Comparison of API 20NE and Biolog GN identification systems assessed by techniques of multivariate analyses

Diagnostic accuracy of automation and non-automation techniques for identifying Burkholderia pseudomallei: A systematic review and meta-analysis

BACKGROUND

Burkholderia pseudomallei, a Gram-negative pathogen, causes melioidosis. Although various clinical laboratory identification methods exist, culture-based techniques lack comprehensive evaluation. Thus, this systematic review and meta-analysis aimed to assess the diagnostic accuracy of culture-based automation and non-automation methods.

METHODS

Data were collected via PubMed/MEDLINE, EMBASE, and Scopus using specific search strategies. Selected studies underwent bias assessment using QUADAS-2. Sensitivity and specificity were computed, generating pooled estimates. Heterogeneity was assessed using I2 statistics.

RESULTS

The review encompassed 20 studies with 2988 B. pseudomallei samples and 753 non-B. pseudomallei samples. Automation-based methods, particularly with updating databases, exhibited high pooled sensitivity (82.79%; 95% CI 64.44-95.85%) and specificity (99.94%; 95% CI 98.93-100.00%). Subgroup analysis highlighted superior sensitivity for updating-database automation (96.42%, 95% CI 90.01-99.87%) compared to non-updating (3.31%, 95% CI 0.00-10.28%), while specificity remained high at 99.94% (95% CI 98.93-100%). Non-automation methods displayed varying sensitivity and specificity. In-house latex agglutination demonstrated the highest sensitivity (100%; 95% CI 98.49-100%), followed by commercial latex agglutination (99.24%; 95% CI 96.64-100%). However, API 20E had the lowest sensitivity (19.42%; 95% CI 12.94-28.10%). Overall, non-automation tools showed sensitivity of 88.34% (95% CI 77.30-96.25%) and specificity of 90.76% (95% CI 78.45-98.57%).

CONCLUSION

The study underscores automation's crucial role in accurately identifying B. pseudomallei, supporting evidence-based melioidosis management decisions. Automation technologies, especially those with updating databases, provide reliable and efficient identification.

Chryseobacterium zhengzhouense sp. nov., isolated from groundwater of the well in a vegetable field, and emended description of the genus Chryseobacterium

A Gram-negative, strictly aerobic, non-motile, asporogenous rod-shaped bacterium, designated M05W1-39A1(T), was isolated from a Chinese cabbage farmland located in Zhengzhou. China, and subjected to a taxonomic study. Strain M05W1-39A1(T) was found to grow optimally at 25-30 °C, at pH 6.0-7.0 and in the presence of 0.5-2.0 % (w/v) NaCl. According to phylogenetic analysis using 16S rRNA gene sequences, strain M05W1-39A1(T) belongs to the genus Chryseobacterium and is closely related to Chryseobacterium arachidis LMG 27813(T) (98.8 %) and Chryseobacterium geocarposphaera LMG 27811(T) (98.1 %). The DNA G + C content was determined to be 35.3 mol%. The respiratory quinone was identified as MK-6 and the predominant cellular fatty acids as iso-C15:0, Summed feature 3 (C16:1 ω7c/C16:1 ω6c), iso-C17:0 3-OH and Summed feature 9 (iso-C17:1 ω9c). Based on the genotypic, chemotaxonomic and phenotypic data, strain M05W1-39A1(T) is concluded to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium zhengzhouense sp. nov. is proposed. The type strain is M05W1-39A1(T) (=HNMC11208(T) = CGMCC 1.15067(T) = JCM 30863(T)).

Glycocaulis alkaliphilus sp. nov., a dimorphic prosthecate bacterium isolated from crude oil

A bacterial strain designated 6B-8T was isolated from crude oil from Daqing oilfield, China. Cells of strain 6B-8T were Gram-negative, aerobic, dimorphic and reproduced by means of binary fission. Strain 6B-8T could grow at 20–37 °C, pH 8–10 and 1–5 % (w/v) NaCl. Its genomic DNA G+C content was 62.0 mol%. The predominant cellular fatty acids were C18 : 1ω7c, C17 : 0, C18 : 0 and 11-methyl C18 : 1ω7c and the main hydroxy fatty acids were C12 : 0 3-OH and C12 : 1 3-OH when grown on marine agar 2216. The major quinone was Q-10 and the major polar lipids were three unidentified glycolipids. Phylogenetic analysis revealed that strain 6B-8T was a member of the family Hyphomonadaceae , sharing 99.6 and 99.4 % 16S rRNA gene sequence similarity with Glycocaulis abyssi LMG 27140T and Glycocaulis albus SLG210-30A1T, respectively, and less than 94.4 % similarity with the type strains of other members of the family Hyphomonadaceae . However, the DNA–DNA relatedness between strain 6B-8T and related strains G. abyssi LMG 27140T and G. albus SLG210-30A1T was 36±5 and 42±5 %, respectively. In addition, several phenotypic and genotypic features allowed differentiation of strain 6B-8T from G. abyssi LMG 27140T and G. albus SLG210-30A1T. Therefore, strain 6B-8T represents a novel species of genus Glycocaulis , for which the name Glycocaulis alkaliphilus sp. nov. is proposed. The type strain is 6B-8T ( = CGMCC 1.12428T = LMG 27410T).

