Biotype Profile Research Articles

Biotypes of major depressive disorder identified by a multiview clustering framework

BackgroundThe advances in resting-state functional magnetic resonance imaging techniques motivate parsing heterogeneity in major depressive disorder (MDD) through neurophysiological subtypes (i.e., biotypes). Based on graph theories, researchers have observed the functional organization of the human brain as a complex system with modular structures and have found wide-spread but variable MDD-related abnormality regarding the modules. The evidence implies the possibility of identifying biotypes using high-dimensional functional connectivity (FC) data in ways that suit the potentially multifaceted biotypes taxonomy. MethodsWe proposed a multiview biotype discovery framework that involves theory-driven feature subspace partition (i.e., “view”) and independent subspace clustering. Six views were defined using intra- and intermodule FC regarding three MDD focal modules (i.e., the sensory-motor system, default mode network, and subcortical network). For robust biotypes, the framework was applied to a large multisite sample (805 MDD participants and 738 healthy controls). ResultsTwo biotypes were stably obtained in each view, respectively characterized by significantly increased and decreased FC compared to healthy controls. These view-specific biotypes promoted the diagnosis of MDD and showed different symptom profiles. By integrating the view-specific biotypes into biotype profiles, a broad spectrum in the neural heterogeneity of MDD and its separation from symptom-based subtypes was further revealed. LimitationsThe power of clinical effects is limited and the cross-sectional nature cannot predict the treatment effects of the biotypes. ConclusionsOur findings not only contribute to the understanding of heterogeneity in MDD, but also provide a novel subtyping framework that could transcend current diagnostic boundaries and data modality.

Bio-typing of Mycobacterium avium subspecies paratuberculosis isolates recovered from the Himalayan sheep and goats.

Information on bio-type profile of Mycobacterium avium subspecies paratubeculosis (MAP) in sheep flocks and goat herds of Himalayan region is not reported earlier. The aim of our study was to determine the bio-type of MAP infecting livestock of this region. A total of 71 faecal samples (sheep-57, goats-14) were screened by Ziehl-Neelsen (ZN) staining and IS900 PCR, and then processed for culture on Herrold's egg yolk medium (HEYM) having mycobactin J (MJ). Out of 71 faecal samples, MAP colonies were seen only in four samples (sheep-3 and goat-1). Isolates were confirmed as MAP on the basis of slow growth, acid fastness, MJ dependency, IS900 and IS1311 PCR. All the IS900 and IS1311 PCR positive samples were bio-typed by IS1311 PCR-REA (restriction endonuclease analysis), which confirmed all four isolates as 'bison type.' In IS1311 based phylogeny of MAP isolates by ClustalW method of the MegAlign program of DNASTAR Lasergene software, the four sequences of MAP isolates (NCBI sequence nos. MH988763, MH988765, MH988766 and MH988764) did not show any distinct clustering/grouping pattern. However, these four isolates showed a bit of closeness to the MAP sequences (KC990353.1 and KC990352.1) of 'bison type' isolated from wood bison in Canada. In conclusion, this is the first report on isolation and bio-type profile of MAP infecting sheep and goats of Himalayan region. Study will help in devising prevention and control strategies against spread of MAP infection in livestock population of Himalayan region.

Profiling of Mycobacterium avium subspecies paratuberculosis in the milk of lactating goats using antigen-antibody based assays

Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis is endemic in the domestic livestock population, still it is not priority for control in the country. First time we used 'multiple assays’ for screening raw milk of 465 goats (farm/farmer's herds) to estimate bio-load and bio-type profile of bacilli. Each sample was screened by six tests and compared their sensitivity and specificity. Of 465 raw milk samples screened, bio-load of bacilli was 65.3% by six assays. Assay-wise bio-load was 49.4 and 62.7% in antigen and antibody detection tests, respectively. Bio-load was 48.8, 46.6, and 13.9% in Indirect Fluorescent Antibody Test (i_FAT), microscopy and IS900 PCR and 39.1, 57.4 and 55.6% in Indirect Enzyme Linked Immuno Sorbant Assay (i_ELISA), Dot Enzyme Linked Immuno Sorbant Assay (d_ELISA) and Latex Agglutination Test (LAT), respectively. Dot-ELISA was most sensitive followed by LAT, i_FAT, microscopy and i_ELISA. Milk DNA samples positive in IS900 PCR on bio-typing using IS1311 PCR_ Restriction Enzyme Analysis (IS1311 PCR_REA) revealed, 72.3% (47/65) were 'Indian Bison Type'. Milk was easy to collect sample and first time we used 'whole milk' as 'test sample' without centrifugation. High bio-load of MAP in milk underlined need for urgent control of disease in lactating goatherds. Bacilli was important 'Milk born' infection and on the basis of sensitivity, specificity, resources and requirements, of the ‘six assays’ most appropriate assay/s (single or in combination) can be chosen for the screening and diagnosis of Johne’s disease in lactating goatherds using whole milk as sample.

