and quinolones in fresh culinary herbs imported from Southeast Asia

Since multidrug resistant bacteria are frequently reported from Southeast Asia, our study focused on the occurrence of ESBL-producing Enterobacteriaceae in fresh imported herbs from Thailand, Vietnam and Malaysia. Samples were collected from fresh culinary herbs imported from Southeast Asia in which ESBL-suspected isolates were obtained by selective culturing. Analysis included identification by MALDI-TOF mass spectrometry, susceptibility testing, XbaI-PFGE, microarray, PCR and sequencing of specific ESBL genes, PCR based replicon typing (PBRT) of plasmids and Southern blot hybridization. In addition, the quinolone resistance genotype was characterized by screening for plasmid mediated quinolone resistance (PMQR) genes and mutations in the quinolone resistance determining region (QRDR) of gyrA and parC. The study encompassed fifty samples of ten batches of culinary herbs (5 samples per batch) comprising nine different herb variants. The herbs originated from Thailand (Water morning glory, Acacia and Betel leaf), Vietnam (Parsley, Asian pennywort, Houttuynia leaf and Mint) and Malaysia (Holy basil and Parsley). By selective culturing 21 cefotaxime resistant Enterobacteriaceae were retrieved. Array analysis revealed 18 isolates with ESBL genes and one isolate with solely non-ESBL beta-lactamase genes. Mutations in the ampC promoter region were determined in two isolates with PCR and sequencing. The isolates were identified as Klebsiella pneumoniae (n = 9), Escherichia coli (n = 6), Enterobacter cloacae complex (n = 5) and Enterobacter spp. (n = 1). All isolates tested were multidrug resistant. Variants of CTX-M enzymes were predominantly found followed by SHV enzymes. PMQR genes (including aac(6')-1b-cr, qnrB and qnrS) were also frequently detected. In almost all cases ESBL and quinolone resistance genes were located on the same plasmid. Imported fresh culinary herbs from Southeast Asia are a potential source for contamination of food with multidrug resistant bacteria. Because these herbs are consumed without appropriate heating, transfer to human bacteria cannot be excluded

Enterobacteriaceae rsistant to third-generation cephalosporins and quinolones in fresh culinary herbs imported from Southeast Asia

Since multidrug resistant bacteria are frequently reported from Southeast Asia, our study focused on the occurrence of ESBL-producing Enterobacteriaceae in fresh imported herbs from Thailand, Vietnam and Malaysia. Samples were collected from fresh culinary herbs imported from Southeast Asia in which ESBL-suspected isolates were obtained by selective culturing. Analysis included identification by MALDI-TOF mass spectrometry, susceptibility testing, XbaI-PFGE, microarray, PCR and sequencing of specific ESBL genes, PCR based replicon typing (PBRT) of plasmids and Southern blot hybridization. In addition, the quinolone resistance genotype was characterized by screening for plasmid mediated quinolone resistance (PMQR) genes and mutations in the quinolone resistance determining region (QRDR) of gyrA and parC. The study encompassed fifty samples of ten batches of culinary herbs (5 samples per batch) comprising nine different herb variants. The herbs originated from Thailand (Water morning glory, Acacia and Betel leaf), Vietnam (Parsley, Asian pennywort, Houttuynia leaf and Mint) and Malaysia (Holy basil and Parsley). By selective culturing 21 cefotaxime resistant Enterobacteriaceae were retrieved. Array analysis revealed 18 isolates with ESBL genes and one isolate with solely non-ESBL beta-lactamase genes. Mutations in the ampC promoter region were determined in two isolates with PCR and sequencing. The isolates were identified as Klebsiella pneumoniae (n = 9), Escherichia coli (n = 6), Enterobacter cloacae complex (n = 5) and Enterobacter spp. (n = 1). All isolates tested were multidrug resistant. Variants of CTX-M enzymes were predominantly found followed by SHV enzymes. PMQR genes (including aac(6')-1b-cr, qnrB and qnrS) were also frequently detected. In almost all cases ESBL and quinolone resistance genes were located on the same plasmid. Imported fresh culinary herbs from Southeast Asia are a potential source for contamination of food with multidrug resistant bacteria. Because these herbs are consumed without appropriate heating, transfer to human bacteria cannot be excluded

qnrB19 Gene Bracketed by IS26 on a 40-Kilobase IncR Plasmid from an Escherichia coli Isolate from a Veal Calf ▿

qnrB19 genes have been reported in Escherichia coli, Escherichia hermannii, Salmonella enterica, and Klebsiella spp., located on IncN, IncL/M (human isolates), and ColE-like (both human and chicken isolates) plasmids (2, 6, 8, 9, 11, 13, 14, 16). This study describes the characterization of the genetic environment of a plasmid-mediated qnrB19 gene identified in E. coli isolated from a veal calf in the Netherlands