Usefulness of multilocus sequence typing for characterization of clinical isolates of Candida albicans

Oral Candida albicans strain diversity and maintenance in HIV positive women in South Africa

OBJECTIVE

This study investigated C. albicans strain diversity and maintenance in the oral cavity of HIV positive women over a 6 month period.

STUDY DESIGN

C. albicans strains were isolated from 17 HIV positive women at Charlotte Maxeke Academic Hospital, Johannesburg at 3 intervals over a 6 month period. Strains were genotyped using ABC and Multilocus Sequence Typing (MLST) techniques. In the MLST technique, for each strain, a Diploid Sequence Type (DST) number was obtained. Using cluster analysis, an Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and a matrix of strain similarities were generated. Strains were also compared to the previous South African isolates documented in the MLST database.

RESULTS

Ninety four percent of women carried the same ABC genotype for 6 months. MLST technique, showed that ten women (58.8%) carried the same DST at 2 visits, while seven (41.2%) carried different DST at all visits. Further analysis showed that 64.7% of women were recolonised with different strains and 35.3% carried the same strains of C. albicans with heterozygosity. A total of 40 diploid sequence types were identified of which 27 DSTs were unique to this study group that were added to the MLST database. Most of the strains were closely related to previously isolated strains from South Africa.

CONCLUSION

Recolonization of the oral cavity with different strains and microevolution of the original strains of C. albicans can occur, which can be a potential problem for HIV patients, in whom highly virulent and drug resistant strains can emerge.

Genetic Diversity and Phylogenetic Study of Leishmania Species in Iran by Multilocus Sequence Typing

Background

Leishmaniasis is an important public health parasitic infection, which is endemic in many parts of the world, including Iran. We aimed to investigate genetic diversity and phylogenetic relationship among different Leishmania isolates using multi-locus sequence typing (MLST).

Methods

Totally, 41 isolates collected either from patients referred to Leishmaniasis Diagnostics and Treatment Center at Tehran University of Medical Sciences, Tehran, Iran or from animals during 2019-2021, were subjected to the study. They included L. major and L. tropica from human, L. infantum from canine, and L. turanica from rodents from different endemic foci of Iran analyzed using MLST including gp63, g6pdh, lack, nagt, and hsp70 genes.

Results

A total of 5010 bps was analyzed from each isolate. The three targets, nagt, lack, and g6pdh, generated better topology comparing to the other genes. In the 44 isolates, 22 haplotypes (STs) were identified. Leishmania tropica contained the highest number of haplotypes (n=12) comparing to L. major (n=8), L. infantum (n=1) and L. turanica (n=1). All five genomic loci caused separation of Iranian Leishmania species at the species level, indicating conservation of these genes in the Leishmania parasite.

Conclusion

The highest number of haplotypes belonged to L. tropica, indicating that the genetic diversity of this species is higher than that of L. major. It was further confirmed that the MLST is a suitable method to examine genetic variation of Leishmania parasites with respect to evolutionary and epidemiological studies.

Multilocus sequence typing of Candida albicans oral isolates reveals high genetic relatedness of mother-child dyads in early life

Candida albicans is a pathogenic fungus recently recognized for its role in severe early childhood caries development (S-ECC). C. albicans oral colonization begins at birth, but the extent of the mother's involvement in yeast transmission to their children is unclear, therefore, this study used a prospective mother-infant cohort to investigate the maternal contribution of C. albicans oral colonization in early life. Oral samples were collected from 160 mother-child dyads during pregnancy and from birth to two years of life. We used whole-genome sequencing to obtain the genetic information of C. albicans isolates and examined the genetic relatedness of C. albicans between mothers and their children using Multilocus Sequence Typing. Multivariate statistical methods were used to identify factors associated with C. albicans' acquisition (horizontal and vertical transmissions). Overall, 227 C. albicans oral isolates were obtained from 93 (58.1%) of mother-child pairs. eBURST analysis revealed 16 clonal complexes, and UPGMA analysis identified 6 clades, with clade 1 being the most populated 124 isolates (54.6%). Significantly, 94% of mothers and children with oral C. albicans had highly genetically related strains, highlighting a strong maternal influence on children's C. albicans acquisition. Although factors such as race, ethnicity, delivery method, and feeding behaviors did not show a significant association with C. albicans vertical transmission, the mother's oral hygiene status reflected by plaque index (PI) emerged as a significant factor; Mothers with higher dental plaque accumulation (PI >=2) had a significantly increased risk of vertically transmitting C. albicans to their infants [odds ratio (95% confidence interval) of 8.02 (1.21, 53.24), p=0.03]. Furthermore, Black infants and those who attended daycare had an elevated risk of acquiring C. albicans through horizontal transmission (p <0.01). These findings highlight the substantial role of maternal transmission in the oral acquisition of C. albicans during early life. Incorporating screening for maternal fungal oral carriage and implementing oral health education programs during the perinatal stage may prove valuable in preventing fungal transmission in early infancy.

Molecular characterization of fungal endophthalmitis and keratitis caused by yeasts

Candida species are the most common causes of sight-threatening fungal ocular infections in temperate regions of the world. Despite their relevance, little is known about the emergence of novel species and the molecular epidemiology of these infections. Here, we molecularly characterized 38 yeast isolates collected from patients diagnosed with endophthalmitis or keratitis at Massachusetts Eye and Ear from 2014 to 2021. Sequencing of the ITS1-5.8S-/ITS2 regions demonstrated that this population of yeasts was dominated by Candida spp. (37 out of 38; 97%), with 58% of the cases caused by C. albicans (n = 22) and the remaining by emerging non-albicans species, predominantly by C. parapsilosis (n = 8) and C. dubliniensis (n = 6). One isolate each was identified as C. tropicalis and Clavispora lusitaniae. Interestingly, all C. dubliniensis were isolated from endophthalmitis and most C. parapsilosis from keratitis. Multilocus sequence typing analysis of C. albicans showed a prevalence of CC-1 isolates that has DST69 as the putative founder, with 64% of them belonging to this clonal complex (CC). Isolates grouped within this cluster were more predominant in endophthalmitis (10 out of 14; 71%). One C. albicans CC-1 isolate was multi-azole resistant. In conclusion, we observed that nearly half of the ocular infections caused by yeasts are associated with C. albicans, with evidence for the emergence of non-albicans species that are differentially enriched in distinct ocular niches. Candida albicans isolates clustered within the predominant CC-1 group were particularly more common in endophthalmitis, demonstrating a potential pattern of ocular disease enrichment within this clade.

Genotyping of candida albicans isolates obtained from vulvovaginal candidiasis patients in Zanjan, Iran, based on ABC and RPS typing systems

Background and Purpose

Genotyping of pathogenic microorganisms is important for epidemiological studies and the adoption of appropriate strategies to control infectious diseases. In this regard, the present study aimed to genotype Candida albicans strains isolated from vulvovaginal candidiasis (VVC) patients using combined ABC type (25SrDNA) and repetitive sequence (RPS) typing systems. using combined typing systems of ABC type (25SrDNA) and repetitive sequence (RPS).

Materials and Methods

In total, 140 patients with VVC were investigated. Vaginal discharges were collected on Sabouraud dextrose agar and identified by CHROMagar. After species identification, a polymerase chain reaction system targeting 25S rDNA as well as ALT repeats in the RPS was designed to determine C. albicans genotypes. The dendrogram was constructed by zero-one matrix data based on the combination of ABC and RPS typing systems. Statistical analysis of data was performed in SPSS software (version 23).