Negadavirga shengliensis gen. nov., sp. nov., a novel member of the family Cyclobacteriaceae isolated from oil-contaminated saline soil

Four novel Gram-stain-negative, rod-shaped, and non-motile bacterial strains, SLG210-21(T), SLG210-4, SLG210-5 and SLG210-14, were isolated from oil-contaminated saline soil in Shengli Oilfield, China. Growth were observed at 25-42 °C (optimum 37 °C), in the presence of 0-10 % (w/v) NaCl (optimum 0-1 %) and at pH 4.0-10.0 (optimum pH 7.6-8.6). All the strains were positive for catalase and α, β-galactosidase activities and nitrogen reduction, and negative for oxidase activity, glucose fermentation and hydrolysis of agar, starch, gelatin, Tween 40, 60 and 80. The DNA G+C contents of the four strains were 41.3-43.0 mol% and the predominant respiratory quinones were all menaquinone-7. The major fatty acids were iso-C15:0, anteiso-C15:0, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:1 ω5c and summed feature 9 (iso-C17:1 ω9c and/or 10-methyl C16:0), while the polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, glycolipid, two unidentified phospholipids and two unidentified amino lipids. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the four strains clustered together to form a stable branch in the family Cyclobacteriaceae, and were most closely related to the genera Cyclobacterium and Echinicola with the 16S rRNA gene sequence similarities being 88.6-90.3 and 89.6-91.4 %, respectively. DNA-DNA hybridization between SLG210-21(T) and the other three strains showed the relatedness of 93.8 ± 4.5, 96.2 ± 4.2 and 82.3 ± 4.8 %, respectively. Based on the polyphasic analysis, a novel species in a new genus, Negadavirga Shengliensis gen. nov., sp. nov., is proposed with SLG210-21(T) (=LMG 27737(T) = CGMCC1.12768(T)) [corrected] as the type strain.

Halodurantibacterium flavum gen. nov., sp. nov., a non-phototrophic bacterium isolated from an oil production mixture

Three Gram-negative bacterial strains, DQW12E6-69-1(T), DQW12E61-22-1, and DQW12E6-22-1-1, were isolated from an oil production mixture from Daqing Oilfield, northeastern China. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that the three strains formed a stable cluster different from the known genus in Rhodobacteraceae of Alphaproteobacteria. In addition, they were most closely related to species in genera Pararhodobacter, Rhodobacter ,and Rhodobaca with the 16S rRNA gene sequence similarities being 95.1-95.9 %. Cells of the three strains were aerobic; they do not require salt to grow but are resistant to high salinity. They could conduct chemoorganoheterotrophic growth on various carbon sources, with non-phototrophic growth observed. The genomic DNA G+C contents of the strains DQW12E6-69-1(T), DQW12E6-22-1-1, and DQW12E61-22-1 were 63.8, 63.7, and 63.6 mol%, respectively. The predominant respiratory ubiquinone of DQW12E6-69-1(T) was Q-10, and the major fatty acids were C18:1 ω7c, C(18:0), and C(10:0) 3-OH. Photosynthetic pigments and photosynthetic reaction center gene pufM were not detected. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified glycolipid, and unidentified phospholipid. On the basis of phenotypic, genotypic, and chemotaxonomic characteristics, strains DQW12E6-69-1(T), DQW12E61-22-1, and DQW12E6-22-1-1 represent a novel genus and a novel species of the family Rhodobacteraceae. The name Halodurantibacterium flavum gen. nov., sp. nov. is proposed with strain DQW12E6-69-1(T) (=LMG 27742(T) = CGMCC 1.12756(T)) as the type strain.