Phenotypic and Genotypic Characterization of Klebsiella pneumoniae Isolated From Retail Foods in China.

Klebsiella pneumoniae is not only a major hospital-acquired pathogen but also an important food-borne pathogen that can cause septicaemia, liver abscesses, and diarrhea in humans. The phenotypic and genotypic characteristics of K. pneumoniae in retail foods have not been thoroughly investigated in China. The objective of this study was to characterize K. pneumoniae isolates through biotyping, serotyping, determination of virulence factors, antibiotic resistance testing, enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR), and (GTG)5-PCR molecular typing. From May 2013 to April 2014, a total of 61 K. pneumoniae isolates were collected from retail foods in China. Using API 20E test strips, five different biotype profiles were identified among these isolates. The majority of isolates belonged to biochemical profile “5215773” (50 isolates, 80.6%). The capsular serotypes of the 61 K. pneumoniae isolates and one reference strain were determined by PCR. Of the seven capsular serotypes tested, four different capsular serotypes were identified. Serotypes K1, K20, K57, and K2 were detected in two, three, two, and one isolates, respectively. Serotypes K3, K5, and K54 were not detected. The presence of 11 virulence genes was assessed by PCR. The most common virulence genes were fimH (85.5%), ureA (79.0%), wabG (77.4%), uge (56.5%), and kfuBC (29.0%). ERIC-PCR and (GTG)5-PCR molecular typing indicated high genetic diversity among K. pneumoniae isolates. We identified 60 different ERIC patterns and 56 distinct (GTG)5 patterns. Genotypic results indicated that isolates carrying similar virulence factors were generally genetically related. Some isolates from the same geographic area have a closer relationship. The isolates showed high levels of resistance to ampicillin (51/62, 82.2%). Resistance to streptomycin (11/62, 17.7%) and piperacillin (10/62, 16.1%) was also common. The presence of virulent and antibiotic-resistant K. pneumoniae in foods poses a potential health hazard for consumers. Our findings highlight the importance of surveillance of K. pneumoniae in foods.

Biotypic Variation among Soybean Aphid Isolates from Four Provinces in China

ABSTRACTThe soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] is an important pest insect of soybean [Glycine max (L.) Merr.] in China and North America. Identification of soybean aphid biotypes would facilitate more effective pest management. Although four soybean aphid biotypes have been discovered in North America to date, biotype determination has not been conducted in China. In this study, we analyzed the biotypes of soybean aphids collected from four different soybean‐growing areas in China in 2011. The responses of four soybean aphid isolates from Changchun (Jilin province), Jinan (Shandong province), and Shanghai and Guiyang (Guizhou province) were assessed by infesting 11 soybean genotypes in noncaged tests during 2 yr and infesting 7 genotypes in a caged test in 1 yr. We distinguished among the four isolates on the basis of their abilities to infest a set of host plants with the known resistance genes Rag1 through Rag6. The results showed that the biotype profiles of the four soybean aphid isolates were different from each other and that there are at least four biotypes of soybean aphid in China.

A biotyping Scheme for Salmonella typhi

Thirty-nine isolates of Salmonella typhi ( S. typhi ) were studied using biotyping and antibiogram typing. Biotyping divided the isolates into six distinct biotypes on the basis of three biochemical tests, which included fermentation of bitter sugars: xylose and rhamnose; and reaction in Stern’s glycerol. Biotype 1 (28.2%) strains were the most wwprevalent, and did not utilize any of the three substrates. They were followed by biotype 2 (23.3%) strains that utilized all the three substrates and biotype 5 (23.3%) strains utilizing only bitter xylose, and biotype 6 (15.3%) strains utilizing bitter xylose and Stern’s glycerol. Biotypes 3 (7.67%) and 4 (2.3%) strains were less prevalent and utilized only Stern’s glycerol or both xylose and rhamnose, respectively. Antibiogram typing of S. typhi revealed the existence of multiple drug resistance to most of the 13 drugs used in the study. All isolates were resistant to oxacillin (1 μg), cephtazidine, 30 μg), erythromycin, 15 μg), vancomycin, 30 μg) and amoxyclaw (30 μ). 92.3% of the isolates were resistant to tetracycline (25 μg), streptomycin (19 μg/ml), and cotrimoxazole (25 μg), whereas 89.7% were resistant to chlorampenicol (30 μg), doxycycline (30 μg) and ampicillin (25 μg), respectively. About 2.6% of the isolates were resistant to gentamicin, whereas none was resistant to kanamycin. There was no correlation between biotype and antibiogram profile. In conclusion, this study has shown that most S. typhi strains in Kenya are multidrug resistant to the conventional drugs used in the treatment of typhoid fever. A reconsideration or temporary withdrawal of these drugs and their substitution with other drugs is highly recommended.

