Genomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico.

Salmonella enterica is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in S. enterica strains from Mexico (n = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (n = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of S. enterica. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating Salmonella strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.

Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype.

Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene-phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene-phenotype associations in M. tuberculosis.

Comparative virulence of the worldwide ST19 and emergent ST213 genotypes of Salmonella enterica serotype Typhimurium strains isolated from food.

Salmonella enterica Typhimurium represents one of the most frequent causal agents of food contamination associated to gastroenteritis. The sequence type ST19 is the founder and worldwide prevalent genotype within this serotype, but its replacement by emerging genotypes has been recently reported. Particularly, the ST213 genotype has replaced it as the most prevalent in clinical and contaminated food samples in Mexico and has been recently reported in several countries. In this study, the in vitro and in vivo virulence of ST213 and ST19 strains isolated from food samples in Mexico was evaluated. Three out of the five analyzed ST213 strains, showed a greater internalization capacity and increased secretion of interleukins IL-8 and IL-6 of Caco-2 cells than the ST19 strains. Microbiological counts in feces and tissues showed the ability of all strains tested to establish infection in the rat model. The ST213 strains also caused histopathological damage, characteristic of gastroenteritis in Wistar rats. In contrast to the in vitro result, one of the ST19 strains showed marked damage in the test animals. The ST213 genotype strains showed in vitro and in vivo virulence variability, but significantly higher than the observed in the ST19 genotype strains, thus such emergent genotype represents a public health concern.

Comparative Genomic Analysis Discloses Differential Distribution of Antibiotic Resistance Determinants between Worldwide Strains of the Emergent ST213 Genotype of Salmonella Typhimurium.

Salmonella enterica constitutes a global public health concern as one of the main etiological agents of human gastroenteritis. The Typhimurium serotype is frequently isolated from human, animal, food, and environmental samples, with its sequence type 19 (ST19) being the most widely distributed around the world as well as the founder genotype. The replacement of the ST19 genotype with the ST213 genotype that has multiple antibiotic resistance (MAR) in human and food samples was first observed in Mexico. The number of available genomes of ST213 strains in public databases indicates its fast worldwide dispersion, but its public health relevance is unknown. A comparative genomic analysis conducted as part of this research identified the presence of 44 genes, 34 plasmids, and five point mutations associated with antibiotic resistance, distributed across 220 genomes of ST213 strains, indicating the MAR phenotype. In general, the grouping pattern in correspondence to the presence/absence of genes/plasmids that confer antibiotic resistance cluster the genomes according to the geographical origin where the strain was isolated. Genetic determinants of antibiotic resistance group the genomes of North America (Canada, Mexico, USA) strains, and suggest a dispersion route to reach the United Kingdom and, from there, the rest of Europe, then Asia and Oceania. The results obtained here highlight the worldwide public health relevance of the ST213 genotype, which contains a great diversity of genetic elements associated with MAR.

Whole-genome comparative analysis at the lineage/sublineage level discloses relationships between Mycobacterium tuberculosis genotype and clinical phenotype.

BACKGROUND: Human tuberculosis (TB) caused by members of the Mycobacterium tuberculosis complex (MTBC) is the main cause of death among infectious diseases worldwide. Pulmonary TB (PTB) is the most common clinical phenotype of the disease, but some patients develop an extrapulmonary (EPTB) phenotype in which any organ or tissue can be affected. MTBC species include nine phylogenetic lineages, with some appearing globally and others being geographically restricted. EPTB can or not have pulmonary involvement, challenging its diagnosis when lungs are not implicated, thus causing an inadequate treatment. Finding evidence of a specific M. tuberculosis genetic background associated with EPTB is epidemiologically relevant due to the virulent and multidrug-resistant strains isolated from such cases. Until now, the studies conducted to establish associations between M. tuberculosis lineages and PTB/EPTB phenotypes have shown inconsistent results, which are attributed to the strain predominance from specific M. tuberculosis lineages/sublineages in the samples analyzed and the use of low-resolution phylogenetic tools that have impaired sublineage discrimination abilities. The present work elucidates the relationships between the MTBC strain lineages/sublineages and the clinical phenotypes of the disease as well as the antibiotic resistance of the strains. METHODS: To avoid biases, we retrieved the raw genomic reads (RGRs) of all (n = 245) the M. tuberculosis strains worldwide causing EPTB available in databases and an equally representative sample of the RGRs (n = 245) of PTB strains. A multiple alignment was constructed, and a robust maximum likelihood phylogeny based on single-nucleotide polymorphisms was generated, allowing effective strain lineage/sublineage assignment. RESULTS: A significant Odds Ratio (OR range: 1.8-8.1) association was found between EPTB and the 1.1.1, 1.2.1, 4.1.2.1 and ancestral Beijing sublineages. Additionally, a significant association between PTB with 4.3.1, 4.3.3, and 4.5 and Asian African 2 and Europe/Russia B0/W148 modern Beijing sublineages was found. We also observed a significant association of Lineage 3 strains with multidrug resistance (OR 3.8; 95% CI [1.1-13.6]), as well as between modern Beijing sublineages and antibiotic resistance (OR 4.3; 3.8-8.6). In this work, it was found that intralineage diversity can drive differences in the immune response that triggers the PTB/EPTB phenotype.