Ottowia shaoguanensis sp. nov., isolated from coking wastewater

A Gram-negative, short rod-shaped, floc-forming bacterial strain J5-66(T) without any flagellum was isolated from coking wastewater collected from Shaoguan, Guangdong, China. It was capable of optimal growth at pH 7, 30 °C, and 1-2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the genus Ottowia in Comamonadaceae, and the highest 16S rRNA gene sequence similarity was 96.2 % with Ottowia pentelensis DSM 21699(T). The major cellular fatty acids of strain J5-66(T) were C₁₆:₁ω7c/C₁₆:₁ ω6c (45.0 %), C₁₆:₀ (21.1 %), C₁₈:₁ ω7c or/and C₁₈:₁ ω6c (19.2 %). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, glycolipid and two unidentified phospholipids (PL1 and PL2). The predominant ubiquinone was Q-8, and the G+C content of the genome DNA was 64.4 mol%. On the basis of genetic, phenotypic and chemotaxonomic analyses, strain J5-66(T) represents a novel species of the genus Ottowia for which the name Ottowia shaoguanensis sp. nov. is proposed. The type strain is J5-66(T) (=CGMCC 1.12431(T) =LMG 27408(T)).

Physiologic and metabolic characterization of a new marine isolate (BM39) of Pantoea sp. producing high levels of exopolysaccharide

Background

Marine environments are the widest fonts of biodiversity representing a resource of both unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, exopolysaccharides (EPS) have many physiological functions and practical applications. Since EPS production by many bacteria is too scarce for practical use and only few species are known for their high levels of production, the search of new high EPS producers is of paramount importance. Many marine bacteria, that produce EPS to cope with strong environmental stress, could be potentially exploited at the industrial level.

Results

A novel bacterium, strain BM39, previously isolated from sediments collected in the Tyrrhenian Sea, was selected for its production of very high levels of EPS. BM39 was affiliated to Pantoea sp. (Enterobacteriaceae) by 16S rRNA gene sequencing and biochemical tests. According to the phylogenetic tree, this strain, being quite far from the closest known Pantoea species (96% identity with P. agglomerans and P. ananatis) could belong to a new species. EPS production was fast (maximum of ca. 21 g/L in 24 h on glucose medium) and mainly obtained during the exponential growth. Preliminary characterization, carried out by thin layer and gel filtration chromatography, showed that the EPS, being a glucose homopolymer with MW of ca. 830 kDa, appeared to be different from those of other bacteria of same genus. The bacterium showed a typical slightly halophilic behavior growing optimally at NaCl 40 ‰ (growing range 0-100 ‰). Flow cytometry studies indicated that good cell survival was maintained for 24 h at 120 ‰. Survival decreased dramatically with the increase of salinity being only 1 h at 280 ‰. The biochemical characterization, carried out with the Biolog system, showed that MB39 had a rather limited metabolic capacity. Its ability, rather lower than that of P. agglomerans, was almost only confined to the metabolization of simple sugars and their derivatives. Few alcohols, organic acids and nitrogen compounds were partially used too.

Conclusions

Strain BM39, probably belonging to a new species, due to its remarkable EPS production, comparable to those of known industrial bacterial producers, could be suggested as a new microorganism for industrial applications.

Effective microbes for simultaneous bio-oxidation of ammonia and manganese in biological aerated filter system

This study determined the most effective microbes acting as ammonia-oxidising (AOB) and manganese-oxidising bacteria (MnOB) for the simultaneous removal of ammonia (NH(4)(+)-N) and manganese (Mn(2+)) from water. Two conditions of mixed culture of bacteria: an acclimatised mixed culture (mixed culture: MC) in a 5-L bioreactor and biofilm attached on a plastic medium (stages of mixed culture: SMC) in a biological aerated filter were isolated and identified using Biolog MicroSystem and 16S rRNA sequencing. A screening test for determining the most effective microbe in the removal of NH(4)(+)-N and Mn(2+) was initially performed using SMC and MC, respectively, and found that Bacillus cereus was the most effective microbe for the removal of NH(4)(+)-N and Mn(2+). Moreover, the simultaneous NH(4)(+)-N and Mn(2+) removal (above 95% removal for both NH(4)(+)-N and Mn(2+)) was achieved using a biological aerated filter under various operating conditions. Thus, the strain could act as an effective microbe of AOB and a MnOB for the simultaneous removal of NH(4)(+)-N and Mn(2+).

Community-level physiological profiles of bacteria and fungi: plate type and incubation temperature influences on contrasting soils

Abstract Temperature sensitivity of community-level physiological profiles (CLPPs) was examined for two semiarid soils from the southwestern United States using five different C-substrate profile microtiter plates (Biolog GN2, GP2, ECO, SFN2, and SFP2) incubated at five different temperature regimes. The CLPPs produced from all plate types were relatively unaffected by these contrasting incubation temperature regimes. Our results demonstrate the ability to detect CLPP differences between similar soils with differing physiological parameters, and these differences are relatively insensitive to incubation temperature. Our study also highlights the importance of using both bacterial and fungal plate types when investigating microbial community differences by CLPP. Nevertheless, it is unclear whether or not the differences in CLPPs generated using these plates reflect actual functional differences in the microbial communities from these soils in situ.