Results

In total, 41 (29.3%) Candida isolates were obtained from 140 VVC patients. The most common Candida species that were identified included C. glabrata (56.1%) and C. albicans (39%). Genotype A3 with five isolates (31.25%) had the highest frequency, followed by B2/3 with three isolates (18.3%), A3/4, C3/4, and B3/4 with two isolates (12.5%), and C2/3 and C3 with one isolate (6.25%), respectively. No significant association was found between the genotypes and antifungal resistance (P<0.05).

Conclusion

The results showed that non-albicans Candida species are more prevalent in VVC patients, compared to C. albicans. The results also indicated that ABC and RPS typings are useful for rapid genotyping and differentiation of C. albicans isolates in regional and small-scale studies.

Specific associations between fungi and bacteria in broncho-alveolar aspirates from mechanically ventilated intensive care unit patients

The detection of fungi in the human respiratory tract may represent contamination, colonization or a respiratory infection. To develop effective management strategies, a more accurate and comprehensive understanding of the lung fungal microbiome is required. Therefore, the objective of the present study was to define the "mycobiome" of mechanically ventilated patients admitted to an intensive care unit (ICU) using broncho-alveolar aspirate ("sputum") samples and correlate this with clinical parameters and the bacterial microbiota. To this end, the mycobiome of 33 sputum samples was analyzed by Internal Transcribed Spacer2 (ITS2) amplicon sequencing of the ribosomal operons. The results show that in the investigated sputa of mechanically ventilated patients Candida spp. were most frequently detected, independent of pneumonia or antimicrobial therapy. The presence of Candida excluded in most cases the presence of Malassezia, which was the second most-frequently encountered fungus. Moreover, a hierarchical clustering of the sequence data indicated a patient-specific mycobiome. Fungi detected by culturing (Candida and Aspergillus) were also detected through ITS2 sequencing, but other yeasts and fungi were only detectable by sequencing. While Candida showed no correlations with identified bacterial groups, the presence of Malassezia and Rhodotorula correlated with oral bacteria associated with periodontal disease. Likewise, Cladosporium correlated with other oral bacteria, whereas Saccharomyces correlated more specifically with dental plaque bacteria and Alternaria with the nasal-throat-resident bacteria Neisseria, Haemophilus and Moraxella. In conclusion, ITS2 sequencing of sputum samples uncovered patient-specific lung mycobiomes, which were only partially detectable by culturing, and which could be correlated to specific nasal-oral-pharyngeal niches.

Multilocus Sequence Typing and Antifungal Susceptibility of Candida albicans Isolates From Milk and Genital Tract of Dromedary Camel

Multilocus sequence typing (MLST) was used to study the genetic diversity and population structure of 48 Candida albicans (C. albicans) isolates from the udder or genital tract of apparently healthy or diseased camels. This study aimed also to determine the frequency of C. albicans isolates in the genital tract and udder of healthy or diseased female dromedary camels. A total of 240 mature dromedary camels (230 females and 10 males) were categorized based on the clinical examination of gentile tract and udder into five groups [fertile females (n = 70), infertile females (n = 115), healthy udder (n = 15), mastitis (n = 30), and fertile males (n = 10)]. Swabs were collected from male and female genital tracts of dromedary camels and milk samples were collected from healthy and diseased udders. C. albicans was isolated from 20% of the samples. The frequency of isolation was significantly higher (p < 0.00001) in disease camels (75%) compared with apparently healthy camels (25%). Most of C. albicans was isolated from infertile female genitalia (62.50%) which was significantly higher than that isolated from fertile female genitalia (16.67%). Multilocus sequence (MLS) analysis identified seven different diploid sequence types (DSTs) including DST2, DST50, DST62, DST69, DST124, DST142, and DST144. The most frequently identified DTS was DST69 (13/48) which significantly higher (p ≤ 0.05) than DST2, DST62, and DST124. The frequency of identification of DST50, DST142, and DST 144 was significantly higher (p ≤ 0.05) than DST62. DST62 and DST124 were isolated only from diseased camels. DST62 was isolated only from mastitic milk. DST124 was isolated only from infertile female genitalia. The percentage of DST50 and DST 142 was significantly higher in diseased camels (infertile females) than in the apparently healthy ones (fertile females). DST2 and DST50 were isolated only from female genitalia of apparent health and diseased camels. The C. albicans isolated from diseased camels had significantly higher biofilm formation, hydrophobicity, phospholipase, proteinase, and hemolysin activities compared with the isolates from apparent healthy camels. All isolates were sensitive to amphotericin B, itraconazole, micafungin, posaconazole and voriconazole. In conclusion, the present study represents the first molecular typing of C. albicans in samples isolated from milk and the genital tract of the dromedary camel. MLST is a useful tool for studying the epidemiology and evolution of C. albicans. Early identification of Candida species and attention to Candida virulence factors and their antifungal susceptibility patterns is very important for establishing strategies to control and/or prevent candidiasis by novel therapeutic management. Amphotericin B, itraconazole, micafungin, posaconazole, or voriconazole can be efficient in treatment of candidiasis.

Candida albicans Multilocus Sequence Typing Clade I Contributes to the Clinical Phenotype of Vulvovaginal Candidiasis Patients

Candida albicans is the most frequent fungal species responsible for vulvovaginal candidiasis (VVC), which exhibits distinct genetic diversity that is linked with the clinical phenotype. This study aimed to assess the genotypes and clinical characteristics of different C. albicans isolates from VVC patients. Based on multilocus sequence typing (MLST), clade 1 was identified as the largest C. albicans group, which appeared most frequently in recurrent VVC and treatment failure cases. Further study of antifungal susceptibility demonstrated that MLST clade 1 strains presented significantly higher drug resistance ability than non-clade 1 strains, which result from the overexpression of MDR1. The mRNA and protein expression levels of virulence-related genes were also significantly higher in clade 1 isolates than in non-clade 1 isolates. Proteomic analysis indicated that the protein stabilization pathway was significantly enriched in clade 1 strains and that RPS4 was a central regulator of proteins involved in stress resistance, adherence, and DNA repair, which all contribute to the resistance and virulence of MLST clade 1 strains. This study was the first attempt to compare the correlation mechanisms between C. albicans MLST clade 1 and non-clade 1 strains and the clinical phenotype, which is of great significance for VVC classification and treatment.

Staphylococcus aureus genotype variation among and within periprosthetic joint infections

Staphylococcus aureus is a common organism in orthopedic infections, but little is known about the genetic diversity of strains during an infectious process. Using periprosthetic joint infection (PJI) as a model, a prospective study was designed to quantify genetic variation among S. aureus strains both among and within patients. Whole genome sequencing and multilocus sequence typing was performed to genotype these two populations at high resolution. In nasal cultures, 78% of strains were of clonal complexes CC5, CC8, and CC30. In PJI cultures, only 63% could be classified in these common clonal complexes. The PJI cultures had a larger proportion of atypical strains, and these atypical strains were associated with poor host status and compromised immune conditions. Mutations in genes involved in fibronectin binding (ebh, fnbA, clfA, and clfB) systematically distinguished later PJI isolates from the first PJI isolate from each patient. Repeated mutations in S. aureus genes associated with extracellular matrix binding were identified, suggesting adaptive, parallel evolution of S. aureus during the development of PJI.