Difference of MreBCD Complex Interactome in Salmonella Typhimurium ST19 and ST213 Genotypes on Pathogenesis and Stress Response Pathways.

BACKGROUND: Salmonella enterica is the etiological agent of salmonellosis, with a high infection rate worldwide in Mexico, ST213 genotype of S. enterica ser. Typhimurium is displacing the ancestral ST19 genotype. Bacterial cytoskeleton protein complex MreBCD plays an important role in S. enterica pathogenesis, but underlying mechanisms are unknown. RESULTS: In this study, 106 interactions among MreBCD and 15 proteins from S. Typhimurium Pathogenicity Islands 1 (SP-I) and 2 (SP-2) involved in both bacterial virulence and stress response were predicted in ST213 and ST19 genotypes, of which 12 interactions were confirmed in vitro. In addition, gene cluster analysis in 100 S. Typhimurium genomes was performed for these genes. RESULTS AND CONCLUSION: The in silico and in vitro results showed a novel MreBCD interactome involved in regulating pathogenesis and stress response through interactions with virulence factors located at SPI-1 and SPI-2. Furthermore, both pseudogene presence and sequence variations in four tested proteins between genotypes resulted in differential interaction patterns involved in Salmonella motility and survival in eukaryotic cells, which could explain the replacement of ST19 by ST213 in Mexico.

Growth Inhibition of Phytopathogenic Fungi and Oomycetes by Basidiomycete Irpex lacteus and Identification of its Antimicrobial Extracellular Metabolites.

In dual culture confrontation assays, basidiomycete Irpex lacteus efficiently antagonized Fusarium spp., Colletotrichum spp., and Phytophthora spp. phytopathogenic strains, with growth inhibition percentages between 16.7-46.3%. Antibiosis assays evaluating the inhibitory effect of soluble extracellular metabolites indicated I. lacteus strain inhibited phytopathogens growth between 32.0-86.7%. Metabolites in the extracellular broth filtrate, identified by UPLC-QTOF mass spectrometer, included nine terpenes, two aldehydes, and derivatives of a polyketide, a quinazoline, and a xanthone, several of which had antifungal activity. I. lacteus strain and its extracellular metabolites might be valuable tools for phytopathogenic fungi and oomycete biocontrol of agricultural relevance.

Detailed epidemiological analysis as a strategy for evaluating the actual behavior of tuberculosis in an apparently low-incidence region.

Tuberculosis control in developing regions with apparent low incidence, like the low-income Mexican state of Michoacán, with mean annual incidence rates below 10/100,000 inhabitants, requires knowledge of the actual behavior of the disease. This can be determined using an epidemiological profile at sub-regional level, allowing disclosure of the clinical and social factors that may be hampering efforts to control tuberculosis. In this work, a detailed epidemiological profile was outlined using data of all new monthly cases registered in the National System of Epidemiological Surveillance Database for Michoacán municipalities from 2000 to 2012. Cases were grouped by gender and age, and sociodemographic data were obtained both from the National Institute of Statistics and Geography and from the United Nations Development Programme. Correlations were calculated by Chi-square, Mann-Whitney U, and Kruskal-Wallis H tests. We observed no statistically significant differences between notification rates for the years 2000, 2005 and 2010 (χ2 = 0.222, p = 0.895). The percentage of cases is similar between all age groups older than 15, while some regions had low notification rates but high proportions of pediatric cases. Higher proportions of cases of extrapulmonary tuberculosis were observed in municipalities in northern Michoacán. No correlation was found between municipal Human Development Index values and municipal notification rates. Michoacán is undergoing an epidemiological transition with three regions having different epidemiological profiles and particular needs for effective prevention and containment of tuberculosis. Our work shows the importance of the spatial scale of epidemiological profiles for determining specific regional needs of surveillance and containment.

