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A total of 244 Candida albicans isolates recovered from vulvovaginal candidiasis (VVC) patients in Suzhou, Eastern China, were investigated. According to CLSI documents M27-A4 and M59-3ed/M60-2ed, the MIC geometric means of nine antifungals in increasing order were micafungin (0.048 mg/L), anidulafungin (0.132 mg/L), caspofungin (0.19 mg/L), itraconazole (0.23 mg/L), posaconazole (0.25 mg/L), voriconazole (0.28 mg/L), 5-flucytosine (0.44 mg/L), amphotericin B (0.49 mg/L) and fluconazole (2.01 mg/L) respectively. Of note, 6.5% (16/244) C. albicans isolates showed resistance mainly to anidulafungin (mono-echinocandin resistance), while voriconazole had the lowest susceptibility rate of 34.8% (85/244), followed by fluconazole 59.4% (145/244), respectively. All isolates were genotyped by allelic combination of 3 microsatellite markers (CEF3, CAIII and LOC4). A total of 129 different allelic genotypes were identified, in which seven different clades were recognized with a discriminatory power of 0.96. Genotypes A-D were present in 35% of the isolates. In conclusion, decrease in antifungal drug susceptibility to C. albicans isolates from VVC is alarming. Our findings revealed the genetic diversity of C. albicans isolates among VVC patients and provided insights into the molecular epidemiology of Candida infections in China.

Rust fungi taxonomically belonging to Pucciniales (Basidiomycota) are important phytopathogens that cause many significant diseases to agricultural crops and forest trees. Hitherto, ca. 8000 and 1200 species have been reported from worldwide and China, respectively. To investigate and document the diversity of rust fungi in China, we have sampled from 86 natural reserves and national parks in the past several years, and 6627 specimens have been collected. Our identification using both morphological and molecular data assigned 1654 collections to 337 species in 43 genera of 15 families, as cataloged in this paper. Among them, 34 new species are formally described based on their morphological distinctions and phylogenetic relationships. In addition, three new families Endoraeciaceae, Neophysopellaceae and Uromycladiaceae are proposed based on their morphological distinctions, phylogenetic independences and divergent times. Considering the traditionally morphologically defined families in Pucciniales have been increasing revealed to be discordant with phylogenetic groupings, taxonomic revisions are needed in future study to establish a natural classification system in Pucciniales. We also discussed the importance of morphologies in spermogonia and aecia for the delimitation of Puccinia and related genera. This study presents a significant contribution to the knowledge of rust flora in China. Taxonomic novelties: new families: Endoraeciaceae P. Zhao & L. Cai; Neophysopellaceae P. Zhao & L. Cai; Uromycladiaceae P. Zhao & L. Cai; new species: Chrysomyxa jinghongensis P. Zhao & L. Cai; Coleosporium sichuanense P. Zhao & L. Cai; Coleosporium smilacis P. Zhao & L. Cai; Cystopsora yunnanense P. Zhao & L. Cai; Gerwasia guanganensis P. Zhao & L. Cai; Gerwasia rubus-playfairianus P. Zhao & L. Cai; Hamaspora rubus-pirifolius P. Zhao & L. Cai; Macruropyxis guizhouensis P. Zhao & L. Cai; Macruropyxis paederiae P. Zhao & L. Cai; Melampsora hyperici-sampsonii P. Zhao & L. Cai; Melampsora linearis P. Zhao & L. Cai; Melampsora salicis-delavayanae P. Zhao & L. Cai; Neophysopella vitis-davidii P. Zhao & L. Cai; Phakopsora sophorae P. Zhao & L. Cai; Phragmidium nonapiculatum P. Zhao & L. Cai; Phragmidium kanas P. Zhao & L. Cai; Phragmidium duchesneae-indicae P. Zhao & L. Cai; Pileolaria medogensis P. Zhao & L. Cai; Puccinia amygdalus-iridis P. Zhao & L. Cai; Puccinia aphananthe-aspera P. Zhao & L. Cai; Puccinia microsorus P. Zhao & L. Cai; Puccinia nandina-domestica P. Zhao & L. Cai; Puccinia persicaria-odorata P. Zhao & L. Cai; Puccinia polygonum-aviculare P. Zhao & L. Cai; Puccinia pulverulentus P. Zhao & L. Cai; Puccinia saposhnikoviae P. Zhao & L. Cai; Puccinia sonchus-oleraceus P. Zhao & L. Cai; Puccinia thalictrum-finetii P. Zhao & L. Cai; Puccinia thalictrum-minus P. Zhao & L. Cai; Puccinia xingwenensis P. Zhao & L. Cai; Puccinia xinjiangensis P. Zhao & L. Cai; Puccinia zanthoxyli-chinensis P. Zhao & L. Cai; Uromyces aconiticola P. Zhao & L. Cai; Uromycladium yunnanense P. Zhao & L. Cai; new combinations: Chrysomyxa purpurea (C.J. You & J. Cao) P. Zhao & L. Cai; Neophysopella verannonae (Beenken) P. Zhao & L. Cai.