Measuring abundance, diversity and parasitic ability in two populations of the nematophagous fungus Pochonia chlamydosporia var. chlamydosporia

Abundance, genetic diversity and parasitic ability in the facultative nematode parasite Pochonia chlamydosporia var. chlamydosporia were compared in soils from two sites in Portugal under long-term tomato cultivation where root-knot nematodes (Meloidogyne sp.) were present. Fungal abundance assessed by selective agar or real-time quantitative PCR with specific primers was similar in both soils. PCR fingerprinting of isolates with ERIC primers indicated that the dominant P. c. var. chlamydosporia biotypes (profiles A and B) in both soils were very closely related, although a second biotype (profile C) was detected in one soil. When tomato plants infected with M. incognita were grown in the two soils, only profiles A and B were recovered from eggs. Primers based on polymorphisms in vcp1 demonstrated that isolates with profiles A and B were likely to prefer root-knot nematodes, whereas profile C preferred cyst nematodes. In the soil containing profiles A, B and C, egg parasitism by P. chlamydosporia was estimated at 1% using water agar plates with antibiotics but fewer than 0.2% of M. incognita eggs were shown to be infected with P. c. var. chlamydosporia when using species-specific β-tubulin-PCR primers. In contrast, the soil containing only profile B showed 22% egg parasitism on water agar plates and more than 2.5% of eggs were confirmed as P. c. var. chlamydosporia by species-specific β-tubulin-PCR primers. The results, which reveal limited diversity within the fungus at the two sites, are discussed in relation to biological control of plant-parasitic nematodes.

Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2005: an 8.5-Year Analysis of Susceptibilities of Candida Species and Other Yeast Species to Fluconazole and Voriconazole Determined by CLSI Standardized Disk Diffusion Testing

ABSTRACT Fluconazole in vitro susceptibility test results for 205,329 yeasts were collected from 134 study sites in 40 countries from June 1997 through December 2005. Data were collected for 147,776 yeast isolates tested with voriconazole from 2001 through 2005. All investigators tested clinical yeast isolates by the CLSI M44-A disk diffusion method. Test plates were automatically read and results recorded with a BIOMIC image analysis system. Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly. Duplicate (same patient, same species, and same susceptible-resistant biotype profile during any 7-day period) and uncontrolled test results were not analyzed. Overall, 90.1% of all Candida isolates tested were susceptible (S) to fluconazole; however, 10 of the 22 species identified exhibited decreased susceptibility (<75% S) on the order of that seen with the resistant (R) species C. glabrata and C. krusei . Among 137,487 isolates of Candida spp. tested against voriconazole, 94.8% were S and 3.1% were R. Less than 30% of fluconazole-resistant isolates of C. albicans , C. glabrata , C. tropicalis , and C. rugosa remained S to voriconazole. The non- Candida yeasts (8,821 isolates) were generally less susceptible to fluconazole than Candida spp. but, aside from Rhodotorula spp., remained susceptible to voriconazole. This survey demonstrates the broad spectrum of these azoles against the most common opportunistic yeast pathogens but identifies several less common yeast species with decreased susceptibility to antifungal agents. These organisms may pose a future threat to optimal antifungal therapy and emphasize the importance of prompt and accurate species identification.

Biotypic Diversity in Greenbug (Hemiptera: Aphididae): Characterizing New Virulence and Host Associations

Biotypic diversity of the greenbug, Schizaphis graminum (Rondani) (Hemiptera: Aphididae), was assessed among populations collected from cultivated wheat, Triticum aestivum L., and sorghum, Sorghum bicolor (L.) Moench, and their associated noncultivated grass hosts. Greenbugs were collected during May through August 2002 from 30 counties of Kansas, Nebraska, Oklahoma, and Texas. Discounting the presumptive biotype A, five of the remaining nine letter-designated greenbug biotypes were collected; however, biotypes C, F, J, and K were not detected. Biotypes E and I exhibited the greatest host range and were the only biotypes collected in all four states. Sixteen greenbug clones, collected from eight plant species, exhibited unique biotype profiles. Eleven were collected from noncultivated grasses, three from wheat, and two from sorghum. The most virulent biotypes were collected from noncultivated hosts. The great degree of biotypic diversity among noncultivated grasses supports the contention that the greenbug species complex is composed of host-adapted races that diverged on grass species independently of, and well before, the advent of modern agriculture.