Corn stover induces extracellular laccase activity in Didymosphaeria sp. (syn. = Paraconiothyrium sp.) and exhibits increased in vitro ruminal digestibility when treated with this fungal species.

Fungi can improve stover digestibility due to their ability to secrete oxidative enzymes that depolymerize lignin, allowing the rumen microorganisms to access the polysaccharides of the plant cell wall. Some ascomycetes have shown good delignification capability; however, they have been scarcely evaluated for their ability to improve corn stover (CS) ruminal digestibility. We evaluated the laccase induction by CS of the CMU-196 strain of the ascomycete fungus Didymosphaeria sp. (syn. = Paraconiothyrium sp.). Also, we analyzed the capacity of such strain to modify the cell wall of CS and to improve its digestion by the ruminal microbiota. The CMU-196 strain showed a maximum extracellular laccase activity of 39.74 ± 0.24 U/L when an aqueous stover extract (SE, 10% v/v) was added to the growth medium. The addition of ground stover (GS, 2% w/v) increased the activity to a maximum of 262.27 ± 0.58 U/L. In solid-state fermentation (SSF) assays of GS, the strain degrades cell walls, destabilizing the vessels and tracheids of plant biomass; the protein content reaches a maximum of 33.2 g/kg dry matter (DM) at 70 days, while the crude fiber content shows the highest level of 314 g/kg DM at 14 days. SSF treatment of the CS increased the in vitro ruminal production of gas in a fraction that was considered nondigestible at 18 h, and gas production increased by 14% with respect to the untreated GS at 14 days. The CMU-196 strain can digest the plant cell wall and improve ruminal CS digestibility at a level equivalent to several basidiomycete species.

Bioinformatic characterization of the extracellular lipases from Kluyveromyces marxianus.

Lipases are hydrolytic enzymes that break the ester bonds of triglycerides, generating free fatty acids and glycerol. Extracellular lipase activity has been reported for the nonconventional yeast Kluyveromyces marxianus, grown in olive oil as a substrate, and the presence of at least eight putative lipases has been detected in its genome. However, to date, there is no experimental evidence on the physiological role of the putative lipases nor their structural and catalytic properties. In this study, a bioinformatic analysis of the genes of the putative lipases from K. marxianus L-2029 was performed, particularly identifying and characterizing the extracellular expected enzymes, due to their biotechnological relevance. The amino acid sequence of 10 putative lipases, obtained by in silico translation, ranged between 389 and 773 amino acids. Two of the analysed putative proteins showed a signal peptide, 25 and 33 amino acids long for KmYJR107Wp and KmLIP3p, and a molecular weight of 44.53 and 58.23 kDa, respectively. The amino acid alignment of KmLIP3p and KmYJR107Wp with the crystallized lipases from a patatin and the YlLip2 lipase from Yarrowia lipolytica, respectively, revealed the presence of the hydrolase characteristic motifs. From the 3D models of putative extracellular K. marxianus L-2029 lipases, the conserved pentapeptide of each was determined, being GTSMG for KmLIP3p and GHSLG for KmYJR107Wp; besides, the genes of these two enzymes (LIP3 and YJR107W) are apparently regulated by oleate response elements. The phylogenetic analysis of all K. marxianus lipases revealed evolutionary affinities with lipases from abH15.03, abH23.01, and abH23.02 families.

Genome Sequence Data of Six Isolates of Phytophthora capsici from Mexico.

Phytophthora capsici is an oomycete plant pathogen with a wide host range. Worldwide, P. capsici is known for causing the principal disease of chili pepper crops. Our goal was to expand the available genome resources for this diverse pathogen by generating whole-genome sequences for six isolates of P. capsici from Mexico.

Comparative stress response to food preservation conditions of ST19 and ST213 genotypes of Salmonella enterica serotype Typhimurium.