Multilocus Sequence Typing Reveals Extensive Genetic Diversity of the Emerging Fungal Pathogen Scedosporium aurantiacum

Scedosporium spp. are the second most prevalent filamentous fungi after Aspergillus spp. recovered from cystic fibrosis (CF) patients in various regions of the world. Although invasive infection is uncommon prior to lung transplantation, fungal colonization may be a risk factor for invasive disease with attendant high mortality post-transplantation. Abundant in the environment, Scedosporium aurantiacum has emerged as an important fungal pathogen in a range of clinical settings. To investigate the population genetic structure of S. aurantiacum, a MultiLocus Sequence Typing (MLST) scheme was developed, screening 24 genetic loci for polymorphisms on a tester strain set. The six most polymorphic loci were selected to form the S. aurantiacum MLST scheme: actin (ACT), calmodulin (CAL), elongation factor-1α (EF1α), RNA polymerase subunit II (RPB2), manganese superoxide dismutase (SOD2), and β-tubulin (TUB). Among 188 global clinical, veterinary, and environmental strains, 5 to 18 variable sites per locus were revealed, resulting in 8 to 23 alleles per locus. MLST analysis observed a markedly high genetic diversity, reflected by 159 unique sequence types. Network analysis revealed a separation between Australian and non-Australian strains. Phylogenetic analysis showed two major clusters, indicating correlation with geographic origin. Linkage disequilibrium analysis revealed evidence of recombination. There was no clustering according to the source of the strains: clinical, veterinary, or environmental. The high diversity, especially amongst the Australian strains, suggests that S. aurantiacum may have originated within the Australian continent and was subsequently dispersed to other regions, as shown by the close phylogenetic relationships between some of the Australian sequence types and those found in other parts of the world. The MLST data are accessible at http://mlst.mycologylab.org. This is a joined publication of the ISHAM/ECMM working groups on “Scedosporium/Pseudallescheria Infections” and “Fungal Respiratory Infections in Cystic Fibrosis”.

A prospective study on vulvovaginal candidiasis: multicentre molecular epidemiology of pathogenic yeasts in China

BACKGROUND

Vulvovaginal candidiasis (VVC) is frequent in women of reproductive age, but very limited data are available on the epidemiology in cases of VVC in China.

OBJECTIVES

The current study has been conducted to reveal the prevalence, species distribution of yeast causing VVC and molecular genetics of Candida albicans in China.

METHODS

Vaginal swabs were collected from 543 VVC outpatients recruited in 12 hospitals in China between September 2017 and March 2018. They were preliminarily incubated on Sabouraud dextrose agar and then positive subjects of which were then transmitted to our institute for further identification. CHROMagar™ was used to isolate Candida species, and all isolates were finally identified by DNA sequencing. Multilocus sequence typing (MLST) was used to analyse phylogenetic relationships of the various C. albicans isolates.

RESULTS

Eleven different yeast species were identified in 543 isolates, among which C. albicans (84.7%) was the most frequent, followed by C. glabrata (8.7%). We obtained 117 unique diploid sequence types from 451 clinical C. albicans isolates and 92 isolates (20.4%) belonged to a New Clade. All the strains appearing in the New Clade were from northern China and they were isolated from non-recurrent VVC.

CONCLUSIONS

Our findings suggest that C. albicans are still the main cause of VVC in China and the majority of C. albicans isolates belongs to Clade 1 with DST 79 and DST 45 being two most common. Moreover, the New Clade revealed in our study seems to be specific to northern China.

Reduction of susceptibility to azoles and 5-fluorocytosine and growth acceleration in Candida albicans in glucosuria

Diabetes mellitus is a chronic metabolic disease characterized by hyperglycemia and glucosuria, and is a risk factor for Candida infections. To reveal the potential effects of glucosuria on Candida spp., we investigated their growth and antifungal susceptibilities in normal human urine to which glucose was added. The viable cell numbers of Candida spp. were more than 10 fold higher in the urine added 3000 mg/dL glucose than in plain urine. In antifungal susceptibility, more than 80% of Candida albicans clinical isolates increased minimum inhibitory concentrations of azoles and 5-fluorocytosine with the addition of glucose, and exceeded their breakpoints. In most of the C. albicans clinical isolates, the mRNA expression of the azole resistance genes ERG11, CDR1, CDR2, and MDR1 in the presence of glucose in urine. These observations provide valuable information about the clinical course and therapeutic effects of azoles against C. albicans infections in patients with diabetes mellitus and hyperglucosuria.

Molecular typing of multi-drug resistant Candida albicans isolated from the Segamat community, Malaysia

In the past decade, researchers have focused on the emergence of drug resistance in fungal pathogens such as Candida albicans, also considered as pathobionts that occur harmlessly in the human body but could potentially be triggered to cause diseases. The increasing rate of antifungal resistance in commensal gut fungi is alarming and should be further investigated. Here, we report seven novel MLST (Multi Locus Sequence Typing) genotypes of multi-drug resistant C. albicans isolates obtained from participants of a community study in Segamat, a district in the state of Johor, Malaysia. A total of eight C. albicans were isolated from four individuals, which were found to express high resistance against fluconazole, itraconazole, voriconazole and 5-fluorocytosine antifungals. MLST was performed to assess the clonal relatedness of these drug resistant isolates among themselves and against other strains isolated from other geographical regions. The novel MLST C. albicans sequence types suggest significant genetic changes compared to previous genotypes.

Molecular genotyping of Candida albicans isolated from different sites may trace the etiological infection routes: Observation in China

BACKGROUND

Invasive candidiasis is a growing concern worldwide, especially in immunocompromised patients, including ICU patients.

OBJECTIVES

As Candida albicans is the leading cause of candidaemia, it is important to investigate the evolution of C. albicans in patients with candidaemia.

METHODS

We analysed 238 strains of C. albicans isolated from different body sites. Antifungal susceptibility testing, CAI loci genotyping and multilocus sequence typing (MLST) of all isolates were performed. The relationships among the total isolates that differed in sequence at only one of the seven housekeeping gene loci were analysed using eBURST.

RESULTS

Multilocus sequence typing analysis in 238 isolates by combining seven housekeeping alleles revealed 175 diploid sequence types, in which 84 were newly identified. eBURST analysis for these data recognised 19 clonal complexes (CCs) and 79 singletons. Besides, seventy-three CAI genotypes were identified. Blood isolates showed maximum genotypes (49), and the dominant genotypes were CAI 17-21 and CAI 21-21. Oral isolates possessed 25 CAI genotypes, and the dominant genotypes were CAI 17-21 and CAI 21-21 as well. Since isolates with CAI allele numbers <30 showed easier transmission, CAI 17-21 and CAI 21-21 were the most frequently transmitted. Finally, the CAI genotypes were classified into six groups.

CONCLUSIONS

This work revealed the oral and blood strains isolated from the patients with candidaemia in ICU shared the identical dominant CAI genotypes. Our data expanded the C. albicans MLST database and helped with understanding the evolution and spread of invasive candidiasis.

Molecular Epidemiology, Genetic Diversity, and Antifungal Susceptibility of Major Pathogenic Dermatophytes Isolated From Human Dermatophytosis

Background

Dermatophytes are a homogeneous group of species with low genetic diversity, and there are still many uncertainties about the boundaries among species.

Objectives

Aiming at clarifying the relationships among species in the genus and introducing suitable genes for multilocus sequence typing (MLST), a new MLST scheme approach was developed to characterize the major pathogenic dermatophytes.

Methods

We performed maximum parsimony (MP), MrBayes, RAxML, and eBURST analyses, based on the MLST scheme to scrutinize the evolution within 95 clinical isolates and four reference strains belonging to the four major dermatophytes species. Then, the discriminatory power, pairwise genetic distances, ratio dN/dS, and sequence types (STs) of these isolates were determined. Also, to study taxonomy, sequences of the internal transcribed spacer (ITS), Beta-tubulin (BT2), and translation elongation factor 1-α (TEF-1α) genes of other dermatophytes species available in the GenBank were analyzed.

