Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study

Mohamed M.A. Nagla; Omer E. El Fadil; Abdel Hamid M. Muzamil; Altayeb N. Hisham; Mohamed B. Bahaeldeen; El-Amin El-Nour

doi:10.12688/f1000research.14019.1

Home Browse Internal transcribed spacer for identification of yeast species isolated...

ALL Metrics

Views

Downloads

Get PDF

Get XML

Export

▬

✚

Research Article

Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study

[version 1; peer review: 1 approved, 1 approved with reservations]

Mohamed M.A. Nagla ¹, Omer E. El Fadil¹, Abdel Hamid M. Muzamil², Altayeb N. Hisham³, Mohamed B. Bahaeldeen⁴, El-Amin El-Nour⁵

Mohamed M.A. Nagla ¹, Omer E. El Fadil¹, [...] Abdel Hamid M. Muzamil², Altayeb N. Hisham³, Mohamed B. Bahaeldeen⁴, El-Amin El-Nour⁵

PUBLISHED 11 Apr 2018

Author details Author details

¹ Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan
² Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
³ Department of Microbiology, College of Medical Laboratory Sciences, Sudan University of Science and Technology, Khartoum, Sudan
⁴ Molecular Biology Unit, National Center for Research, Khartoum, Sudan
⁵ Department of Microbiology and Molecular biology, Faculty of Sciences and Technology, Al-Neelain University, Khartoum, Sudan

Mohamed M.A. Nagla
Roles: Conceptualization, Funding Acquisition, Investigation, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation

Omer E. El Fadil
Roles: Conceptualization, Supervision

Abdel Hamid M. Muzamil
Roles: Resources

Altayeb N. Hisham
Roles: Methodology, Software

Mohamed B. Bahaeldeen
Roles: Methodology

El-Amin El-Nour
Roles: Supervision, Validation, Writing – Review & Editing

OPEN PEER REVIEW

REVIEWER STATUS

Abstract

Background: Cancer patients have a high risk of fungal infections, especially by Candida species. Non-C. albicans Candida infections and less common yeast infections have been increasing in recent years. Identification by conventional methods can be difficult and sometimes inconclusive. This study aimed to detect the prevalence of oral yeast species isolated from cancer patients, from oral swab, sputum and urine, using Internal Transcribed Spacer (ITS) sequence analysis, since little is known about this problem in Sudan.
Methods: The study involved 333 cancer patients (168 patients under treatment [study group] and 165 patients before treatment [control group]). Oral swabs were collected from all patients. Urine or sputum specimens were collected from patients under treatment showing clinical features of UTI or lower respiratory tract infection, respectively. ITS1 and ITS2 region of isolated yeast were amplified by PCR and sequenced. The obtained sequences were compared to reference sequence available in the GenBank database using BLAST.
Results: Culture results showed oral yeast species were isolated from 69/168 (41.1%) and 74/165 (44.8%) of patients among study and control groups, respectively (P value > 0.05). 2/9 (22.2%) patients were urine growth positive and 8/14 (57.1%) patients were sputum culture positive. Sequence analysis showed, C. albicans was the most prevalent organism (93; 52.5%) followed by C. tropicalis (29; 16.4%), and C. glabrata (24; 13.6%). Non-C. albicans Candida and uncommon rare yeast were found to be associated with oral infections and colonization among the study and control groups, whereas C.albicans was the most common species (66.7%) associated with oral candidiasis among the treated patients.
Conclusion: Cancer patients were highly colonized with different oral yeast species, which indicates that ITS sequence analysis is an accurate method for identification. This will aid effective management to prevent dissemination of disease especially among those who are under chemo and/or radiotherapy treatment.

Keywords

Yeast species, ITS sequencing, Cancer patients.

Corresponding author: Mohamed M.A. Nagla

Competing interests: No competing interests were disclosed.

Grant information: The project was financially supported by Ministry of Higher Education and Scientific Research, Sudan.

Copyright: © 2018 Nagla MMA et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

How to cite: Nagla MMA, El Fadil OE, Muzamil AHM et al. Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2018, 7:443 (https://doi.org/10.12688/f1000research.14019.1) First published: 11 Apr 2018, 7:443 (https://doi.org/10.12688/f1000research.14019.1) Latest published: 11 Apr 2018, 7:443 (https://doi.org/10.12688/f1000research.14019.1)

Introduction

As a result of the immunocompromised state and the effect of chemotherapy, cancer patients are more susceptible to fungal infections, especially by Candida species (AI-Dwairi et al., 2014). Candida species are commensal in human bodies, and become opportunistic pathogens in immunodefective patients. Sometimes they can cause systemic infections and colonize different organs due to their dissemination from the mucosal infected regions (Miceli et al., 2011). Pfaller et al. (2006) and Wilson et al., (2002) reported that the systemic infections have considerable morbidity among those with severely paralyzed immune system.

The most common fungal infection is oropharyngeal candidiasis, which is more prevalent among cancer patients (Akapan & Morgan, 2002). Recently infections with non-Candida albicans and rare common yeast genera, such as Pichia, Rhodotorula, and Saccharomyces, have been implicated; however, C. albicans remains the most prevalent species (Han et al., 2004 and Walsh et al., 2004).

Yeast identification is of great importance for targeting proper treatments (Ramani et al., 1998), since different species yield different antifungal response (Pfaller et al., 2003). Conventional methods for yeast identification may be difficult and inconclusive (Reiss et al., 1998) especially for less common yeast. Thus more rapid and accurate molecular methods have been developed, among which ITS sequence analysis is found to be more accurate for species delineation (Chen et al., 2001 and Iwen et al., 2002).

The ITS region is located between the highly conserved genes coding for 18S and 28S rRNA. The ITS region includes two none coding regions ITS1 and ITS2, which are separated by the highly conserved 5.8SrRNA gene (White et al., 1990). The more genetic variability of ITS1 and ITS2 regions enables better identification of closely related species other than the adjacent rRNA gene (Ciardo et al., 2006).

This study aimed to detect the prevalence of oral yeast species isolated from cancer patients by oral swab, in addition to other specimens (sputum and urine), using ITS sequence analysis, since little is known about this problem in Sudan.

Methods

Study design and participants

This was a cross-sectional, case-control study conducted in a period between April 2013 and December 2017.

The study involved 333 cancer patients referred to Isotope and Radiation Center, Khartoum, who were seeking anticancer treatment and during a routine check-up were enrolled in this study. The participants were classified into 168 patients under chemo and/or radiotherapy treatment (study group) and 165 cancer patients prior to starting anticancer treatment (control group). Study participants included 185 females and 148 males (mean age, 48 years old).