The Microbe: The Basics of Structure, Morphology, and Physiology as They Relate to Microbial Characterization and Attribution

This chapter is meant to (1) review classical methods used to characterize and classify microbes and (2) introduce new molecular methods used in microbial characterization. The fundamental composition of microbes is discussed as well as their importance in classification of microbes into genus and species. Classical microbiological methods in general seek to define the common features of specific bacterial groups as a means of classification and identification of microbes. Thus, the focus was to describe the common features which discriminated closely related groups of organisms. In contrast, the newer molecular methods often seek to expand the classification of microbes not only as a means to organize microbial phylogeny but also to differentiate signatures between microbes identified within a species in greater detail. Molecular biology tools are used both as an adjunct to established methods and as replacement for classical methods for detection, discrimination, or identification of bacterial and viral species.

Metabolic characterization of a strain (BM90) of Delftia tsuruhatensis showing highly diversified capacity to degrade low molecular weight phenols

A novel bacterium, strain BM90, previously isolated from Tyrrhenian Sea, was metabolically characterized testing its ability to use 95 different carbon sources by the Biolog system. The bacterium showed a broad capacity to use fatty-, organic- and amino-acids; on the contrary, its ability to use carbohydrates was extremely scarce. Strain BM90 was identified and affiliated to Delftia tsuruhatensis by molecular techniques based on 16S rRNA gene sequencing. D. tsuruhatensis BM90, cultivated in shaken cultures, was able to grow on various phenolic compounds and to remove them from its cultural broth. The phenols used, chosen for their presence in industrial or agro-industrial effluents, were grouped on the base of their chemical characteristics. These included benzoic acid derivatives, cinnamic acid derivatives, phenolic aldehyde derivatives, acetic acid derivatives and other phenolic compounds such as catechol and p-hydroxyphenylpropionic acid. When all the compounds (24) were gathered in the same medium (total concentration: 500 mg/l), BM90 caused the complete depletion of 18 phenols and the partial removal of two others. Only four phenolic compounds were not removed. Flow cytometry studies were carried out to understand the physiological state of BM90 cells in presence of the above phenols in various conditions. At the concentrations tested, a certain toxic effect was exerted only by the four compounds that were not metabolized by the bacterium.

Comparison of biochemical and molecular methods for the identification of bacterial isolates associated with failed loggerhead sea turtle eggs

AIMS

Comparison of biochemical vs molecular methods for identification of microbial populations associated with failed loggerhead turtle eggs.

METHODS AND RESULTS

Two biochemical (API and Microgen) and one molecular methods (16s rRNA analysis) were compared in the areas of cost, identification, corroboration of data with other methods, ease of use, resources and software. The molecular method was costly and identified only 66% of the isolates tested compared with 74% for API. A 74% discrepancy in identifications occurred between API and 16s rRNA analysis. The two biochemical methods were comparable in cost, but Microgen was easier to use and yielded the lowest discrepancy among identifications (29%) when compared with both API 20 enteric (API 20E) and API 20 nonenteric (API 20NE) combined. A comparison of API 20E and API 20NE indicated an 83% discrepancy between the two methods.

CONCLUSIONS

The Microgen identification system appears to be better suited than API or 16s rRNA analysis for identification of environmental isolates associated with failed loggerhead eggs.

SIGNIFICANCE AND IMPACT OF THE STUDY

Most identification methods are not intended for use with environmental isolates. A comparison of identification systems would provide better options for identifying environmental bacteria for ecological studies.

Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

AIMS

Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus.

METHODS AND RESULTS

For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%).

CONCLUSIONS

Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.

Incidence of antibiotic resistance in coliforms from drinking water and their identification using the Biolog and the API identification systems

Antibiotic-resistant bacteria were common in samples collected from an intermittent water distribution system in Lebanon. Multiply-resistant isolates were also present and most commonly to amoxycillin, cephalexin and sulfamethoxazole/trimethoprim. The aminoglycosides (amikacin, gentamicin and kanamycin) were the most effective, with almost all tested strains showing susceptibility to these antimicrobial agents. Both the Biolog GN MicroPlates and the API 20E strips can be used for the identification of coliform bacteria isolated from potable water, but the outcome of the identification should be viewed with caution. 51% of isolates were assigned similar identities by both the Biolog MicroPlates and the API 20E strips. The similarity at the species level was lower (33%) compared to that at the genus level (67%). The identification of Escherichia coli strains, which represented 30% of all tested organisms, showed 95% similarity in the assigned genus and species using both identification schemes.