Results

Findings of the present study indicated that three genes: BT2, ITS, and TEF−1α, which showed the greatest diversity among dermatophyte species, were suitable for MLST. The most prevalent STs were seen among the species of Trichophyton interdigitale. Also, two new genotypes, i.e., XXVII and XXVIII, were introduced for T. interdigitale and Trichophyton mentagrophytes. The least informative sites were found in Epidermophyton floccosum, Trichophyton rubrum, and T. mentagrophytes, while the most informative sites were observed in T. interdigitale. Furthermore, the most informative locus was TEF-1α. The phylogenetic tree, constructed by the combination of the three genes, shows a new topological pattern that confirms the derivation of the anthropophilic and zoophilic genera from the geophilic genus. Also, the phylogenetic analyses and pairwise distances of the combination of the three loci showed that Trichophyton tonsurans and Trichophyton equinum were a species complex, where T. equinum is derived from T. tonsurans.

Conclusions

Results of this study showed that MLST is very effective in determining the boundaries between species and taxonomy. Considering that there is no database for MLST dermatophytes, further studies are needed to determine the suitable genes for MLST. Also, the determination of STs in epidemiological studies and raising epidemiological information are helpful. This study was a new starting point to determine the ST and a foundation for a dermatophyte MLST database.

Association between CAI microsatellite, multilocus sequence typing, and clinical significance within Candida albicans isolates

Candida albicans bloodstream infection (BSI) is epidemiologically important because of its increasing frequency and serious outcome. Strain typing and delineation of the species are essential for understanding the phylogenetic relationship and clinical significance. Microsatellite CAI genotyping and multilocus sequence typing (MLST) were performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Data regarding demographics, comorbidities, risk factors, and clinical outcomes were recorded within adult patients with C. albicans BSI. Both CAI genotyping and MLST yielded comparable discriminatory power for C. albicans characterization. Besides, the distribution of CAI repetition showed a satisfactory phylogenetic association, which could be a good alternative method in the molecular phylogenetics of C. albicans and epidemiological studies. As for the clinical scenario, clade 17 isolates with CAI alleles either possessing 29 or more repetitions were related to higher 14-day and 30-day mortality, and shorter median survival days.

Diversity of the diploid sequence type of Candida albicans clinical isolates from a tertiary-care hospital in Mwanza, Tanzania

Geographical strain variations of Candida albicans causing different clinical conditions in susceptible individuals have been reported. In this study, the distribution of diploid sequence type of C. albicans was investigated in Mwanza, Tanzania. A total of 64 C. albicans were selected on the basis of their antifungal susceptibility patterns, followed by multilocus sequence typing (MLST) to establish the circulating sequence types (STs). Forty-eight MLST were obtained out of 64 isolates amounting to 75% population structure differences. Out of these STs, 27 (56.3%) were new diploid ST types. C. albicans isolates with new ST were more diverse than isolates with known STs (27/29, 93.1% vs. 21/35, 60%, p 0.002). In conclusion, C. albicans from clinical specimens were highly diverse, with more than half of the detected diploid ST not previously reported in the MLST database, thus confirming the genetic differences of C. albicans from different geographical regions.

Development of a Multilocus Sequence Typing Scheme for Giardia intestinalis

Giardia intestinalis is an intestinal protozoan most commonly found in humans. It has been grouped into 8 assemblages (A-H). Markers such as the glutamate dehydrogenase gene, triose phosphate isomerase and beta-giardin (β-giardin) have been widely used for genotyping. In addition, different genetic targets have been proposed as a valuable alternative to assess diversity and genetics of this microorganism. Thus, our objective was to evaluate new markers for the study of the diversity and intra-taxa genetic structure of G. intestinalis in silico and in DNA obtained from stool samples. We analysed nine constitutive genes in 80 complete genome sequences and in a group of 24 stool samples from Colombia. Allelic diversity was evaluated by locus and for the concatenated sequence of nine loci that could discriminate up to 53 alleles. Phylogenetic reconstructions allowed us to identify AI, AII and B assemblages. We found evidence of intra- and inter-assemblage recombination events. Population structure analysis showed genetic differentiation among the assemblages analysed.

Investigation of Genetic Relationships Between Hanseniaspora Species Found in Grape Musts Revealed Interspecific Hybrids With Dynamic Genome Structures

Hanseniaspora, a predominant yeast genus of grape musts, includes sister species recently reported as fast evolving. The aim of this study was to investigate the genetic relationships between the four most closely related species, at the population level. A multi-locus sequence typing strategy based on five markers was applied on 107 strains, confirming the clear delineation of species H. uvarum, H. opuntiae, H. guilliermondii, and H. pseudoguilliermondii. Huge variations were observed in the level of intraspecific nucleotide diversity, and differences in heterozygosity between species indicate different life styles. No clear population structure was detected based on geographical or substrate origins. Instead, H. guilliermondii strains clustered into two distinct groups, which may reflect a recent step toward speciation. Interspecific hybrids were detected between H. opuntiae and H. pseudoguilliermondii. Their characterization using flow cytometry, karyotypes and genome sequencing showed different genome structures in different ploidy contexts: allodiploids, allotriploids, and allotetraploids. Subculturing of an allotriploid strain revealed chromosome loss equivalent to one chromosome set, followed by an auto-diploidization event, whereas another auto-diploidized tetraploid showed a segmental duplication. Altogether, these results suggest that Hanseniaspora genomes are not only fast evolving but also highly dynamic.

Persistence of Clonal Azole-Resistant Isolates of Candida albicans from a Patient with Chronic Mucocutaneous Candidiasis in Colombia

PURPOSE

The present article describes retrospectively a case of a patient with chronic mucocutaneous candidiasis (CMC) who presented recurrent Candida albicans infection since he was 6 months old. We obtained 16 isolates recovered during a 4-year period. Our purpose was to determinate the susceptibility, genotyping, and the pathogenicity profile in all the isolates.

METHODS

Sixteen C. albicans were isolated from a 25-year-old male with several recurrent fungal infections admitted to Hospital. The isolates were recovered during 4 years from a different anatomical origin. We typified them by multilocus sequence typing, also we evaluated susceptibility to fluconazole, itraconazole, voriconazole, posaconazole, isavuconazole, caspofungin, and amphotericin B by microdilution method and we also test the pathogenic capacity in the Galleria mellonella model.

RESULTS

Genotyping of all clinical isolates showed the persistence of the same diploid sequence type (DST). Isolates changed their susceptibility profile over time, but there were no significant statistical differences in pathogenicity.

CONCLUSION

Herein, a persistent clonal isolates of C. albicans (DST 918) in a patient with CMC, showed changes in its susceptibility profile after several antifungal treatments acquiring gradual resistance to the azole drugs, which did not affect their pathogenicity.

Genetic diversity of Candida albicans isolates recovered from hospital environments and patients with severe acquired brain injuries

Although the epidemiology of pathogenic Candida species causing invasive human diseases is changing, Candida albicans still remains the most common cause of bloodstream infections worldwide. The propensity of this pathogen to cause infections is undoubtedly the result of its unique genetic plasticity that allow it to adapt and respond quickly to a myriad of changing conditions both in the host and in the environment. For this reason, we decided to investigate the genetic diversity of this important fungal pathogen in a particular category of patients with severe neurological deficits including the hospital environments where they are hospitalized. Genetic diversity of 21 C. albicans isolates recovered from blood, hands of healthcare workers and hospital environments was evaluated by using multilocus sequence typing (MLST) which revealed a high genetic heterogeneity with a set of 18 diploid sequence types (DSTs) recovered among 21 isolates investigated. Interestingly, 13 of these 18 MLST genotypes were completely new and added to the C. albicans MLST central database. Six eBURST clonal complexes (CC-1, CC-2, CC-6, CC-9, CC-27 and CC-42) and three singletons contained all DSTs found in this study. Among all the new DSTs identified, DST3388 was the most intriguing as this genotype was recovered from a typical C. albicans isolate clustering within the MLST-Clade 13, the most divergent evolutionary lineage within C. albicans population containing only isolates with unusual phenotypes originally known as Candida africana. In conclusion, the results of this study expand our understanding of the molecular epidemiology and global population structure of C. albicans suggesting that further studies on different categories of patients and hospital environments are needed to better understand how the population of this species adapts and evolves in heterogeneous hosts and changing environments.

