Liquid chromatography mass spectrometry-based proteomics of Escherichia coli single colony

The Escherichia coli proteome is the most extensively characterized and studied of all prokaryotic proteomes. Despite this, large scale bacterial proteomics experiments performed on E. coli cells grown in liquid cultures have failed to identify key virulence factors thought to be important determinants in establishing bacterial infections. It seems likely that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth in biofilms, which can be crudely mimicked on solid media. This method describes a simple workflow to characterize the unique proteome signature of individual, isolated single colonies, using E. coli K12 strain grown on solid media as a model system. The workflow thus provides a means to explore the proteomes of minimally passaged clinical isolates of bacteria grown on primary culture plates and to identify both unique and differentially expressed proteins contained therein.

Value of the method:

- Simple mass spectrometry-based proteomics workflow to characterise the proteome of single colony forming units

- Enables exploration of the proteomes of minimally passaged clinical isolates from primary culture plates

- Identification of virulence factors expressed in true or mimicked biofilms that may be missed in liquid cultures

Method name: E. coli single colony proteome analysis

Prenatal diagnosis of trisomy 11 in a single colony of cultured amniocytes at amniocentesis in a pregnancy with a favorable outcome

OBJECTIVE

We present prenatal diagnosis of trisomy 11 in a single colony of cultured amniocytes at amniocentesis and the perinatal outcome.

CASE REPORT

A 36-year-old, gravida 2, para 1, woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XX,+11[1]/46,XX[16]. In 17 colonies of cultured amniocytes, all five cells in one colony had a karyotype of 47,XX,+11, while the rest 16 colonies had a normal karyotype. The parental karyotypes were normal. Repeat amniocentesis was performed at 21 weeks of gestation. Interphase fluorescence in situ hybridization (FISH) was applied on the uncultured amniocytes, and the result revealed 0.9% mosaicism (1/101 cells) for trisomy 11 with only one cell with three signals, while the other 100 cells had two signals, compared with no trisomy 11 signals (0/100 cells) in the normal control. Uniparental disomy (UPD) 11 was excluded by polymorphic DNA marker analysis on the DNAs extracted from uncultured amniocytes and parental bloods. The cultured amniocytes at repeat amniocentesis revealed a karyotype of 46, XX in 28/28 colonies. Prenatal ultrasound findings were unremarkable. The pregnancy was continued to 38 weeks of gestation, and a 2724-g healthy female baby was delivered. The cord blood had a karyotype of 46,XX. The interphase FISH analysis on buccal mucosal cells revealed no trisomy 11 signals (0/100 cells). When follow-up at three months of age, the neonate manifested normal psychomotor and physical development.

CONCLUSION

Prenatal diagnosis of mosaic trisomy 11 in a single colony at amniocentesis without abnormal fetal ultrasound and UPD 11 can be associated with a favorable outcome.

Prenatal diagnosis of mosaicism for trisomy 12 in a single colony at amniocentesis in a pregnancy with a favorable outcome

OBJECTIVE

We present prenatal diagnosis of mosaicism for trisomy 12 in a single colony at amniocentesis with a favorable outcome.

CASE REPORT

A 36-year-old woman underwent amniocentesis at 18 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XY,+12[1]/46,XY[14]. In 15 colonies of cultured amniocytes, all three cells in one colony had the karyotype of 47,XY,+12, while the rest 14 colonies had the karyotype of 46,XY. The parental karyotypes were normal. Prenatal ultrasound findings were unremarkable. Polymorphic DNA marker analysis using the DNAs extracted from cultured amniocytes and parental bloods excluded uniparental disomy (UPD) 12. At 37 weeks of gestation, a healthy 2,828-g male baby was delivered with no phenotypic abnormality. The cord blood had a karyotype of 46,XY in 40/40 lymphocytes. Postnatal interphase fluorescence in situ hybridization (FISH) analysis on buccal cells and urinary cells revealed normal signals in 72/72 buccal cells, and trisomy 12 signals in 1/47 (2.1%) urinary cells compared with 0% (0/75 cells) of trisomy 12 signals in the normal control.

CONCLUSION

Mosaicism for trisomy 12 in a single colony at amniocentesis without UPD 12 and fetal ultrasound abnormalities can be associated with a favorable outcome.

Prenatal diagnosis of mosaicism for double trisomies of trisomy 11 and trisomy 12 in a single colony at amniocentesis in a pregnancy with a favorable outcome

OBJECTIVE

We present prenatal diagnosis of mosaicism for double trisomies of trisomy 11 and trisomy 12 in a single colony at amniocentesis with a favorable outcome.

CASE REPORT

A 23-year-old woman underwent amniocentesis at 24 weeks of gestation because of congenital bowel dilation in the fetus. Amniocentesis revealed a karyotype of 48,XX,+11,+12[1]/46,XX[24]. In 25 colonies of cultured amniocytes, all five cells in one colony had the karyotype of 48,XX,+11,+12, while the rest 24 colonies had the karyotype of 46,XX. The parental karyotypes were normal. Repeat amniocentesis was performed at 26 weeks of gestation. Interphase fluorescence in situ hybridization (FISH), array comparative genomic hybridization (aCGH) and quantitative fluorescent polymerase chain reaction (QF-PCR) were applied on the uncultured amniocytes, and conventional cytogenetic analysis was applied on cultured amniocytes. Interphase FISH analysis showed no trisomy 11 signal and no trisomy 12 signal in 102 uncultured amniocytes. QF-PCR analysis excluded uniparental disomy (UPD) 11 and UPD 12. aCGH analysis showed no genomic imbalance. The cultured amniocytes at repeat amniocentesis had the karyotype of 46,XX in 13/13 colonies. At term, a healthy 3445-g female baby was delivered with no phenotypic abnormality except imperforate anus and a perianal fistula. The cord blood had a karyotype of 46,XX in 40/40 lymphocytes. Postnatal interphase FISH analysis of buccal cells and urinary cells revealed trisomies 11 and 12 signals in 11/111 (9.9%) buccal cells compared with 3% in normal control, and in 3/103 (2.9%) urinary cells compared with 0.98% in normal control.