Written informed consent and structural questionnaire (see Supplementary File 1), including demographical data, site of cancer and cancer treatments, was obtained from each patient. The participants were ensured of anonymity and that only group findings will be reported.

To reduce any possible bias matching criteria was done, which included age, sex and type of cancer. Inclusion criteria: Any patient diagnosed with any type of cancer during or before starting cancer treatment, having age equal or above 18 year old, attending Isotope and Radiation Center, Khartoum was included in this study. Exclusion criteria: Patients on antifungal therapy for past two weeks were excluded from the study.

Sample collection

Oral swabs were collected from each patient (333 patients) to detect the prevalence of yeast infections and colonization among the treated and non-treated patients. Urine (n=9) and sputum (n=14) samples were collected from patients under treatment (study group), who exhibited the clinical features of urinary tract infection (UTI) and/or lower respiratory tract infection (LRT), respectively. These samples were taken in order to detect whether there is any dissemination from a patient’s own oral yeast due to action of cancer treatments.

All specimens (n=356) were cultured without delay in Sabouraud’s dextrose agar plates (SDA) to which chloramphenicol (0.05g/l) was added. Then the plates were incubated at 37°C for 24–48 hours. Phenotypic identification was made using Gramʹs stain and germ tube test. Purified colonies were preserved on glycerol stock solution for molecular identification (Sherman et al., 1986).

DNA extraction

The isolated strains were subbed from the stock solution on Sabouraud’s dextrose agar medium and DNA extraction was performed from colonies that had been incubated for 48 hrs using Guanidine Chloride method as described by Gassoum et al. (2014). Three to five colonies were washed with 5 ml phosphate buffer saline (PBS) (Sigma Aldrich) for three times. 2 ml white cell lysis buffer and 20 µl of proteinase K (10 mg/ml; iNtRON Inc, Korea) were added, vortexed and incubated at 37°C for overnight. Then 1 ml from Guanidine chloride (7M; iNtRON Inc, Korea) and 350 µl of ammonium acetate (7M; Loba Chemie, India) were added. The tubes were vortexed and incubated at 65°C in an oven for 2 hours. Then the supernatant was mixed with 2ml pre chilled chloroform (sd Fine-Chem limited, India) at 6000 RPM for 20 minutes and this was transferred into a new Falcon tube and completed to 10 ml volume with pre chilled absolute ethanol (Carlo Erba, France) and incubated overnight at -20°C for completion of DNA precipitation.

After incubation the tubes were centrifuged at 6000 RPM for 20 minutes, then the ethanol was poured off and the same step was repeated with 70% ethanol. After that the tubes were left to air dry. Finally DNA was suspended in 80 µl TE buffer (iNtRON Inc, Korea) and incubated at 4 °C until used. Nanodrop ND 1000 Spectrophotometer (NanoDrop Technologies, Inc.) was used to measure quality and quantity of DNA.

PCR amplification procedure

The universal fungal primers ITS1 (5′-TCC GTA GGT GAA CCT GCG G-3′) and ITS4 (5′-TCC TCC GCT TAT TGA TAT GC-3′) (Macrogen Inc. Korea) were used to amplify the entire ITS rDNA region (Zimbeck et al., 2010). PCR mixture contained 5 μl pre mix (iNtRON Inc., Korea), 22μl deionized sterile water, 1 μl from each forward and reverse primer, and 1 μl of genomic DNA, which served as the DNA template in a final volume of 25 μl.

PCR cycling conditions were as follows: an initial denaturation step of 5 min at 95°C followed by 35 cycles of 45 s at 94°C, 45 s at 55°C, and 45 s at 72°C, with a final extension of 5 min at 72°C. The reactions were carried out in an ESCO thermocycler (AERIS-BG096, China).

The PCR products were analyzed on 2% agarose gels (iNtRON Inc., Korea) stained with ethidium bromide (10 ng/100 ml; Fisher Scientific, USA) and visualized under a UV transilluminator apparatus (Saratoga, CA.95070, USA Gel Documentation System) and Biodoct BDA system (Biometra, Germany).

DNA sequencing

PCR products of 90 isolates from the cases and 87 isolates from the control group were purified and commercially sequenced using forward primer ITS1 and backward primer ITS4 by Macrogen Company (Seoul, Korea).

The sequences obtained in this study were identified by searching databases using BLAST sequence analysis tool (http://www.ncbi nlm.nih.gov/BLAST/). The sequences were compared using nucleotide-nucleotide BLAST (blastn) with default setting except that sequences were not filtered for low complexity. Species were identified based on the highest similarity score (100%) with reference database sequence.

Statistical analysis

Data was analyzed using SPSS 21. Frequencies and percent were obtained for frequency tables, Chi-squared test was used for goodness of fit. The relationships between variables tested were obtained using cross tables and Chi-squared (Fisher exact) test for independence. P-value ≤0.05 was considered as significant.

Ethical statement

Scientific approval was obtained from Faculty and Department of Medical Microbiology Management, Al-Neelain University (No AU/FMLS/7/1). Ethical clearance was obtained from the Directorate of Research Department, Ministry of Health, Khartoum (dated on 21-04-2013).

Results

The collected oral swabs (333 specimens), from 168 cancer patients with chemo and/or radiotherapy treatment (study group) and from 165 cancer patients (control group) without treatment were examined by cultural technique. Oral Candida species were isolated from 69/168 (41.1%) and 74/165 (44.8%) of patients among study and control groups, respectively.

Of the 168 study group, 23 patients with clinical symptoms of UTI and/or LRT infection had urine (n=9) and sputum (n=14) samples collected for detection of Candida species. The results showed that 2 out of 9 patients and 8 out of 14 patients were culture positive for Candida spp. (Table 1).

Table 1. Culture results of urine and sputum specimens collected from the study group.

	Specimens
Growth	Sputum N (%)	Urine N (%)	Total N (%)
Positive	8 (57.1)	2 (22.2)	10 (43.5)
Negative	6 (42.9)	7 (77.8)	13 (56.5)
Total	14 (100)	9 (100)	23 (100)

Among the culture positive patients (n=69 study group; n= 74 control group), the prevalence of oral candidiasis were 33.3% and 10.8% ,while the prevalence of oral colonization were 66.7% and 89.2% among the study and control patients, respectively (Table 2).

Table 2. Prevalence of oral candidiasis and colonization among the study and control groups.