Fresh produce imported by Qatar are mostly sold at the wholesale produce market (WPM) located in open-air and near major animal markets and slaughterhouses. This study was the first in Qatar to monitor the effect of environmental conditions on the microbial quality and safety of fresh produce sold at the WPM over 1 year. The monitoring involved the collection of 540 produce samples along with samples of air, soil, and surface swabs. Samples were analyzed for total aerobic bacteria (TAB); generic Listeria spp., Staphylococcus spp., Salmonella spp.; total coliforms and total fungi. Bacterial and fungal isolates were identified using 16S rRNA/ITS rRNA markers. Environmental/sanitary factors significantly impacted the prevalence of microorganisms in all samples tested. Produce quality was rated 'poor' during the months of November-February or May-August, with TAB and coliform counts exceeding 6 and 4 log10 CFU/g, respectively. Bacillus subtilus, Enterobacter cloacae, E. faecium, P. expansium, P. aurantiocandidum, and A. niger were the most abundant species with prevalence rate of 11-30%. The high microbial load of environmental samples indicates that the location of the WPM near livestock markets is likely impacting the microbial quality of fresh produce. Therefore, effective control measures need to be implemented at WPM to improve produce safety yearlong.

The emergence of carbapenem-resistant (CR) hypervirulent Klebsiella pneumoniae (hvKp) is a new threat to healthcare. In this study, we studied the molecular epidemiology of CR Klebsiella isolates in Qatar using whole genome sequence data. We also characterised the prevalence and genetic basis of hypervirulent phenotypes, and established the virulence potential using a Galleria mellonella model. One hundred CR Klebsiella isolates were recovered, and NDM and OXA-48 were the most common carbapenemases. Phylogenetic analysis indicated the presence of diverse sequence types and clonal lineages; one of them belonged to K. quaisipneumoniae ST196 that may be disseminated among several health care centres. Ten K. pneumoniae isolates carrying rmpA and/or rmpA2, and 2 isolates belonged to KL2, indicating the prevalence of classical hypervirulent (hv) isolates was not high. Isolates carrying CR and hv genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated the blaNDM was located on an IncHI1B type plasmid (pFQ61_ST383_NDM-5), which also harbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from inversion and recombination events. In contrast, blaOXA-48 was located in an IncL-type plasmid. Comparative genomes indicated the recent evolution and emergence of CR-hv Kp ST383 via the acquisition of hybrid plasmids with both carbapenemase and virulence genes. CR-hv K. pneumoniae ST383 pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.

Complementing whole genome sequencing strategies with high-throughput multiplex RT-qPCR genotyping allows for more comprehensive and real-time tracking of SARS-CoV-2 variants of concern. During the second and third waves of COVID-19 in Qatar, PCR genotyping, combined with Sanger sequencing of un-typeable samples, was employed to describe the epidemiology of the Alpha, Beta and Delta variants. A total of 9792 nasopharyngeal PCR-positive samples collected between April-June 2021 were successfully genotyped, revealing the importation and transmission dynamics of these three variants in Qatar.