The replacement of the most prevalent Salmonella enterica genotypes has been documented worldwide. Here we tested the hypothesis that the current prevalent sequence type ST213 of serotype Typhimurium in Mexico has a higher resistance to stressful food preservation conditions than the displaced sequence ST19. ST19 showed higher cell viability percentages than ST213 in osmotic (685 mM NaCl) and acidic (pH 3.5) stress conditions and in combination with refrigeration (4 °C) and ambient (≈22 °C) temperatures. Both genotypes showed the same poststress recovery growth. ST213 formed biofilm and filamentous cells (FCs) under stress, whereas ST19 did not. ST213 cells also showed higher motility. The capacity of ST213 to form FCs may explain its lower viability percentages when compared with ST19, i.e., ST213 cells divided less under stress conditions, but FCs had the same recovery capacity of ST19 cells. ST213 presented a higher unsaturated/saturated fatty acids ratio (0.5-0.6) than ST19 (0.2-0.5), which indicates higher membrane fluidity. The transcript levels of the rpoS gene were similar between genotypes under the experimental conditions employed. Biofilm formation, the generation of FCs, cell motility and membrane modification seem to make ST213 more resistant than ST19 to food preservation environments.

Sequencing and Annotation of the Genome of Mycobacterium tuberculosis MYC004, a Strain Causing Meningitis in Mexico.

Mycobacterium tuberculosis strain MYC004 was isolated from a Mexican patient with tuberculous meningitis, the most aggressive form of tuberculosis. The draft genome sequence is the first of a meningeal strain of M. tuberculosis reported from Latin America and consists of 4,411,530 bp, including 4,251 protein-encoding genes.

Identification and characterization of the biotechnological potential of a wild strain of Paraconiothyrium sp.

The isolation and characterization of fungal strains from poorly described taxa allows undercover attributes of their basic biology useful for biotechnology. Here, a wild fungal strain (CMU-196) from recently described Paraconiothyrium genus was analyzed. CMU-196 was identified as Paraconiothyrium brasiliense by phylogenetic analysis of the rDNA internal transcribed spacer region (ITS). CMU-196 metabolized 57 out of 95 substrates of the Biolog FF microplates. Efficient assimilation of dextrins and glycogen indicates that CMU-196 is a good producer of amylolytic enzymes. It showed a remarkably assimilation of α-d-lactose, substrate described as inducer of cellulolytic activity but poorly assimilated by several fungi. Metabolically active mycelium of the strain decolorized broth supplemented with direct blue 71, Chicago sky blue and remazol brilliant blue R dyes. The former two dyes were also well removed from broth by mycelium inactivated by autoclaving. Both mycelia had low efficiency for removing fuchsin acid from broth and for decolorizing wastewater from the paper industry. CMU-196 strain showed extracellular laccase activity when potato dextrose broth was supplemented with Cu+2 , reaching a maximum activity of 46.8 (±0.33) U L-1 . Studied strain antagonized phytopathogenic Colletotrichum spp. fungi and Phytophthora spp. oomycetes in vitro, but is less effective towards Fusarium spp. fungi. CMU-196 antagonism includes overgrowing the mycelia of phytopathogens and growth inhibition, probably by hydrosoluble extracellular metabolites. The biotechnological potential of strain CMU-196 here described warrants further studies to have a more detailed knowledge of the mechanisms associated with its metabolic versatility, capacity for environmental detoxification, extracellular laccase production, and antagonism against phytopathogens. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:846-857, 2018.

An ascomycota coculture in batch bioreactor is better than polycultures for cellulase production.

Efficient hydrolysis of holocellulose depends on a proper balance between cellulase (endoglucanase, exoglucanase, ß-glucosidase) and xylanase activities. The present study aimed to induce the production of cellulases and xylanases using liquid cultures (one, two, three, and four fungal strains on the same bioreactor) of wild strains of Trichoderma harzianum, Aspergillus niger, and Fusarium oxysporum. The strains were identified by amplification and analysis of the ITS rDNA region and the obtained sequences were deposited in Genbank. Enzymes (endoglucanase, exoglucansae, ß-glucosidase, and xylanase activities) and the profile of extracellular protein isoforms (SDS-PAGE) produced by different fungal combinations (N = 14) were analyzed by Pearson's correlation matrix and principal component analysis (PCA). According to our results, induction of endoglucanase (19.02%) and ß-glucosidase (6.35%) were obtained after 4 days when A. niger and F. oxysporum were cocultured. The combination of A. niger-T. harzianum produced higher endoglucanase in a shorter time than monocultures. On the contrary, when more than two strains were cultured in the same reactor, the relationships of competition were established, trending to diminish the amount of enzymes and the extracellular protein isoforms produced. The xylanase production was sensible to stress produced by mixed cultures, decreasing their activity. This is important when the aim is to produce cellulase-free xylanase. In addition, exoglucanase activity did not change in the combinations tested.