Results from the ARTEMIS DISK Global Antifungal Surveillance Study: a 6.5-year analysis of susceptibilities of Candida and other yeast species to fluconazole and voriconazole by standardized disk diffusion testing.

Fluconazole in vitro susceptibility test results for 140,767 yeasts were collected from 127 participating investigators in 39 countries from June 1997 through December 2003. Data were collected on 79,343 yeast isolates tested with voriconazole from 2001 through 2003. All investigators tested clinical yeast isolates by the CLSI (formerly NCCLS) M44-A disk diffusion method. Test plates were automatically read and results were recorded with the BIOMIC Vision Image Analysis System. Species, drug, zone diameter, susceptibility category, and quality control results were collected quarterly via e-mail for analysis. Duplicate (the same patient, same species, and same susceptible-resistant biotype profile during any 7-day period) and uncontrolled test results were not analyzed. The 10 most common species of yeasts all showed less resistance to voriconazole than to fluconazole. Candida krusei showed the largest difference, with over 70% resistance to fluconazole and less than 8% to voriconazole. All species of yeasts tested were more susceptible to voriconazole than to fluconazole, assuming proposed interpretive breakpoints of > or =17 mm (susceptible) and < or =13 mm (resistant) for voriconazole. MICs reported in this study were determined from the zone diameter in millimeters from the continuous agar gradient around each disk, which was calibrated with MICs determined from the standard CLSI M27-A2 broth dilution method by balanced-weight regression analysis. The results from this investigation demonstrate the broad spectrum of the azoles for most of the opportunistic yeast pathogens but also highlight several areas where resistance may be progressing and/or where previously rare species may be "emerging."

Use of Biochemical Kinetic Data To Determine Strain Relatedness among Salmonella enterica subsp. enterica Isolates

Classical biotyping characterizes strains by creating biotype profiles that consider only positive and negative results for a predefined set of biochemical tests. This method allows Salmonella subspecies to be distinguished but does not allow serotypes and phage types to be distinguished. The objective of this study was to determine the relatedness of isolates belonging to distinct Salmonella enterica subsp. enterica serotypes by using a refined biotyping process that considers the kinetics at which biochemical reactions take place. Using a Vitek GNI+ card for the identification of gram-negative organisms, we determined the biochemical kinetic reactions (28 biochemical tests) of 135 Salmonella enterica subsp. enterica strains of pig origin collected in Spain from 1997 to 2002 (59 Salmonella serotype Typhimurium strains, 25 Salmonella serotype Typhimurium monophasic variant strains, 25 Salmonella serotype Anatum strains, 12 Salmonella serotype Tilburg strains, 7 Salmonella serotype Virchow strains, 6 Salmonella serotype Choleraesuis strains, and 1 Salmonella enterica serotype 4,5,12:-:- strain). The results were expressed as the colorimetric and turbidimetric changes (in percent) and were used to enhance the classical biotype profile by adding kinetic categories. A hierarchical cluster analysis was performed by using the enhanced profiles and resulted in 14 clusters. Six major clusters grouped 94% of all isolates with a similarity of > or =95% within any given cluster, and eight clusters contained a single isolate. The six major clusters grouped not only serotypes of the same type but also phenotypic serotype variations into individual clusters. This suggests that metabolic kinetic reaction data from the biochemical tests commonly used for classic Salmonella enterica subsp. enterica biotyping can possibly be used to determine the relatedness between isolates in an easy and timely manner.

Streptococcal Pyrogenic Exotoxin A, Streptolysin O, Exoenzymes, Serotype and Biotype Profiles of Streptococcus pyogenes Isolates from Patients with Toxic Shock Syndrome and other Severe Infections