Whole-genome sequencing was used to characterize carbapenemase-producing Enterobacterales (CPE) strains recovered from rectal screening swab samples obtained from children at a tertiary-care pediatric hospital in Qatar during a 3-year period. A total of 72 CPE isolates recovered from 61 fecal carriers were characterized. Escherichia coli (47 isolates [65.3%]) and Klebsiella pneumoniae (22 isolates [30.6%]) were the most common species identified. High levels of genetic diversity were observed for both species. These 72 isolates produced 78 carbapenemases, characterized as either NDM-type (41 enzymes [52.6%]) or OXA-48-type (37 enzymes [47.4%]). NDM-5 (24 enzymes [30.8%]), NDM-1 (15 enzymes [19.2%]), and OXA-181 (15 enzymes [19.2%]) were the most common variants detected within each type. Twenty-three NDM producers exhibited difficult-to-treat resistance, compared with only 2 of the OXA-48 producers. Multiple comorbidities were identified in 88.5% of the patients, whereas recent travel history to countries in which CPE are endemic was documented for 57.4% of the patients. All 9 blaOXA-48-type-gene-containing E. coli sequence type 38 (ST38) strains were isolated from patients without international travel history. The mean quarterly incidence of fecal carriage decreased more than 6-fold after the implementation of coronavirus disease 2019 (COVID-19)-related international travel restrictions in Qatar in mid-March 2020. Our data suggest that NDM-type and OXA-48-type carbapenemases expressed by a large diversity of E. coli and K. pneumoniae genotypes are largely dominant in the pediatric population of Qatar. Although our data indicate successful local expansion of E. coli ST38 strains harboring blaOXA-244 genes, at least within health care settings, blaOXA-48-type and blaNDM-type genes appear to have been mainly introduced sporadically by asymptomatic carriers who visited or received health care in some nearby countries in which the genes are endemic. IMPORTANCE To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.

Complementing whole genome sequencing strategies with high-throughput multiplex RT-qPCR genotyping allows for more comprehensive and real-time tracking of SARS-CoV-2 variants of concern. During the second and third waves of COVID-19 in Qatar, PCR genotyping, combined with Sanger sequencing of un-typeable samples, was employed to describe the epidemiology of the Alpha, Beta and Delta variants. A total of 9792 nasopharyngeal PCR-positive samples collected between April-June 2021 were successfully genotyped, revealing the importation and transmission dynamics of these three variants in Qatar.

Peritoneal dialysis (PD)–associated peritonitis constitutes a major complication associated with the procedure. PD-associated peritonitis caused by nontuberculous mycobacteria, usually as a result of an infection related to the PD catheter, has been reported in adults and is associated with significant complications and poor outcome. The management of PD-associated peritonitis caused by Mycobacterium abscessus is particularly challenging because this species is resistant to many antimicrobials commonly used to treat mycobacterial species. We present here the second reported case of PD-associated peritonitis caused by M. abscessus in children. Our patient was a 9-year-old boy with end-stage renal disease (ESRD) who presented with suspected peritonitis, and his PD fluid cultures eventually grew M. abscessus. The patient received a 3-week course of triple therapy with clarithromycin, amikacin, and meropenem in addition to PD catheter removal. The infection completely resolved even though a susceptibility report at the end of treatment revealed that the isolate was resistant to clarithromycin and had decreased susceptibility to carbapenems. Our observations suggest that PD catheter removal is important in PD-associated peritonitis caused by M. abscessus in children and that more studies are needed to define the optimal length of treatment.

Introduction: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim: To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods: Whole-genome sequencing (WGS) was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results: A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-beta-lactam antibiotics for both species were: 18.1% and 30.1% for gentamicin, 0.8% and 4.1% for amikacin, 41.3% and 41.1% for ciprofloxacin, and 65.8% and 76.1% for co-trimoxazole. The most common sequence types (ST) were ST131 (16.9%), ST38 and ST10 (8.2 % each) in E. coli and ST307 (9.7%), ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBL were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other beta lactamases, TEM-1B and OXA-1 were co-produced in 41% and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes co-carried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only 2 of 57 isolates harboring aac(6’)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. Conclusions: Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited given the frequent co-production of OXA-1 and TEM-1B enzymes and co-resistance to antibiotic classes other than β-lactams.

The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p

Additional file 1. Supplemental methods.