Characterization of ligninolytic enzyme production in white-rot wild fungal strains suitable for kraft pulp bleaching.

Fungal strains identified by phylogenetic analysis of the ITS rDNA region as Trametes versicolor (CMU-TA01), Irpex lacteus (CMU-84/13), and Phlebiopsis sp. (CMU-47/13) are able to grow on and bleach kraft pulp (KP) in a simple solid-state fermentation (SSF) assay conducted in Petri dishes. Kappa number reductions obtained with Phlebiopsis sp. (48.3%), T. versicolor (43%), and I. lacteus (39.3%), evidence their capability for lignin breakdown. Scanning electron microscopy images of KP fibers from SSF assays demonstrated increased roughness and striation, evidencing significant cell wall modification. T. versicolor produces laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) in potato dextrose broth (PDB), PDB + CuSO4, and PDB + KP, whereas Phlebiopsis sp. and I. lacteus showed no Lac and low LiP activities in all media. Compared to PDB, the highest increase in Lac (7.25-fold) and MnP (2.37-fold) activities in PDB + CuSO4 occur in T. versicolor; for LiP, the greatest changes (6.95-fold) were observed in I. lacteus. Incubation in PDB + KP shows significant increases in Lac and MnP for T. versicolor, MnP and LiP for Phlebiopsis sp., and none for I. lacteus. SSF assays in Petri plates are a valuable tool to select fungi that are able to delignify KP. Here, delignification by Phlebiopsis sp. of this substrate is reported for the first time, and MnP activity was strongly associated with the delignification ability of the studied strains. The obtained results suggest that the studied fungal strains have biotechnological potential for use in the paper industry.

Extending GelJ for interoperability: Filling the gap in the bioinformatics resources for population genetics analysis with dominant markers.

BACKGROUND AND OBJECTIVE: The manual transformation of DNA fingerprints of dominant markers into the input of tools for population genetics analysis is a time-consuming and error-prone task; especially when the researcher deals with a large number of samples. In addition, when the researcher needs to use several tools for population genetics analysis, the situation worsens due to the incompatibility of data-formats across tools. The goal of this work consists in automating, from banding patterns of gel images, the input-generation for the great diversity of tools devoted to population genetics analysis. METHODS: After a thorough analysis of tools for population genetics analysis with dominant markers, and tools for working with phylogenetic trees; we have detected the input requirements of those systems. In the case of programs devoted to phylogenetic trees, the Newick and Nexus formats are widely employed; whereas, each population genetics analysis tool uses its own specific format. In order to handle such a diversity of formats in the latter case, we have developed a new XML format, called PopXML, that takes into account the variety of information required by each population genetics analysis tool. Moreover, the acquired knowledge has been incorporated into the pipeline of the GelJ system - a tool for analysing DNA fingerprint gel images - to reach our automatisation goal. RESULTS: We have implemented, in the GelJ system, a pipeline that automatically generates, from gel banding patterns, the input of tools for population genetics analysis and phylogenetic trees. Such a pipeline has been employed to successfully generate, from thousands of banding patterns, the input of 29 population genetics analysis tools and 32 tools for managing phylogenetic trees. CONCLUSIONS: GelJ has become the first tool that fills the gap between gel image processing software and population genetics analysis with dominant markers, phylogenetic reconstruction, and tree editing software. This has been achieved by automating the process of generating the input for the latter software from gel banding patterns processed by GelJ.

Multi-Typing of Enterobacteria Harboring LT and ST Enterotoxin Genes Isolated from Mexican Children.