	Symptoms
Patients	Yes (infection) N (%)	No (colonization) N (%)	Total N (%)	P- value
Study	23 (33.3)	46 (66.7)	69 (100)	< 0.05
Control	8 (10.8)	66 (89.2)	74 (100)	< 0.05

Among the 69 positive cases in the study group, 13 patients exhibited mixed growth of oral yeast, while among the control group 25 patients exhibited mixed growth out of 74. As a result, the numbers of total isolates collected from different specimens from the study group were 92 and 99 isolates from the control group.

PCR products of ITS polymerized region revealed different band size for different species. C. albicans exhibited 500 bp (Figure 1). In contrast, non-C. albicans Candida and less common yeast represented different band sizes ranging from 400–750 bp (Figure 2).

Figure 1. Agarose gel showing the results obtained for conventional PCR of isolated yeast genomic DNA.

From left to right lanes: L, 100bp DNA ladder, L1 negative control, L2,4,5,6 C. albicans (500bp).

Figure 2. Agarose gel showing the results obtained for conventional PCR of isolated yeast genomic DNA.

From right to left lanes: L, 100bp DNA ladder, L1,2,3,6 C. glabrata (750bp), L9,11 C. galbrata (600bp), L4,8 P. kudriavzevii (450bp), L10,12 P. kudriavzevii (400bp), L5,7 C. tropicalis (450bp), L13 L. fermentati (500bp).

DNA sequencing was performed for isolated yeast species (only 90 isolates from 67 out of 69 positive patients in study group and 87 isolates from 66 out of 74 positive patients in the control group). The result of the BLAST sequence analysis for species identification is shown in Table 3.

Table 3. Species distribution among the study and control groups.

Species	Study N (%)	Control N (%)	Total N (%)
*Clavispora lusitaniae*	0 (0.00)	4 (4.60)	4 (2.30)
*C. albicans*	59 (65.6)	34 (39.1)	93 (52.50)
*C. glabrata*	7 (7.80)	17 (19.50)	24 (13.60)
*C. tropicalis*	13 (14.40)	16 (18.40)	29 (16.40)
*Pichia.sporocuriosa*	1(1.1)	0 (0.00)	1(0.60)
*Saccharomyces cervisiae*	0 (0.00)	2 (2.30)	2 (1.10)
*Magnusiomyces capitatus*	2 (2.20)	2 (2.30)	4 (2.30)
*Pichia kudriavzevii*	7 (7.80)	11 (12.60)	18 (10.20)
*C. dobliensis*	0 (0.00)	1 (1.10)	1 (0.60)
*Lachancea fermentati*	1 (1.10)	0 (0.00)	1 (0.60)
Total	90 (100)	87 (100)	177 (100)

The distribution of oral mixed species among the 67 study and 66 control groups is shown in Table 4.

Table 4. Frequency of mixed oral yeast species among Sudanese cancer patients.

Species	Study N (%)	Control N (%)	Total N (%)
*Clavispora lusitaniae*	0 (0.0)	4 (6.1)	4 (3.0)
*C. albicans*	42 (62.7)	23 (34.8)	65(48. 9)
*C. glabrata*	3 (4.5)	6 (9.1)	96.8)
*C. tropicalis*	3 (4.5)	4 (6.1)	6 (4.5)
*Saccharo cervisiae*	0 (0.0)	2 (3.0)	2 (1.5)
*Magnusiomyces capitatus*	2 (3.0)	2 (3.0)	4 (3.0)
*Pichia kudriavzevii*	3 (4.5)	4(6.1)	7 (5.3)
*C.dobliensis*	0 (0.0)	1 (1.5)	1 (0.8)
*Lachane fermentati*	1 (1.5)	0 (0.0)	1 (0.8)
*C. tropicalis+C. glabrata*	3 (4.5)	3 (4.5)	6 (4.5)
*C. albicans+C. albicans*	4 (6.0)	2 (3.0)	6 (4.5)
*C. tropicalis+C. tropicalis*	3 (4.5)	2 (3.0)	5 (3.8)
*Pichi kudriavzevii+Pichi* *kudriavzevii*	1 (1.5)	0 (0.0)	1 (0.8)
*C. glabrata+C. glabrata*	0 (0.0)	4 (6.1)	4 (3.0)
*C. albicans+C. tropicalis*	0 (0.0)	2 (3.0)	2 (1.5)
*Pichi kudriavzevii+* *C. tropicalis*	0 (0.0)	2 (3.0)	2 (1.5)
*C.albicans+pichia* *sporocuriosa*	1(1.5%)	0(0.0%)	1(0.8%)
*C.albicans+Pichi.* *kudriavzevii*	1(1.5%)	5(7.6%)	6(4.5%)
Total	67 (100)	66 (100)	133 (100)

Table 4 shows the distribution of oral mixed species among the (67) study and (66) control groups. It was found that although some patients represented different colonial morphology of mixed oral isolated yeast, they exhibited the same species on sequence identification.

The identified species were classified according to presence or absence of symptoms of oral candidiasis among the study and control group to detect their association with oral infection and colonization as in Figure 3. This showed that C. albicans was the most common organism associated with oral infection (14 out of 21) and colonization (28 out of 46) among the study group. In the control group it had the same percentage (2/8; 25%) as C. tropicalis and mixed C. glabrata among oral symptomatic patients, whereas it was found to be the most common cause of colonization (21/58; 36.2%).

Figure 3.

Frequency of yeast species associated with oral Candida infection (symptoms) and colonization (no symptoms) among the (A) study group and (B) control group.

Identification of sputum isolates showed that C. albicans was isolated from both oral and sputum specimens from four patients, while three patients exhibited C. albicans from sputum specimens only (oral swabs were negative), and C. tropicalis was isolated from sputum specimen only from one patient. Regarding urine specimens, C. albicans was isolated from both oral and urine samples from one patient in contrast to mixed infections (Pichia kudriavzevii and Pichia kudriavzevii) that were isolated from oral swabs. C. glabrata was also isolated from the urine of another patient.

Dataset 1.Demographical data of cancer patients.

Sheet 1: For case group (168 cancer patients under treatments); Sheet 2: For control group (165 cancer patients); Sheet 3: Pictures demonstrated the colonial morphology for different isolated yeast species.