The determination of protein M and T serotypes, biotypes and pyrogenic (erythrogenic) exotoxin A (SPE A), streptolysin O (SLO), streptokinase (SK), hyaluronidase (HA) and cysteine proteinase release by 212 S. pyogenes isolates from patients with severe invasive group A streptococcal (GAS) infections, among them 74 cases of streptococcal toxic shock syndrome (STSS) has been investigated. M1 or M3 serotypes were expressed by 25% of the isolates (53/212), whereas 59% (125/212) belonged to 15 other different serotypes and 16% (34/212) were untypeable. Of the 74 isolates from STSS patients, 42% (31/74) expressed M1 and to a lesser extent M3 serotypes versus 19% of the non STSS isolates (26/138). Among the ten different biotypes known, biotypes 1 and 3 were prevalent, particularly the former in the case of STSS isolates. SPE A was detectably produced by about 25% (54/212) of the strains. However, as high as 40.5% of the STSS isolates (30/74) versus 17.4% of non STSS isolates (24/138) released SPE A. Moreover, 67% of the SPE A producing strains were of serotype M1 or M3. SK and HA were released by 71% and 10% of the isolates respectively. All strains released SLO (4 to 256 HU/ml) and 85% cysteine proteinase. No relationship between toxin or enzyme titer and the type of disease or clinical origin of the strains was found. Culture supernatants of all isolates showed moderate to high lymphocyte transforming activity with index values ranging from 14.5 to 50.3 including those strains which did not release detectable amounts of SPE A suggesting that SPE C and other mitogenic factor(s) are released by the isolates investigated.

Biotypes of oral Candida albicans isolates in a Tanzanian child population

Although biotypes of Candida albicans from adult populations, especially in the West, have been described, there are no data either from a child population, or from the African continent. Hence a total of 200 oral C. albicans isolates from Tanzanian children aged 6-24 months were biotyped using two commercially available API micromethod kit systems and a boric acid resistance test. The predominant biotypes, which comprised two thirds of the organisms isolated, were J1S (19.5%), A1S (16.0%), J1R (14.5%), A1R (9.5%) and P1R (7.5%). In total, 16 new biotypes comprising 44 (22%) isolates which have not hitherto been described were found in this Tanzanian population and, of these, the P1R biotype predominated with 15 (7.5%) isolates. There was no significant association between predominant biotypes (with clusters > or = 15 isolates) and age, gender, breast feeding and malnutrition. These data indicate that the biotype profile of C. albicans isolates may differ in paediatric and adult populations, and/or global distribution of various subtypes of this common opportunistic pathogen.

Bacteriocin Typing and Biotyping of Clinical Isolates of Serratia marcescens

A total of 727 clinical isolates of Serratia marcescens from 474 patients were typed for bacteriocin susceptibility; 707 of the isolates (97.25%) were typable and comprised 46 different bacteriocin types. The biotyping method of Grimont and Grimont permitted categorization of 726 of the 727 isolates into 50 biotype profiles. However, 98 of the 726 biotypable isolates (13.5%) yielded previously unknown biotype profiles; similarly, 24 out of 59 reference strains of S. marcescens gave biotype profiles that had not been encountered before. Multiple S. marcescens isolates (366 of the 727 isolates) had been recovered from 113 patients. Phenotypic variation in bacteriocin susceptibility occurred in 15 of these patients, whereas phenotypic variation in biotype profiles was noted in 26 of these patients. In 5 of the 113 patients, phenotypic variation accounted for changes both in bacteriocin type and in biotype profile. It is suggested that serotyping should remain the method of choice until new methods have been evaluated accordingly.

A concise biotyping system for differentiating strains of Escherichia coli.

A six test biotyping system comprising fermentation of dulcitol, sorbose, raffinose, and 5 ketogluconate, motility and production of beta-haemolysis was used to obtain biotype profiles for 514 strains of Escherichia coli isolated from the urinary tract. This profile was suffixed to the API-20E code, recorded when the strains were originally identified. An expanded and reliable biotyping system was thus created giving a greater number of possible biotypes than with either system alone. The sensitivity in terms of distinguishing the organisms studied was therefore greatly increased. The use of O-serotyping in combination with biotyping is discussed. Biotyping can also be usefully supplemented by the determination of the eight commonest E coli O-serotypes. This is of value in many clinical situations where differentiation of organisms is vital to the proper analysis of results.

Biotyping of Escherichia coli

We examined the results of tests with 22 substrates for their ability to discriminate a series of 917 strains of Escherichia coli collected from different sources. The tests with three of the substrates were discarded because of difficulties in performance or interpretation, and another nine substrates because they provided little discrimination. The tests used to obtain biotype profiles for strains were those for the fermentation of dulcitol, D-raffinose or sucrose or both, L-rhamnose and L-sorbose, the decarboxylation of L-lysine and L-ornithine, the hydrolysis of aesculin, motility, and prototrophy. Observations on several series of cultures from different sources showed that biotype characters were stable in vivo and after storage on non-selective medium. The biotype profiles obtained were as reliable as partial O serotyping for the routine subtyping of strains of E. coli isolated from the urine of patients with long-term urinary-tract infections and those from other sources in different patients. Biotyping and O serotyping used in conjuction offered a very fine degree of strain discrimination.