Revision of the medically relevant species of the yeast genus Diutina

Diutina (Candida) rugosa is emerging as a causative agent of human infections. Recently some close relatives have been described, that is, D. mesorugosa, D. pseudorugosa, and D. neorugosa, some of which have also been implicated in human infection. Phylogenetic relationships of 24 clinical isolates of the D. rugosa complex are reconstructed using multilocus sequence analysis of five housekeeping genes, supplemented with phenotypic studies of CandiSelect™ 4 Agar and nutritional physiology. Diutina mesorugosa could not meaningfully be distinguished from D. rugosa and is regarded as a synonym. Diutina neorugosa and D. pseudorugosa represent separate, distantly related species within the genus Diutina, but have as yet not been encountered in clinical settings.

A Predominance of Clade 17 Candida albicans Isolated From Hemocultures in a Tertiary Care Hospital in Thailand

Candida albicans is one of the most common human fungal pathogens. Candidemia has significant mortality globally. No epidemiological study of C. albicans based on multilocus sequence typing (MLST) has been conducted in Thailand. Therefore, MLST was used to study the molecular epidemiology of C. albicans blood strains in a large Thai teaching hospital. In vitro virulence phenotypes and antifungal susceptibility testing by broth microdilution were also conducted. Forty-six C. albicans blood strains from 37 patients were collected from the Department of Microbiology, Siriraj Hospital, in 2016 and 2017. Most patients (71.8%) were more than 60 years old, and the case fatality rate was 54.8%. The male-to-female ratio was 5:3. Thirty-four diploid sequence types (DSTs), including six new DSTs, were identified, with DST2514 (8.7%) and DST2876 (8.7%) as the most common DSTs. Strains were clustered into nine clades. Unlike other studies of C. albicans blood strains in Asia, clade 17 was the most common (13 strains, 28.3%). Sequential allelic changes were evident in sequential strains from one patient. All strains produced phospholipase and hemolysin, while none produced proteinase. The ability to form biofilm was found in 82.6% of the strains. Clade 17 strains showed significantly stronger hemolytic activity than non–clade 17 strains (69.2% versus 27.3%; p = 0.022). However, no significant association existed between clades and patient mortalities. All were susceptible or wild type to anidulafungin (MIC range = 0.015–0.12 and GM = 0.030), micafungin (MIC range = ≤ 0.008–0.015 and GM = 0.008), caspofungin (MIC range = 0.008–0.12 and GM = 0.036), and amphotericin B (MIC range = 0.25–0.5 and GM = 0.381). Only one strain was resistant to voriconazole (MIC range = ≤ 0.008 to ≥ 8 and GM = 0.010) and fluconazole (MIC range = 0.12–16 and GM = 0.398). In conclusion, a high prevalence of clade 17 C. albicans blood strains was found in Thailand, in contrast to other Asian countries. This unique finding might be explained by the strong hemolytic activity that is required for bloodstream infection of C. albicans.

Candida albicans Biofilms Are Generally Devoid of Persister Cells

Candida albicans is known for its ability to form biofilms, which are communities of microorganisms embedded in an extracellular matrix developing on different surfaces. Biofilms are highly tolerant to antifungal therapy. This phenomenon has been partially explained by the appearance of so-called persister cells, phenotypic variants of wild-type cells, capable of surviving very high concentrations of antimicrobial agents. Persister cells in C. albicans were found exceptionally in biofilms, while none were detected in planktonic cultures of this fungus. Yet, this topic remains controversial, as others could not observe persister cells in biofilms formed by the C. albicans SC5314 laboratory strain. Due to ambiguous data in the literature, this work aimed to reevaluate the presence of persister cells in C. albicans biofilms. We demonstrated that the isolation of C. albicans "persister cells" as described previously was likely to be the result of the survival of biofilm cells that were not reached by the antifungal. We tested biofilms of SC5314 and its derivatives, as well as 95 clinical isolates, using an improved protocol, demonstrating that persister cells are not a characteristic trait of C. albicans biofilms. Although some clinical isolates are able to yield survivors upon the antifungal treatment of biofilms, this phenomenon is rather stochastic and inconsistent.

Can Saccharomyces cerevisiae keep up as a model system in fungal azole susceptibility research?

The difficulty of manipulation and limited availability of genetic tools for use in many pathogenic fungi hamper fast and adequate investigation of cellular metabolism and consequent possibilities for antifungal therapies. S. cerevisiae is a model organism that is used to study many eukaryotic systems. In this review, we analyse the potency and relevance of this model system in investigating fungal susceptibility to azole drugs. Although many of the concepts apply to multiple pathogenic fungi, for the sake of simplicity, we will focus on the validity of using S. cerevisiae as a model organism for two Candida species, C. albicans and C. glabrata. Apart from the general benefits, we explore how S. cerevisiae can specifically be used to improve our knowledge on azole drug resistance and enables fast and efficient screening for novel drug targets in combinatorial therapy. We consider the shortcomings of the model system, yet conclude that it is still opportune to use S. cerevisiae as a model system for pathogenic fungi in this era.

Genotyping of clinical isolates of Candida glabrata from Iran by multilocus sequence typing and determination of population structure and drug resistance profile

Candida glabrata is often the second most common causative agent for candidiasis following Candida albicans. Despite the importance of C. glabrata infections, few epidemiological studies have been conducted on this issue. The goal of this study was genotyping of clinical isolates of C. glabrata by multilocus sequence typing (MLST) technique for determination of the endemic prevalent genotypes and any association between isolation source and drug resistance. A total of 50 C. glabrata clinical isolates from Iran were analyzed by MLST and tested for in-vitro susceptibilities to amphotericin-B, caspofungin, fluconazole, and voriconazole according to the Clinical Laboratory Standards Institute (CLSI) M27-A4 document guidelines. Among these isolates, 16 distinct STs were identified, indicating a discriminatory power index of 0.9029. The three major sequence types (STs) were ST-59, ST-74, and ST-7 with 10, 8, and 7 isolates, respectively. Furthermore, a total of 11 new sequences were found, to which no allele numbers were assigned in the MLST database. All the isolates were susceptible to amphotericin B and caspofungin. Fluconazole resistance was shown in four isolates. Also, a sole isolate was voriconazole resistant. This study shows that the population structure of C. glabrata in Iran consists of groups closely related to the global database as well as to some new clonal clusters and STs. Regarding the high prevalence of 11 new sequences found in this study, it can be concluded that, these new alleles are among the endemic genotypes of Iran. The genotypes or STs were independent of drug susceptibility and anatomic sources.