Discussion

In the present study it was found that oral Candida isolates were obtained from 69 (41.1%) patients who were under treatment with chemo and/or radiotherapy treatments and from 74 (44.8%) patients without cancer treatment. Xu et al. (2013) found that oral infection was prevalent in 46% (391/850) of all cancer patients, while another study reported the incidence of oral candidiasis ranging from 7 to 52% in cancer patients on chemotherapy and/or radiotherapy (Lone et al., 2014)

The present study revealed that 8 out of 14 patients were positive for sputum culture among the study group (Table 1). Mohammed et al. (2016) and Ungureanu et al. (2016) reported slightly lower percentages of 30.50% and 33.75%, respectively, in comparison to this study (57.15%). This may be due to differences in study population, since cytotoxic and immunosuppressive therapies promote dissemination of Candida spp. through induction of cytopenias and/or immune cell dysfunction (Blot et al., 2008; Cruciani & Serpelloni, 2008). Also this was expressed in the isolation of 22.2% of Candida species from urine culture of the treated patients among this study, which is relatively similar to Nigar et al. (2016), who found out of 64 culture positive clinical specimens Candida species were identified from 18.75% urine specimens.

Among the study and control groups, the present study found that oral colonization was significantly (p<0.05) more common than oral Candida infection (66.7% vs 33.3% and 89.2% vs 10.8%, in both groups, respectively). Similar results have been reported by Lone et al. (2014), who found the total colonization to be prevalent in 50% and oral candidiasis in 30% of all cancer patients. In contrast, oral Candida infection was more common (p<0.05) among the study group compared with the control group (33.3% vs 10.8%). A systematic review carried out by Lalla et al. (2010) reported that for all cancer treatments, the weighed prevalence of clinical oral fungal infection was found to be 7.5% pretreatment and 39.1% during treatment. This may be due to chemotherapeutic agents and therapeutic radiation that disrupts the mucosal banner of the mouth, leading to severe oral mucositis, gingivitis, and oral candidiasis. Blasting results of ITS sequence analysis in the present study revealed C. albicans was the most prevalent organism in the two groups (65.6% and 39.1%, study and control groups, respectively). These results are in agreement with previous reports (Ismet et al., 2016 and Aldossary et al., 2016) that studied the prevalence of oral Candida spp and demonstrated that C. albicans was the most prevalent organism.

The majority of oral infections are due to C. albicans but non-albicans strains, such as C. glabrata and C. tropicalis, have increasingly been implicated in causing disease (Bagg et al., 2003). Similar findings were observed in this study C. tropicalis was found to be the second most common isolate among the study group (14.4%) followed equally (7.8%) by C.glabrata and P. kudriavzevii, whereas among the control group C.glabrata was the second most common isolate (19.5%) followed by C. tropicalis (18.4%).

It was found that P. kudriavzevii (anamorph of Candida krusei) represented 12.6% among the control group, and P. sporocuriosa was isolated once from the study group only. In addition, C. lusitaniae (teleomorph of Candida lusitaniae) represented 4.6%, and C. dubliniensis represented 1.1% among the control group only (Table 3). These findings are in agreement with Pfaller et al. (2010), who performed a recent ten-year analysis of the worldwide distribution of non-albicans Candida species, and indicated that C. glabrata remains the most common non-albicans species and that C. parapsilosis, C. tropicalis, and C. krusei are also frequently isolated.

Less common yeast species were also detected in small numbers. L. fermentati appeared only once and M. capitatus twice among the study group, while among the control group the later along with S. cervisiae were detected among two patients (2.2%). These findings were in agreement with a study done by Han et al., 2004 and Walsh et al., 2004, who reported that, recently, infections caused by less common yeast species such as Pichia, Rhodotorula, Trichosporon, and Saccharomyces spp. and other rarely encountered species have been reported.

Table 4 shows the presence of identified mixed oral yeast species among the study and control groups. Similarly de Sousa et al. (2016) found the presence of more than one yeast among orogastric cancer patients.

Regarding distribution of species according to presence or absence of symptoms of oral candidiasis, it was found that C. albicans was the most common isolate associated with infection 14/21 (66.7%) and colonization 28/46 (60.9%) among the study group. While among non-albicans Candida, the prevalence of C. tropicalis was 9.5% vs. 2.2% and C. glabrata was 4.8% vs. 4.3% among the oral symptomatic and non-symptomatic study patients, respectively (Figure 3A). Similarly Lone et al., (2014) observed C. albicans to be the most common species (74.39% vs. 65.4%) causing colonization and candidiasis in cancer patients, respectively. Whereas they found C. glabrata was the second most common species followed by C. tropicalis and C. parapsilosis to cause colonization as well as candidiasis in cancer patients. This may be due to geographical region variation.

In contrast, among the control group C. albicans was detected as the same percentage (2/8; 25%) as C. tropicalis and the mixed C. glabrata among oral symptomatic patients, whereas it represents the most common cause of colonization (21/58; 36.2%) followed by C. glabrata (Figure 3B). This may be due to small number of symptomatic control patients due to the absence of any cancer treatment since it is a predisposing factor for initiation of oral infection by the colonized organisms, mainly by C. albicans, which is the most virulent organism.

Among the isolated Candida species from sputum and urine specimens, C. albicans was isolated from both oral and sputum specimens from four patients and from both oral and urine from one patient. These patients may have gained the infection or colonization in these organs from their own oral colonized Candida species. Other studies reported that colonized Candida can invade the underlying mucosa and enter the blood stream leading onto disseminated disease with considerable morbidity and mortality if not treated promptly (Lalla et al., 2010 and Shokohi et al., 2011).

Conclusion

The present study demonstrates that cancer patients were highly colonized with oral yeast species. C. albicans was the most common isolate associated with oral infection and colonization among the treated cancer patients. In contrast with control group it occupied a higher percent among the colonized species only. As the control group were not under cancer treatment, this lead to oral infection and disseminations to other organs. So early detection and identification of colonized yeast is of great value especially among patients undergoing cancer treatments.

Although C. albicans was the most prevalent species, other non-albicans Candida and rarely encountered yeast were also isolated. This indicates that use of proper and accurate molecular methods for yeast identification, especially for unusual yeast species, and prior antifungal treatment as required in cancer patients.

Data availability

Dataset 1: Demographical data of cancer patients. Sheet 1: For case group (168 cancer patients under treatments); Sheet 2: For control group (165 cancer patients); Sheet 3: Pictures demonstrated the colonial morphology for different isolated yeast species. DOI, 10.5256/f1000research.14019.d199685 (Nagla et al., 2018).

Sequences from the patients are available on GenBank under accession numbers: MH037201 to MH037237, MH019244 to MH019255, MH016295-MH016371, MH061321-MH061334, MH084778-MH084790, MH016252 to MH016274 and MH104613.

Competing interests

No competing interests were disclosed.

Grant information

The project was financially supported by Ministry of Higher Education and Scientific Research, Sudan.