CONCLUSION

Mosaicism for double trisomies of trisomy 11 and trisomy 12 in a single colony at amniocentesis without UPD 11 and UPD 12 can be associated with a favorable outcome.

Prenatal diagnosis of mosaicism for trisomy 11 in a single colony at amniocentesis in a pregnancy with a favorable outcome

OBJECTIVE

We present prenatal diagnosis of mosaicism for trisomy 11 in a single colony at amniocentesis with a favorable outcome.

CASE REPORT

A 34-year-old woman underwent amniocentesis at 16 weeks of gestation because of advanced maternal age. Amniocentesis revealed a result of 47,XY,+11[1]/46,XY[9]. In 10 colonies of cultured amniocytes, all five cells in one colony had a karyotype of trisomy 11, while the rest nine colonies had a normal karyotype. The parental karyotypes were normal. Repeat amniocentesis was performed at 19 weeks of gestation. Interphase fluorescence in situ hybridization (FISH) was applied on the uncultured amniocytes, and the result showed no trisomy 11 signals in 56/56 uncultured amniocytes. Uniparental disomy (UPD) 11 was excluded by polymorphic DNA marker analysis. The cultured amniocytes at repeat amniocentesis had a karyotype of 46,XY. Prenatal ultrasound findings were unremarkable. A healthy 3084-g male baby was delivered at 38 weeks of gestation. The karyotype of cord blood lymphocytes was 46,XY. The boy was phenotypically normal at age 10 months at follow-ups. The interphase FISH analysis on urinary cells revealed no trisomy 11 signal.

CONCLUSION

Mosaicism for trisomy 11 in a single colony at amniocentesis without UPD 11 can be associated with a favorable outcome.

Multi-directional Morphological Assessment of Single Bacterial Colonies Through Non-invasive Optical Imaging

A bacterium in bacterial colony is a basal component of bacterial studies and is therefore of considerable importance. The morphological characteristics of a single colony have been widely used as the standard to identify diverse bacterial species. However, the conventional methods for obtaining morphological information, such as microscopic techniques, cannot provide tomographic views. This study utilizes spectral-domain optical coherence tomography (SD-OCT) to observe both external and internal structures for single colonies. OCT imaging provided a clear top (projection) and lateral (cross-sectional) images, which can identify distinct features in the fifteen different bacterial species examined. Through the acquired OCT images, the elevation type in each genus was confirmed, and the quantitative measurements for morphology including a diameter, height, and elevation angle were achieved. Moreover, the OCT raw data was used to build three-dimensional images to observe outer appearances in all direction. As a result, the averaged angles of 7.92°, 14.40°, 6.78°, and 11.92° of the genus Hymenobacter, Spirosoma, Bacillus, and Deinococcus, respectively, were calculated. In conclusion, we have demonstrated that OCT is a highly feasible, non-invasive method for the identification of bacterial species, providing detailed morphological and visual information. It thus has strong potential for applications in bacteriology, as well as biomedical and food sciences.

Comparison between the proteome of Escherichia coli single colony and during liquid culture

Most bacterial proteomic studies done to date utilise bacterial cells harvested from liquid culture media. However, it is widely accepted that many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media, as a crude mimic of true biofilms. Here, we compare the observed proteome of Escherichia coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. A total of 2044 protein groups covering approximately 47% of the total proteome were identified across all studied conditions, including 1650 proteins identified from single colonies and 1679 proteins from liquid cultured cells. Label-free quantitative analysis revealed that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture. Notably, the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles, whereas proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. The data presented here provide a valuable resource for understanding the role of key proteins within microenvironments surrounding E. coli single colonies. SIGNIFICANCE: To date, most proteomics studies have used E. coli cells harvested from liquid culture media even though many important determinants associated with virulence and host cell adhesion are exclusively expressed during growth on solid media. In this study, we compare the observed proteome of E. coli K12 from isolated single colonies on solid media with those observed at different growth phases in liquid culture; i.e. early-log, mid-log, early-, mid- and late-stationary growth phases. By using label-free quantitative analysis we demonstrate that the E. coli proteome of single colonies on a solid agar differs from that observed in liquid culture with an overlap of 68% of proteins between the two culture conditions. Our analysis further reveal the presence of proteins in the Suf-operon that are involved in iron mobilisation and swarming motility was associated exclusively with single colony profiles. While those proteins involved in motility such as motA, motB, fliH, flip, fliD and fliJ were associated exclusively with cells grown in liquid culture. By comparison to E. coli proteomic data available on liquid culture and solid media, this research represents a first effort to describe the differential expression of key E. coli proteins within microenvironments surrounding single colonies.