Enterotoxigenic Escherichia coli is the most common cause of diarrhea in children younger than 5 years in the developing world. We used 16S rRNA gene sequencing, the Biolog® system, and an Amplified Ribosomal DNA Restriction Analysis (ARDRA) to identify 69 enterobacteria isolated from the feces of healthy children up to 12 years old and 54 enterobacteria isolated from stool samples obtained from children up to 5 years old with diarrhea from Morelia, Michoacán, Mexico. In the diarrheic group, 18 isolates belonged to the enterotoxigenic pathotype, 1 isolate had both LT (heat labile toxin) gene and ST (heat stable toxin) gene, and 17 had the ST gene. The identity of most of the strains harboring the ST gene was E. coli, and 3 of the strains were identified as Morganella morganii. The ST toxin gene of one of the strains identified as M. morganii showed 100% identity with an ST toxin gene of E. coli. The ARDRA was a very useful tool to differentiate between E. coli and M. morganii. The phenotypic and genetic analyses of the isolates using the Biolog® system and Random Amplified Polymorphic DNA, respectively, showed physiological variation among the studied strains and genetic differences between subgroups.

Typing and selection of wild strains of Trichoderma spp. producers of extracellular laccase.

Using the ITS region and the gene tef1, 23 strains of the genus Trichoderma were identified as belonging to the species T. harzianum (n = 14), T. olivascens (n = 1), T. trixiae (n = 1), T. viridialbum (n = 1), T. tomentosum (n = 2), T. koningii (n = 1), T. atroviride (n = 1), T. viride (n = 1), and T. gamsii (n = 1). Strains expressing extracellular laccase activity were selected by decolorization/oxidation assays in solid media, using azo, anthraquinone, indigoid, and triphenylmethane dyes, and the phenolic substances tannic acid and guaiacol. No strain decolorized Direct Blue 71 or Chicago Blue 6B, but all of them weakly oxidized guaiacol, decolorized Methyl Orange, and efficiently oxidized tannic acid. Based in decolorization/oxidation assays, strains CMU-1 (T. harzianum), CMU-8 (T. atroviride), CMU-218 (T. viride), and CMU-221 (T. tomentosum) were selected for evaluating their extracellular laccase activity in liquid media. Strain CMU-8 showed no basal laccase activity, while strains CMU-1, CMU-218, and CMU-221 had a basal laccase activity of 1,313.88 mU/mL, 763.88 mU/mL, and 799.53 mU/mL, respectively. Addition of sorghum straw inhibited laccase activity in strain CMU-1 by 34%, relative to the basal culture, while strains CMU-8, CMU-21, and CMU-221 increased their laccase activity by 1,321.5%, 64%, and 47%, respectively. These results show that assayed phenolic substrates are good tools for selecting laccase producer strains in Trichoderma. These same assays indicate the potential use of studied strains for bioremediation processes. Straw laccase induction suggests that analyzed strains have potential for straw delignification in biopulping and other biotechnological applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:787-798, 2016.

Investigation of a food-borne Salmonella Oranienburg outbreak in a Mexican prison.

INTRODUCTION: Gastroenteritis outbreaks in prisons represent a public health risk worldwide. Identifying and characterizing the etiological agents of gastroenteritis outbreaks in prisons is important for implementing effective prevention and infection control measures. We present the first studied case of a gastroenteritis outbreak in a Mexican prison. METHODOLOGY: Rectal swab samples were obtained from affected inmates. Standard microbiological techniques were used for isolating Salmonella enterica. Isolates were typed by PCR assays of DNA repetitive elements (ERIC, BOX, REP) and RAPD. Antibiotic resistance profiles were performed by the Kirby-Bauer method. RESULTS: S. enterica serotype Oranienburg was responsible for the outbreak affecting 150 inmates. All patients presented diarrhea, and 70% of them also presented vomiting, with no fatal cases. The origin of the outbreak was undetermined due to the difficulty of gathering epidemiological information, but was likely the result of consumption of shrimp broth or a cantaloupe melon beverage. REP, BOX, and ERIC analyses of 26 serotype Oranienburg strains resulted in Simpson discrimination index (D) values of 0, 0.5507, and 0.5661, respectively. The D values from DG93-RAPD analyses and from the combined ERIC-BOX-DG93 markers were 0.7753 and 0.6092, respectively. All strains showed multiresistance to antibiotics. CONCLUSIONS: This is the only studied case of a gastroenteritis outbreak in a Mexican prison, and of the first such outbreak caused by serotype Oranienburg. The combined ERIC, BOX, and RAPD markers adequately assessed the genotype diversity of analyzed strains. Penitentiary personnel or inmates involved in outbreaks might spread multiresistant strains outside of the facility.