Supplementary material

Supplementary File 1: Demographic questionnaire.

Click here to access the data.

Faculty Opinions recommended

References

Akapan A, Morgan R: Oral candidiasis. Postgard Med J. 2002; 78(922): 455–459. PubMed Abstract | Publisher Full Text | Free Full Text
Al-Dwairi ZN, Darwazeh MG, Shukri LA: Isolation of Candida species from the oral cavity and fingertips of complete and partial dentures wearers. J Dent Health Oral Disord Ther. 2014; 1(3): 1–6. Publisher Full Text
Aldossary MA, Almansour NA, Abdulraheem BS: Isolation and identification of Candida species from the oral cavity of cancer patients undergoing chemotherapy in Basrah, Irag. J Of Biol Agricul And Healthca. 2016; 6(18). Reference Source
Bagg J, Sweeney MP, Lewis MA, et al.: High prevalence of non-albicans yeasts and detection of anti-fungal resistance in the oral flora of patients with advanced cancer. Palliat Med. 2003; 17(6): 477–81. PubMed Abstract | Publisher Full Text
Blot S, Dimopoulos G, Rello J, et al.: Is Candida really a threat in the ICU? Curr Opin Crit Care. 2008; 14(5): 600–604. PubMed Abstract | Publisher Full Text
Chen YC, Eisner JD, Kattar MM, et al.: Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol. 2001; 39(11): 4042–4051. PubMed Abstract | Publisher Full Text | Free Full Text
Ciardo DE, Schär G, Böttger EC, et al.: Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts. J Clin Microbiol. 2006; 44(1): 77–84. PubMed Abstract | Publisher Full Text | Free Full Text
Cruciani M, Serpelloni G: Management of Candida infections in the adult intensive care unit. Expert Opin Pharmacother. 2008; 9(2): 175–191. PubMed Abstract | Publisher Full Text
de Sousa LVNF, Santos VL, de Souza Monteiro A, et al.: Isolation and identification of Candida species in patients with orogastric cancer: susceptibility to antifungal drugs, attributes of virulence in vitro and immune response phenotype. BMC Infect Dis. 2016; 16: 86. PubMed Abstract | Publisher Full Text | Free Full Text
Gassoum A, Arbab MA, Aldeaf SAH, et al.: Allele Frequency Of P53 Gene Arg72Pro In Sudanese Meningioma Patients And Controls. IJSTR. 2014; 6(3): 243–248. Reference Source
Han XY, Tarrand JJ, Escudero E: Infections by the yeast Kodomaea (Pichia) ohmeri: two cases and literature review. Eur J Clin Microbiol Infect Dis. 2004; 23(2): 127–130. PubMed Abstract | Publisher Full Text
Ismet N, Shirin T, Rehana RK, et al.: Species identification of Candida isolated from clinical specimens in tertiary care hospital. BSMMU J. 2016; 9(1): 20–25. Publisher Full Text
Iwen PC, Hinrichs SH, Rupp ME: Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol. 2002; 40(1): 87–109. PubMed Abstract | Publisher Full Text
Lalla RV, Latortue MC, Hong CH, et al.: A systematic review of oral fungal infections in patients receiving cancer therapy. Support Care in Cancer. 2010; 18(8): 985–992. PubMed Abstract | Publisher Full Text | Free Full Text
Lone MS, Bashir G, Bali N, et al.: Oral Candida colonization and infection in cancer patients and their antifungal susceptibility in a tertiary care hospital. Int J Adv Res. 2014; 2(5): 541–550. Reference Source
Miceli MH, Díaz JA, Lee SA: Emerging opportunistic yeast infections. Lancet Infect Dis. 2011; 11(2): 142–151. PubMed Abstract | Publisher Full Text
Mohammed AB, Ali JH, Abdullah SK: Multiplex polymerase chain reaction identification of Candida species colonized sputum of patients suffering from various respiratory tract disorders in Duhok, Iraq. Int J Res Med Sci. 2016; 4(5): 1558–1563. Publisher Full Text
Nagla MMA, El Fadil OE, Muzamil AHM, et al.: Dataset 1 in: Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study. F1000Research. 2018. Data Source
Nigar I, Tarafder S, Khan RR, et al.: Species identification of Candida isolated from clinical specimens in a tertiary care hospital. BSMMU J. 2016; 9(1): 20–25. Publisher Full Text
Pfaller MA, Diekema DJ, Gibbs DL, et al.: Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: a 10.5-year analysis of susceptibilities of Candida Species to fluconazole and voriconazole as determined by CLSI standardized disk diffusion. J Clin Microbiol. 2010; 48(4): 1366–1377. PubMed Abstract | Publisher Full Text | Free Full Text
Pfaller MA, Diekema DJ, Messer SA, et al.: In vitro activities of caspofungin compared with those of fluconazole and itraconazole against 3,959 clinical isolates of Candida spp., including 157 fluconazole-resistant isolates. Antimicrob Agents Chemother. 2003; 47(3): 1068–1071. PubMed Abstract | Publisher Full Text | Free Full Text
Pfaller MA, Pappas PG, Wingard JR: Invasive fungal pathogens: current epidemiological trends. Clin Infect Dis. 2006; 43(1): S3–S14. Publisher Full Text
Ramani R, Gromadzki S, Pincus DH, et al.: Efficacy of API 20C and ID 32C systems for identification of common and rare clinical yeast isolates. J Clin Microbiol. 1998; 36(11): 3396–3398. PubMed Abstract | Free Full Text
Reiss E, Tanaka K, Bruker G, et al.: Molecular diagnosis and epidemiology of fungal infections. Med Mycol. 1998; 36 Suppl 1: 249–257. PubMed Abstract
Sherman F, fink JR, Hick JB: The laboratory course manual for methods in yeast genetics. Cold spring harbor press, cold spring harber, NY P179. 1986. Reference Source
Shokohi T, Bandalizadeh Z, Hedayati MT, et al.: In vitro antifungal susceptibility of Candida species isolated from oropharyngeal lesions of patients with cancer to some antifungal agents. Jundishapur J Microbiol. 2011; 4(1): S19–S26. Reference Source
Ungureanu A, Gaman AE, Turculeanu A, et al.: Incidence and Antifungal Susceptibility of Candida albicans infections. Curr Health Sci J. 2016; 42(2): 164–168. Publisher Full Text
Walsh TJ, Groll JA, Hiemenz JE, et al.: Infections due to emerging and uncommon medically important fungal pathogens. Clin Microbiol Infect. 2004; 10 Suppl 1: 48–66. PubMed Abstract | Publisher Full Text
White TJ, Bruns T, Lee S, et al.: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In MA Innis, DH Gelfand, JJ Sninsky and TJ White (ed.), PCR protocols: a guide to methods and applications. Academic Press, Inc., San Diego, Calif. 1990. Reference Source
Wilson LS, Reyes CM, Stolpman M, et al.: The direct cost and incidence of systemic fungal infections. Value Health. 2002; 5(1): 26–34. PubMed Abstract | Publisher Full Text
Xu L, Zhang H, Liu J, et al.: Investigation of the oral infections and manifestations seen in patients with advanced cancer. Pak J Med Sci. 2013; 29(5): 1112–1115. PubMed Abstract | Free Full Text
Zimbeck AJ, Iqbal N, Ahlquist AM, et al.: FKS mutations and elevated echinocandin MIC values among Candida glabrata isolates from U.S. population-based surveillance. Antimicrob Agents Chemother. 2010; 54: 5042–7. PubMed Abstract | Publisher Full Text | Free Full Text

Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 11 Apr 2018

Author details Author details

Mohamed M.A. Nagla
Roles: Conceptualization, Funding Acquisition, Investigation, Resources, Software, Validation, Visualization, Writing – Original Draft Preparation

Omer E. El Fadil
Roles: Conceptualization, Supervision

Abdel Hamid M. Muzamil
Roles: Resources

Altayeb N. Hisham
Roles: Methodology, Software

Mohamed B. Bahaeldeen
Roles: Methodology

El-Amin El-Nour
Roles: Supervision, Validation, Writing – Review & Editing

Competing interests

No competing interests were disclosed.

Grant information

The project was financially supported by Ministry of Higher Education and Scientific Research, Sudan.

Article Versions (1)

version 1

Published: 11 Apr 2018, 7:443

https://doi.org/10.12688/f1000research.14019.1

© 2018 Nagla MMA et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).

Download

Export To

metrics

	Views	Downloads
F1000Research	-	-
PubMed Central Data from PMC are received and updated monthly.	-	-

Citations

SEE MORE DETAILS

CITE

how to cite this article

Nagla MMA, El Fadil OE, Muzamil AHM et al. Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Research 2018, 7:443 (https://doi.org/10.12688/f1000research.14019.1)

NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.

track

receive updates on this article

Track an article to receive email alerts on any updates to this article.

Open Peer Review

Version 1

VERSION 1

PUBLISHED 11 Apr 2018

Views

Reviewer Report 30 Jan 2019

Lucia Bulacio, Centro de Referencia en Micología - CEREMIC, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina; Facultad Católica de Química e Ingeniería Santa María de los Buenos Aires, Universidad Católica Argentina, Buenos Aires, Argentina

Approved

https://doi.org/10.5256/f1000research.15237.r41097

The subject is very interesting since the early study of the epidemiology of infectious diseases in immunocompromised patients contributes to reduced frequency of complications due to invasion and dissemination, which cause increased morbidity and mortality of patients.

Saccharo genus does not

Saccharo genus does not exist (Saccaromyces?)
C. dobliensis does not exist (C. dubliniensis?)
Pichi kudriavzevii does not exist (Picchia?)
P. sporocuriosa? L. fermentati?

The first time they are mentioned in the text, all isolates must be named using the complete nomenclature; this is the name of the genus followed by the specific epithet, e.g. Candida albicans, Saccharomyces cerevisiae.

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Yes
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Yes

Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Mycology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

CITE

Report a concern

Respond or Comment

Views

Reviewer Report 02 Nov 2018

Dimitrios Farmakiotis, Transplant and Oncology Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, RI, USA

Zoe Weiss, Department of Internal Medicine and Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, RI, USA

Approved with Reservations

https://doi.org/10.5256/f1000research.15237.r40051

This is an interesting study, but it is rather poorly analyzed. Also, some of the definitions need to be readdressed.

First of all, even in cancer patients, growth of Candida from sputum or urine does not mean

This is an interesting study, but it is rather poorly analyzed. Also, some of the definitions need to be readdressed.

First of all, even in cancer patients, growth of Candida from sputum or urine does not mean dissemination; rather colonization. Even if the patients have symptoms, Candida UTIs and even less pneumonia are extremely rare. The authors need to provide solid data such as histopathology, define that there were no other potential pathogens, and symptoms resolved only after antifungal.
I am not sure how appropriate it is to use chi-square to document that one condition (colonization) is more frequent than another (infection) within the same group. Besides, so what? If infection is properly defined, the authors should investigate if there was a statistically significant difference in % between their "case" and "control" groups.
Speaking of infection, any cases of candidemia? This is the main clinical syndrome that can result from heavy Candida colonization, mucosal breech, foreign bodies, especially lines, immunosuppression, elimination of other flora with antibacterials etc.
More clinical information is required and needs to be properly analyzed (e.g. risk factors for non-albicans species, different clinical syndromes etc.).
It might be good to analyze the data on different species presented in the article tables for statistically significant differences in the frequencies of different Candida species.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

No
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

No
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

No

Competing Interests: No competing interests were disclosed.

We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

CITE

Report a concern

Author Response 07 Nov 2018

nagla masaad, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan

07 Nov 2018

Author Response
1. The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the
... Continue reading
The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the oral cavity and urine or sputum in symptomatic patients so I recommend for further investigation so as to confirm it.

Point number 2: The authors stated that there was a statistical significant difference between infection and colonization among the case and control group.

Point number 4: It would be good to investigate that but, it wasn't one of my objectives.

Thanks for your good comment.

Nagla
The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the oral cavity and urine or sputum in symptomatic patients so I recommend for further investigation so as to confirm it.

Point number 2: The authors stated that there was a statistical significant difference between infection and colonization among the case and control group.

Point number 4: It would be good to investigate that but, it wasn't one of my objectives.

Thanks for your good comment.

Nagla
Competing Interests: No competing interests were disclosed. Close
Report a concern
Respond or Comment

COMMENTS ON THIS REPORT

Author Response 07 Nov 2018

nagla masaad, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan

07 Nov 2018

Author Response
1. The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the
... Continue reading
The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the oral cavity and urine or sputum in symptomatic patients so I recommend for further investigation so as to confirm it.

Point number 2: The authors stated that there was a statistical significant difference between infection and colonization among the case and control group.

Point number 4: It would be good to investigate that but, it wasn't one of my objectives.

Thanks for your good comment.

Nagla
The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the oral cavity and urine or sputum in symptomatic patients so I recommend for further investigation so as to confirm it.