Multilocus sequence typing of Candida albicans isolates from the oral cavities of patients undergoing haemodialysis

This study evaluates the prevalence, diversity, and genetic profiles of Candida albicans isolates recovered from the oral cavities of haemodialysis patients. Oral swab samples were obtained from haemodialysis patients (n = 126) and healthy control subjects (n = 233) and Candida species were characterised. There was no significant difference between the haemodialysis and control groups in the prevalence of yeast carriers (23.6% vs. 31.0%, respectively) or C. albicans carriers (19.8% vs. 21.0%, respectively). C. albicans was the most populous species in both cohorts, followed by C. parapsilosis. C. parapsilosis and C. glabrata were more prevalent in the haemodialysis group than in the control group (C. parapsilosis 5.6% vs. 0.9% and C. glabrata 3.2% vs. 0.4%, respectively; P < 0.05). C. albicans isolates were analysed by multilocus sequence typing and the results were used to construct a phylogenetic tree. Most haemodialysis isolates were placed into Clade 4 (20.0%) and Clade 19 (16.0%) and most control isolates into Clade 8 (17%) and Clade 4 (14.9%). Differences in the strain abundance in each clade were not statistically significant between the two groups. Moreover, there was no significant association between the health status or diagnosis and either the sequence types or clades.

Genotype and homology analysis of pathogenic and colonization strains of Candida albicans from hospitalized neonates

BACKGROUND

To detect the genotypes of pathogenic and colonization Candida albicans strains and to reveal whether there was a homologous relationship between these strains.

METHODS

Pathogenic and colonization isolates were collected from infants in the NICU of Shenzhen People's Hospital (Shenzhen, People's Republic of China). rDNA identification, multilocus sequence typing (MLST), and multi-loci variable number tandem repeat analysis (MLVA) were used for species confirmation, strain identification, phylogenetic tree clustering, and assessment of homology among the pathogenic and colonization strains.

RESULTS

All 48 isolates belonged to C. albicans species; 12 were collected from premature infants with fungal sepsis. These isolates generated 5 sequence types (ST1867, ST2551, ST2552, ST2937, and ST2945) and were designated as pathogenic strains. The other 36 isolates were collected from the infants without fungal infection; 9 sequence types were detected and designated as the colonization strains. In the phylogenetic tree, the upper branch consisted of a 4° clade composed of 20 colonization isolates designated to 3 strains, and 4 pathogenic isolates designated to 1 strain; a 5° clade composed of 8 pathogenic isolates designated to 3 strains; and a 4° clade consisting 1 pathogenic isolate designated to 1 strain and 4 colonization isolates designated to 2 strains. The lower branch consisted of a 3° clade composed of 6 colonization isolates designated to 2 strains and a control pathogenic isolate, and a 3° clade composed of 5 colonization isolates designated to 2 strains.

CONCLUSION

Although there was no core ST detected to specify pathogenicity or colonization of C. albicans, the genotypes of the colonization strains were different from those of the pathogenic strains. Most of the colonization and pathogenic strains were highly homologous within their classifications while some pathogenic strains had genomes highly homologous with those of colonization strains and clustered in heterogeneous groups.

Gene flow contributes to diversification of the major fungal pathogen Candida albicans

Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. Candida albicans is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. albicans isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. albicans shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. Candida albicans thus takes advantage of both clonality and gene flow to diversify.

The fungal pathogen Candida albicans can undergo a parasexual process that may contribute to genetic diversity, but its actual relevance is unclear. Here, Ropars et al. analyse the genomic sequences of 182 C. albicans isolates collected worldwide and find evidence of gene flow and thus parasexuality in nature.

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses

The yeast Kluyveromyces marxianus possesses advantageous traits like rapid growth, GRAS (generally regarded as safe) status and thermotolerance that make it very suitable for diverse biotechnological applications. Although physiological studies demonstrate wide phenotypic variation within the species, there is only limited information available on the genetic diversity of K. marxianus. The aim of this work was to develop a multilocus sequence typing (MLST) method for K. marxianus to improve strain classification and selection. Analysis of housekeeping genes in a number of sequenced strains led to the selection of five genes, IPP1, TFC1, GPH1, GSY2 and SGA1, with sufficient polymorphic sites to allow MLST analysis. These loci were sequenced in an additional 76 strains and used to develop the MLST. This revealed wide diversity in the species and separation of the culture collection and wild strains into multiple distinct clades. Two subsets of strains that shared sources of origin were subjected to MLST and split decomposition analysis. The latter revealed evidence of recombination, indicating that this yeast undergoes mating in the wild. A public access web-based portal was established to allow expansion of the database and application of MLST to additional K. marxianus strains. This will aid understanding of the genetic diversity of the yeast and facilitate biotechnological exploitation.

Investigating Clinical Issues by Genotyping of Medically Important Fungi: Why and How?

Genotyping studies of medically important fungi have addressed elucidation of outbreaks, nosocomial transmissions, infection routes, and genotype-phenotype correlations, of which secondary resistance has been most intensively investigated. Two methods have emerged because of their high discriminatory power and reproducibility: multilocus sequence typing (MLST) and microsatellite length polymorphism (MLP) using short tandem repeat (STR) markers. MLST relies on single-nucleotide polymorphisms within the coding regions of housekeeping genes. STR polymorphisms are based on the number of repeats of short DNA fragments, mostly outside coding regions, and thus are expected to be more polymorphic and more rapidly evolving than MLST markers. There is no consensus on a universal typing system. Either one or both of these approaches are now available for Candida spp., Aspergillus spp., Fusarium spp., Scedosporium spp., Cryptococcus neoformans, Pneumocystis jirovecii, and endemic mycoses. The choice of the method and the number of loci to be tested depend on the clinical question being addressed. Next-generation sequencing is becoming the most appropriate method for fungi with no MLP or MLST typing available. Whatever the molecular tool used, collection of clinical data (e.g., time of hospitalization and sharing of similar rooms) is mandatory for investigating outbreaks and nosocomial transmission.

Multilocus sequence typing (MLST) analysis of Candida albicans isolates colonizing acrylic dentures before and after denture replacement

Yeast, in particular Candida albicans, are the principal fungal cause of denture stomatitis, and can also be present as a commensal in many individuals. Few studies, however, have examined oral retention of yeast strains over time. We analyzed the yeast present in saliva samples and from the dentures of 10 individuals colonized with yeast but with no signs of stomatitis, before new complete maxillary dentures were fitted and also at 1, 3, and 6 months after denture replacement. Yeast species were presumptively identified on selective agar plates and were present in nine individuals before denture replacement and in six at the 6-month time point. C. albicans was detected in seven individuals pre-replacement, and in three by 6 months post-replacement. Sixty-two isolates (up to five from each C. albicans-positive sample) were analyzed by multilocus sequence typing (MLST) (33 from saliva and 29 from dentures). Six MLST allele profiles were identified that were common to several individuals. These profiles included three previously reported diploid sequence types (DSTs) and three novel DSTs. Two of the novel DSTs were closely related variants of a previously reported DST, and both showed loss of heterozygosity polymorphisms within one of the seven MLST gene sequences. For three individuals, at least one DST that was present before denture replacement was still detected in either saliva or on dentures at subsequent sampling times. Our results indicate that denture replacement reduces but does not remove, colonising yeast and confirm previous observations of C. albicans strain microevolution.

A Combination Fluorescence Assay Demonstrates Increased Efflux Pump Activity as a Resistance Mechanism in Azole-Resistant Vaginal Candida albicans Isolates

Candida albicans is a pathogenic fungus causing vulvovaginal candidiasis (VVC). Azole drugs, such as fluconazole, are the most common treatment for these infections. Recently, azole-resistant vaginal C. albicans isolates have been detected in patients with recurring and refractory vaginal infections. However, the mechanisms of resistance in vaginal C. albicans isolates have not been studied in detail. In oral and systemic resistant isolates, overexpression of the ABC transporters Cdr1p and Cdr2p and the major facilitator transporter Mdr1p is associated with resistance. Sixteen fluconazole-susceptible and 22 fluconazole-resistant vaginal C. albicans isolates were obtained, including six matched sets containing a susceptible and a resistant isolate, from individual patients. Using quantitative real-time reverse transcriptase PCR (qRT-PCR), 16 of 22 resistant isolates showed overexpression of at least one efflux pump gene, while only 1 of 16 susceptible isolates showed such overexpression. To evaluate the pump activity associated with overexpression, an assay that combined data from two separate fluorescent assays using rhodamine 6G and alanine β-naphthylamide was developed. The qRT-PCR results and activity assay results were in good agreement. This combination of two fluorescent assays can be used to study efflux pumps as resistance mechanisms in clinical isolates. These results demonstrate that efflux pumps are a significant resistance mechanism in vaginal C. albicans isolates.