Point number 2: The authors stated that there was a statistical significant difference between infection and colonization among the case and control group.

Point number 4: It would be good to investigate that but, it wasn't one of my objectives.

Thanks for your good comment.

Nagla
Competing Interests: No competing interests were disclosed. Close
Report a concern

Comments on this article Comments (0)

Version 1

VERSION 1 PUBLISHED 11 Apr 2018

Open Peer Review

Reviewer Status

Reviewer Reports

	Invited Reviewers
	1	2
Version 1 11 Apr 18	read	read

Dimitrios Farmakiotis, Brown University, Providence, USA

Zoe Weiss, Brown University, Providence, USA
Lucia Bulacio, Universidad Nacional de Rosario, Rosario, Argentina; Universidad Católica Argentina, Buenos Aires, Argentina

Comments on this article

All Comments(0)

Add a comment

Browse by related subjects

Back to all reports

Reviewer Report

4 Views

30 Jan 2019 | for Version 1

4 Views Cite this report Responses(0)

Approved

Saccharo genus does not exist (Saccaromyces?)
C. dobliensis does not exist (C. dubliniensis?)
Pichi kudriavzevii does not exist (Picchia?)
P. sporocuriosa? L. fermentati?

Is the work clearly and accurately presented and does it cite the current literature?

Yes
Is the study design appropriate and is the work technically sound?

Yes
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

Yes
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

Yes

Competing Interests

No competing interests were disclosed.

Reviewer Expertise

Mycology

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Respond to this report

Responses (0)

Back to all reports

Reviewer Report

8 Views

02 Nov 2018 | for Version 1

Dimitrios Farmakiotis, Transplant and Oncology Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, RI, USA

Zoe Weiss, Department of Internal Medicine and Division of Infectious Diseases, Warren Alpert Medical School, Brown University, Providence, RI, USA

8 Views Cite this report Responses(1)

Approved With Reservations

This is an interesting study, but it is rather poorly analyzed. Also, some of the definitions need to be readdressed.

First of all, even in cancer patients, growth of Candida from sputum or urine does not mean dissemination; rather colonization. Even if the patients have symptoms, Candida UTIs and even less pneumonia are extremely rare. The authors need to provide solid data such as histopathology, define that there were no other potential pathogens, and symptoms resolved only after antifungal.
I am not sure how appropriate it is to use chi-square to document that one condition (colonization) is more frequent than another (infection) within the same group. Besides, so what? If infection is properly defined, the authors should investigate if there was a statistically significant difference in % between their "case" and "control" groups.
Speaking of infection, any cases of candidemia? This is the main clinical syndrome that can result from heavy Candida colonization, mucosal breech, foreign bodies, especially lines, immunosuppression, elimination of other flora with antibacterials etc.
More clinical information is required and needs to be properly analyzed (e.g. risk factors for non-albicans species, different clinical syndromes etc.).
It might be good to analyze the data on different species presented in the article tables for statistically significant differences in the frequencies of different Candida species.

Is the work clearly and accurately presented and does it cite the current literature?

Partly
Is the study design appropriate and is the work technically sound?

No
Are sufficient details of methods and analysis provided to allow replication by others?

Yes
If applicable, is the statistical analysis and its interpretation appropriate?

No
Are all the source data underlying the results available to ensure full reproducibility?

Yes
Are the conclusions drawn adequately supported by the results?

No

Competing Interests

No competing interests were disclosed.

Respond to this report

Responses (1)

Author Response

07 Nov 2018

nagla masaad, Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan

The first point of referee comment. Answer: I didn't confirm that it was dissemination. I suggested it may be dissemination due to the presence of the same strain in the oral cavity and urine or sputum in symptomatic patients so I recommend for further investigation so as to confirm it.
Point number 2: The authors stated that there was a statistical significant difference between infection and colonization among the case and control group.
Point number 4: It would be good to investigate that but, it wasn't one of my objectives.

Thanks for your good comment.

Nagla

View more View less

Competing Interests

No competing interests were disclosed.

Alongside their report, reviewers assign a status to the article:

Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested

Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.

Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions

Click here to access the data.

Downloaded data do not display as expected? Download the data

[1] Akapan A, Morgan R: Oral candidiasis. Postgard Med J. 2002; 78(922): 455–459. PubMed Abstract | Publisher Full Text | Free Full Text

[2] Al-Dwairi ZN, Darwazeh MG, Shukri LA: Isolation of Candida species from the oral cavity and fingertips of complete and partial dentures wearers. J Dent Health Oral Disord Ther. 2014; 1(3): 1–6. Publisher Full Text

[3] Aldossary MA, Almansour NA, Abdulraheem BS: Isolation and identification of Candida species from the oral cavity of cancer patients undergoing chemotherapy in Basrah, Irag. J Of Biol Agricul And Healthca. 2016; 6(18). Reference Source

[4] Bagg J, Sweeney MP, Lewis MA, et al.: High prevalence of non-albicans yeasts and detection of anti-fungal resistance in the oral flora of patients with advanced cancer. Palliat Med. 2003; 17(6): 477–81. PubMed Abstract | Publisher Full Text

[5] Blot S, Dimopoulos G, Rello J, et al.: Is Candida really a threat in the ICU? Curr Opin Crit Care. 2008; 14(5): 600–604. PubMed Abstract | Publisher Full Text

[6] Chen YC, Eisner JD, Kattar MM, et al.: Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol. 2001; 39(11): 4042–4051. PubMed Abstract | Publisher Full Text | Free Full Text

[7] Ciardo DE, Schär G, Böttger EC, et al.: Internal transcribed spacer sequencing versus biochemical profiling for identification of medically important yeasts. J Clin Microbiol. 2006; 44(1): 77–84. PubMed Abstract | Publisher Full Text | Free Full Text

[8] Cruciani M, Serpelloni G: Management of Candida infections in the adult intensive care unit. Expert Opin Pharmacother. 2008; 9(2): 175–191. PubMed Abstract | Publisher Full Text

[9] de Sousa LVNF, Santos VL, de Souza Monteiro A, et al.: Isolation and identification of Candida species in patients with orogastric cancer: susceptibility to antifungal drugs, attributes of virulence in vitro and immune response phenotype. BMC Infect Dis. 2016; 16: 86. PubMed Abstract | Publisher Full Text | Free Full Text

[10] Gassoum A, Arbab MA, Aldeaf SAH, et al.: Allele Frequency Of P53 Gene Arg72Pro In Sudanese Meningioma Patients And Controls. IJSTR. 2014; 6(3): 243–248. Reference Source