Using genomics data to reconstruct transmission trees during disease outbreaks

Genetic sequence data from pathogens present a novel means to investigate the spread of infectious disease between infected hosts or infected premises, complementing traditional contact-tracing approaches, and much recent work has gone into developing methods for this purpose. The objective is to recover the epidemic transmission tree, which identifies who infected whom. This paper reviews the various approaches that have been taken. The first step is to define a measure of difference between sequences, which must be done while taking into account such factors as recombination and convergent evolution. Three broad categories of method exist, of increasing complexity: those that assume no withinhost genetic diversity or mutation, those that assume no within-host diversity but allow mutation, and those that allow both. Until recently, the assumption was usually made that every host in the epidemic could be identified, but this is now being relaxed, and some methods are intended for sparsely sampled data, concentrating on the identification of pairs of sequences that are likely to be the result of direct transmission rather than inferring the complete transmission tree. Many of the procedures described here are available to researchers as free software.

Multilocus sequence typing of Candida tropicalis shows clonal cluster enrichment in azole-resistant isolates from patients in Shanghai, China

To explore the putative correlation between the multilocus sequence types (MLST) and antifungal susceptibility of clinical Candida tropicalis isolates in Mainland China. Eighty-two clinical C. tropicalis isolates were collected from sixty-nine patients at Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China, from July 2012 to February 2015, and antifungal susceptibility tests were performed. Genetic profiles of those 82 isolates (30 azole-resistant and 52 azole-susceptible) were characterised by multilocus sequence typing. Phylogenetic analysis of the data was conducted with the clustering method, using UPGMA (unweighted pair group method with arithmetic averages) and the minimal spanning tree algorithm. MLST clonal clusters were analysed using the eBURST V3 package. Of the six gene fragments identified in multilocus sequence typing, SAPT4 presented the highest typing efficiency, whereas SAPT2 was the least efficient. Of the 44 diploid sequence types (DSTs) differentiated, 32 DSTs and 12 genotypes were identified as new to the C. tropicalis DST database. Twenty (45.45%) of the 44 DSTs were assigned to seven major groups based on eBURST analysis. Of these, Group 6, which contained DST 376, DST 505, DST 506 and DST 507, accounted for 76.7% of the 30 azole-resistant isolates. However, the genetic relationships among the azole-susceptible isolates were relatively decentralised. This MLST analysis of the putative correlation between the MLST types and antifungal susceptibility of clinical C. tropicalis isolates in Mainland China shows that DSTs 376, 505, 506 and 507 are closely related azole-resistant C. tropicalis clones.

Typing Candida Species Using Microsatellite Length Polymorphism and Multilocus Sequence Typing

To gain more insight into the epidemiological relationships between isolates of Candida spp. obtained from various origins, several molecular typing techniques have been developed. Two methods have emerged in the 2000s as soon as enough knowledge of the Candida spp. genomes was available to choose adequate loci and primers, namely microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST). To contrast with previous PCR-based methods, specific amplifications with stringent conditions easily reproducible are the basis of MLP and MLST. MLST relies on Sanger sequencing to detect single-nucleotide polymorphisms within housekeeping genes. MLP needs a first in silico step to select tandemly repeated stretches of two to five nucleotides. One of the two primers used to amplify a microsatellite locus is labeled and fragment sizing is automatically performed using high-resolution electrophoresis platforms. MLST provides results easily comparable between laboratories and active MLST schemes are publicly available for the main Candida species. For comparative studies, MLP needs standards to compensate for the electrophoretic variations depending on the platforms used. Both methods can help us gain insight into the genetic relatedness of fungal isolates, both with advantages and drawbacks, and the choice of one method rather than the other depends on the task in question.

Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients

Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.

Posttreatment Antifungal Resistance among Colonizing Candida Isolates in Candidemia Patients: Results from a Systematic Multicenter Study

The prevalence of intrinsic and acquired resistance among colonizing Candida isolates from patients after candidemia was investigated systematically in a 1-year nationwide study. Patients were treated at the discretion of the treating physician. Oral swabs were obtained after treatment. Species distributions and MIC data were investigated for blood and posttreatment oral isolates from patients exposed to either azoles or echinocandins for <7 or ≥ 7 days. Species identification was confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and internal transcribed spacer (ITS) sequencing, susceptibility was examined by EUCAST EDef 7.2 methodology, echinocandin resistance was examined by FKS sequencing, and genetic relatedness was examined by multilocus sequence typing (MLST). One hundred ninety-three episodes provided 205 blood and 220 oral isolates. MLST analysis demonstrated a genetic relationship for 90% of all paired blood and oral isolates. Patients exposed to azoles for ≥ 7 days (n = 93) had a significantly larger proportion of species intrinsically less susceptible to azoles (particularly Candida glabrata) among oral isolates than among initial blood isolates (36.6% versus 12.9%; P < 0.001). A similar shift toward species less susceptible to echinocandins among 85 patients exposed to echinocandins for ≥ 7 days was not observed (4.8% of oral isolates versus 3.2% of blood isolates; P > 0.5). Acquired resistance in Candida albicans was rare (<5%). However, acquired resistance to fluconazole (29.4%; P < 0.05) and anidulafungin (21.6%; P < 0.05) was common in C. glabrata isolates from patients exposed to either azoles or echinocandins. Our findings suggest that the colonizing mucosal microbiota may be an unrecognized reservoir of resistant Candida species, especially C. glabrata, following treatment for candidemia. The resistance rates were high, raising concern in general for patients exposed to antifungal drugs.

A multilocus sequence analysis scheme for characterization of Flavobacterium columnare isolates

Background

Columnaris disease caused by Flavobacterium columnare is a serious problem in aquaculture, annually causing large economic losses around the world. Despite considerable research, the molecular epidemiology of F. columnare remains poorly understood.

Methods

We investigated the population structure and spatiotemporal changes in the genetic diversity of F. columnare population in Finland by using a multilocus sequence typing (MLST) and analysis (MLSA) based on DNA sequence variation within six housekeeping genes. A total of 83 strains of F. columnare were collected from eight different areas located across the country between 2003 and 2012.

Results

Partial sequencing of six housekeeping genes (trpB, tuf, atpA, rpoD, gyrB and dnaK) revealed eight sequence types and a moderate level of genetic diversity (H = 0.460). Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 3,509 nucleotides) formed two lineages, which could be further divided into five clusters. All analysed F. columnare strains appeared to have a genetic origin distinct from that of another important fish pathogen form the genus Flavobacterium, F. psychrophilum. Although the value of the index of association between alleles, 0.292 (P < 0.001), supports some degree of clonality for this species in Finland, recombination has introduced molecular diversity to the population almost three times more than mutation.

Conclusion

The results suggest that Finnish F. columnare strains have an epidemic population structure followed by clonal expansion of successful genotypes. Our study with reproducible methodology and comparable results establishes a robust framework for the discrimination and phylogenetic analysis of F. columnare isolates, which will help to improve our understanding about geographic distribution and epidemiology of columnaris disease.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0576-4) contains supplementary material, which is available to authorized users.