[11] Han XY, Tarrand JJ, Escudero E: Infections by the yeast Kodomaea (Pichia) ohmeri: two cases and literature review. Eur J Clin Microbiol Infect Dis. 2004; 23(2): 127–130. PubMed Abstract | Publisher Full Text

[12] Ismet N, Shirin T, Rehana RK, et al.: Species identification of Candida isolated from clinical specimens in tertiary care hospital. BSMMU J. 2016; 9(1): 20–25. Publisher Full Text

[13] Iwen PC, Hinrichs SH, Rupp ME: Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol. 2002; 40(1): 87–109. PubMed Abstract | Publisher Full Text

[14] Lalla RV, Latortue MC, Hong CH, et al.: A systematic review of oral fungal infections in patients receiving cancer therapy. Support Care in Cancer. 2010; 18(8): 985–992. PubMed Abstract | Publisher Full Text | Free Full Text

[15] Lone MS, Bashir G, Bali N, et al.: Oral Candida colonization and infection in cancer patients and their antifungal susceptibility in a tertiary care hospital. Int J Adv Res. 2014; 2(5): 541–550. Reference Source

[16] Miceli MH, Díaz JA, Lee SA: Emerging opportunistic yeast infections. Lancet Infect Dis. 2011; 11(2): 142–151. PubMed Abstract | Publisher Full Text

[17] Mohammed AB, Ali JH, Abdullah SK: Multiplex polymerase chain reaction identification of Candida species colonized sputum of patients suffering from various respiratory tract disorders in Duhok, Iraq. Int J Res Med Sci. 2016; 4(5): 1558–1563. Publisher Full Text

[18] Nagla MMA, El Fadil OE, Muzamil AHM, et al.: Dataset 1 in: Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study. F1000Research. 2018. Data Source

[19] Nigar I, Tarafder S, Khan RR, et al.: Species identification of Candida isolated from clinical specimens in a tertiary care hospital. BSMMU J. 2016; 9(1): 20–25. Publisher Full Text

[20] Pfaller MA, Diekema DJ, Gibbs DL, et al.: Results from the ARTEMIS DISK Global Antifungal Surveillance Study, 1997 to 2007: a 10.5-year analysis of susceptibilities of Candida Species to fluconazole and voriconazole as determined by CLSI standardized disk diffusion. J Clin Microbiol. 2010; 48(4): 1366–1377. PubMed Abstract | Publisher Full Text | Free Full Text

[21] Pfaller MA, Diekema DJ, Messer SA, et al.: In vitro activities of caspofungin compared with those of fluconazole and itraconazole against 3,959 clinical isolates of Candida spp., including 157 fluconazole-resistant isolates. Antimicrob Agents Chemother. 2003; 47(3): 1068–1071. PubMed Abstract | Publisher Full Text | Free Full Text

[22] Pfaller MA, Pappas PG, Wingard JR: Invasive fungal pathogens: current epidemiological trends. Clin Infect Dis. 2006; 43(1): S3–S14. Publisher Full Text

[23] Ramani R, Gromadzki S, Pincus DH, et al.: Efficacy of API 20C and ID 32C systems for identification of common and rare clinical yeast isolates. J Clin Microbiol. 1998; 36(11): 3396–3398. PubMed Abstract | Free Full Text

[24] Reiss E, Tanaka K, Bruker G, et al.: Molecular diagnosis and epidemiology of fungal infections. Med Mycol. 1998; 36 Suppl 1: 249–257. PubMed Abstract

[25] Sherman F, fink JR, Hick JB: The laboratory course manual for methods in yeast genetics. Cold spring harbor press, cold spring harber, NY P179. 1986. Reference Source

[26] Shokohi T, Bandalizadeh Z, Hedayati MT, et al.: In vitro antifungal susceptibility of Candida species isolated from oropharyngeal lesions of patients with cancer to some antifungal agents. Jundishapur J Microbiol. 2011; 4(1): S19–S26. Reference Source

[27] Ungureanu A, Gaman AE, Turculeanu A, et al.: Incidence and Antifungal Susceptibility of Candida albicans infections. Curr Health Sci J. 2016; 42(2): 164–168. Publisher Full Text

[28] Walsh TJ, Groll JA, Hiemenz JE, et al.: Infections due to emerging and uncommon medically important fungal pathogens. Clin Microbiol Infect. 2004; 10 Suppl 1: 48–66. PubMed Abstract | Publisher Full Text

[29] White TJ, Bruns T, Lee S, et al.: Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In MA Innis, DH Gelfand, JJ Sninsky and TJ White (ed.), PCR protocols: a guide to methods and applications. Academic Press, Inc., San Diego, Calif. 1990. Reference Source

[30] Wilson LS, Reyes CM, Stolpman M, et al.: The direct cost and incidence of systemic fungal infections. Value Health. 2002; 5(1): 26–34. PubMed Abstract | Publisher Full Text

[31] Xu L, Zhang H, Liu J, et al.: Investigation of the oral infections and manifestations seen in patients with advanced cancer. Pak J Med Sci. 2013; 29(5): 1112–1115. PubMed Abstract | Free Full Text

[32] Zimbeck AJ, Iqbal N, Ahlquist AM, et al.: FKS mutations and elevated echinocandin MIC values among Candida glabrata isolates from U.S. population-based surveillance. Antimicrob Agents Chemother. 2010; 54: 5042–7. PubMed Abstract | Publisher Full Text | Free Full Text

Internal transcribed spacer for identification of yeast species isolated from cancer patients at the Isotope and Radiation Center, Khartoum, Sudan: A cross-sectional, case-control study

Abstract

Keywords

Introduction

Methods

Study design and participants

Sample collection

DNA extraction

PCR amplification procedure

DNA sequencing

Statistical analysis

Ethical statement

Results

Table 1. Culture results of urine and sputum specimens collected from the study group.

Table 2. Prevalence of oral candidiasis and colonization among the study and control groups.

Figure 1. Agarose gel showing the results obtained for conventional PCR of isolated yeast genomic DNA.

Figure 2. Agarose gel showing the results obtained for conventional PCR of isolated yeast genomic DNA.

Table 3. Species distribution among the study and control groups.

Table 4. Frequency of mixed oral yeast species among Sudanese cancer patients.

Figure 3.

Discussion

Conclusion

Data availability

Competing interests

Grant information

Supplementary material

References

Comments on this article Comments (0)

Open Peer Review

Comments on this article Comments (0)

Open Peer Review

Reviewer Status

Reviewer Reports

Comments on this article

Browse by related subjects

The problem

How to fix it

Competing Interests Policy

Stay Updated