Molecular epidemiology of invasive Candida albicans at a tertiary hospital in northern Taiwan from 2003 to 2011

Candida albicans is a common cause of bloodstream fungal infections in hospitalized patients. To investigate its epidemiology, multilocus sequence typing (MLST) was performed on 285 C. albicans bloodstream isolates from patients in Chang Gung Memorial Hospital at Linkou (CGMHL), Taiwan from 2003 to 2011. Among these isolates, the three major diploid sequence types (DSTs) were 693, 659, and 443 with 19, 16, and 13 isolates, respectively. The 179 DSTs were classified into 16 clades by unweighted pair-group method using arithmetic averages (UPGMA). The major ones were clades 1, 4, 3, and 17 (54, 49, 31, and 31 isolates, respectively). Further analyses with eBURST clustered the 285 isolates into 28 clonal complexes (CC). The most common complexes were CC8, CC20, and CC9. DST 693 that had the highest number of isolates was determined to be the cluster founder of CC20, which belonged to clade 3. So far, 33 isolates worldwide including 29 from Taiwan and 4 from Korea, are CC20, suggesting that CC20 is an Asian cluster. Two fluconazole-resistant isolates belonging to CC12 and CC19 were detected. All other CGMHL isolates were susceptible to 5-flucytosine, amphotericin B, anidulfungin, caspofungin, fluconazole, itraconazole, micafungin, posaconazole, and voriconazole. However, CC20 isolates exhibited significantly lower susceptibility to fluconazole. In conclusion, the 285 CGMHL C. albicans isolates displayed geographically clustering with Asian isolates, and most of them are susceptible to common antifungal drugs. Isolates of DST 693, a Taiwanese major genotype belonging to MLST clade 3, were more resistant to fluconazole than other isolates.

Molecular Diversity of Candida albicans Isolated from Immunocompromised Patients, Based on MLST Method

BACKGROUND

As regards multilocus sequence typing (MLST) method directly analyze the polymorphism within DNA sequences; we performed the first nationwide study on the genotypic relationships of Candida albicans strains obtained from oropharynx and bronchoalveolar lavage (BAL) samples from immunocompromised patients.

METHODS

Fourteen epidemiologically unrelated clinical strains of C. albicans were obtained from three hospitals in Mazandaran Province, Iran (2006 to 2012) from seven patients with pulmonary infections and the rest with oropharyngeal samples of immunocompromised patients. Seven loci of housekeeping genes were sequenced for all fourteen isolates.

RESULTS

MLST was applied to a subset of 14 unrelated isolates. Seventy-one (2.5%) nucleotide sites were found to be variable. Accordingly, 60 different alleles were identified in seven loci among the isolates, among which two new alleles were obtained. Furthermore, 12 independent diploid sequence types (DSTs) including five novel DSTs were identified. The fourteen unrelated isolates were placed in 10 clonal clusters (CC) while two isolates were singletons, by eBURST analysis. Most of the isolates belonged to CC461 of eBURST analysis from the clade 11 and two isolates assigned to CC172 from the clade 15.

CONCLUSION

Pathogen distribution and relatedness for determining the epidemiology of nosocomial infections is highly recommended for pathogen control methods.

Candida albicans bloodstream isolates in a German university hospital are genetically heterogenous and susceptible to commonly used antifungals

From an eight-year-span, 99 Candida bloodstream isolates were collected at the University Hospital Wuerzburg, Germany. In this study, all strains were analyzed using molecular and phenotypic typing methods. Confirmatory species identification revealed three isolates that were initially diagnosed as C. albicans to be actually C. dubliniensis. Two isolates contained a mixed culture of C. albicans and C. glabrata, in one of the specimens both species could be separated while it was not possible to recover C. albicans in the other sample. The remaining 95 C. albicans isolates were profiled by multilocus sequence typing (MLST). Phylogenetic analyses showed a highly heterogenous collection of strains, associated with many different clades and constituting a set of new diploid sequence types (DST). For all strains with identical DST, patient data were reviewed for potential nosocomial transmission. In addition, all isolates were tested for their susceptibility to amphotericin B, caspofungin, fluconazole, itraconazole, posaconazole and voriconazole. No clinically relevant resistance could be detected. Furthermore, these data underline that correlation between minimal inhibitory concentrations for caspofungin and anidulafungin is low.

Stepwise emergence of azole, echinocandin and amphotericin B multidrug resistance in vivo in Candida albicans orchestrated by multiple genetic alterations

OBJECTIVES

The objective of this study was to characterize the underlying molecular mechanisms in consecutive clinical Candida albicans isolates from a single patient displaying stepwise-acquired multidrug resistance.

METHODS

Nine clinical isolates (P-1 to P-9) were susceptibility tested by EUCAST EDef 7.2 and Etest. P-4, P-5, P-7, P-8 and P-9 were available for further studies. Relatedness was evaluated by MLST. Additional genes were analysed by sequencing (including FKS1, ERG11, ERG2 and TAC1) and gene expression by quantitative PCR (CDR1, CDR2 and ERG11). UV-spectrophotometry and GC-MS were used for sterol analyses. In vivo virulence was determined in the insect model Galleria mellonella and evaluated by log-rank Mantel-Cox tests.

RESULTS

P-1 + P-2 were susceptible, P-3 + P-4 fluconazole resistant, P-5 pan-azole resistant, P-6 + P-7 pan-azole and echinocandin resistant and P-8 + P-9 MDR. MLST supported genetic relatedness among clinical isolates. P-4 harboured four changes in Erg11 (E266D, G307S, G450E and V488I), increased expression of ERG11 and CDR2 and a change in Tac1 (R688Q). P-5, P-7, P-8 and P-9 had an additional change in Erg11 (A61E), increased expression of CDR1, CDR2 and ERG11 (except for P-7) and a different amino acid change in Tac1 (R673L). Echinocandin-resistant isolates harboured the Fks1 S645P alteration. Polyene-resistant P-8 + P-9 lacked ergosterol and harboured a frameshift mutation in ERG2 (F105SfsX23). Virulence was attenuated (but equivalent) in the clinical isolates, but higher than in the azole- and echinocandin-resistant unrelated control strain.

CONCLUSIONS

C. albicans demonstrates a diverse capacity to adapt to antifungal exposure. Potentially novel resistance-inducing mutations in TAC1, ERG11 and ERG2 require independent validation.

Multilocus Sequence Typing of Pathogenic Candida albicans Isolates Collected from a Teaching Hospital in Shanghai, China: A Molecular Epidemiology Study

Molecular typing of Candida albicans is important for studying the population structure and epidemiology of this opportunistic yeast, such as population dynamics, nosocomial infections, multiple infections and microevolution. The genetic diversity of C. albicans has been rarely studied in China. In the present study, multilocus sequence typing (MLST) was used to characterize the genetic diversity and population structure of 62 C. albicans isolates collected from 40 patients from Huashan Hospital in Shanghai, China. A total of 50 diploid sequence types (DSTs) were identified in the 62 C. albicans isolates, with 41 newly identified DSTs. Based on cluster analysis, the 62 isolates were classified into nine existing clades and two new clades (namely clades New 1 and New 2). The majority of the isolates were clustered into three clades, clade 6 (37.5%), clade 1 (15.0%) and clade 17 (15.0%). Isolates of clade New 2 were specifically identified in East Asia. We identified three cases of potential nosocomial transmission based on association analysis between patients' clinical data and the genotypes of corresponding isolates. Finally, by analyzing the genotypes of serial isolates we further demonstrated that the microevolution of C. albicans was due to loss of heterozygosity. Our study represents the first molecular typing of C. albicans in eastern China, and we confirmed that MLST is a useful tool for studying the epidemiology and evolution of C. albicans.