Background There are limited data describing carbapenem-resistant Enterobacteriaceae (CRE) from the Arabian Gulf region. Our aims were to describe the clinical, microbiological and molecular characteristics of CRE infections and to characterize the gene displaying resistance to carbapenem. Methods Retrospective and prospective review of clinical, microbiological and molecular characteristics of CRE isolated between April 2015 and November 2017 at 7 tertiary hospitals in Qatar. Susceptibility testing was performed and interpreted according to Clinical Laboratory Standards Institute methodology and breakpoints. Carbapenemase genes were identified using PCR. Whole-genome sequencing followed by bioinformatics analysis was performed on a subset of samples for accurate detection of resistant genes. SPSS V.21.0 was used for all statistical analyses. Results A total of 144 nonrepeating CRE strains were recovered from 137 individuals over the study period, of which 35 (24.3%) represented colonization. Klebsiella spp. (98, 68.1%) and E. coli (38, 26.4%) were the most predominant. The most prevalent carbapenemases were NDM (69, 47.9%), OXA-48 (36, 25.0%), and KPC (15, 10.4%). Sixteen (11.1%) strains possessed multiple carbapenemase genes but none were detected in 37 (25.7%) strains. Genomic analysis also detected the presence of NDM-7, NDM-5, NDM1, VIM4, and OXA48-like carbapenemase genes among 34 clinical samples. The majority of the strains were susceptible to tigecycline (124, 86.1%), fosfomycin (122, 84.7%) and amikacin (102, 70.8%). There were 109 CRE infections involving the urinary tract (40, 36.7%), bloodstream (31, 28.4%), and respiratory tract (17, 15.6%). Fifty-seven (52.3%) were males and the median age was 57 years (range 3–97). Baseline comorbidities included diabetes (57, 52.3%), chronic kidney disease (27, 24.8%), and cancer (27, 24.8%) (Table 1). Within the 30 days preceding CRE infection, 38 (34.9%) had received carbapenem therapy, 65 (59.6%) had undergone invasive procedures and 33 (30.3%) had had surgery. All-cause 30-day mortality was 29.4%. The only variable independently associated with mortality was baseline SAPS Score (Table 2). Conclusion NDM and OXA-48 are the predominant carbapenemases in Qatar. CRE infections are associated with high overall mortality. Disclosures All authors: No reported disclosures.

Fungi interact with plants in various ways, with each interaction giving rise to different alterations in both partners. While fungal pathogens have detrimental effects on plant physiology, mutualistic fungi augment host defence responses to pathogens and/or improve plant nutrient uptake. Tropic growth towards plant roots or stomata, mediated by chemical and topographical signals, has been described for several fungi, with evidence of species-specific signals and sensing mechanisms. Fungal partners secrete bioactive molecules such as small peptide effectors, enzymes and secondary metabolites which facilitate colonization and contribute to both symbiotic and pathogenic relationships. There has been tremendous advancement in fungal molecular biology, omics sciences and microscopy in recent years, opening up new possibilities for the identification of key molecular mechanisms in plant–fungal interactions, the power of which is often borne out in their combination. Our fragmentary knowledge on the interactions between plants and fungi must be made whole to understand the potential of fungi in preventing plant diseases, improving plant productivity and understanding ecosystem stability. Here, we review innovative methods and the associated new insights into plant–fungal interactions., The diversity of fungal–plant interactions are reviewed as a function of biochemical, physiological and evolutionary adaptation, which are interconnected at various stages.

Contains fulltext : 182411.pdf (Publisher’s version ) (Open Access) This study investigated the triazole phenotype and genotypic of clinical Aspergillus fumigatus isolates from China. We determined the triazole susceptibility profiles of 159 A. fumigatus isolates collected between 2011 and 2015 from four different areas in China tested against 10 antifungal drugs using the Clinical Laboratory Standard Institute M38-A2 method. For the seven itraconazole-resistant A. fumigatus isolates identified in the study, the cyp51A gene, including its promoter region, was sequenced and the mutation patterns were characterized. The resistant isolates were genotyped by microsatellite typing to determine the genetic relatedness to isolates from China and other countries. The frequency of itraconazole resistance in A. fumigatus isolates in our study was 4.4% (7/159). Six of the seven triazole-resistant isolates were recovered from the east and southeast of China, and one from was recovered from the west of China. No resistant isolates were found in the north. Three triazole-resistant isolates exhibited the TR34/L98H mutation, two carried the TR34/L98H/S297T/F495I mutation and one harbored a G54V mutation in the cyp51A gene. Analysis of the microsatellite markers from seven non-wild-type isolates indicated the presence of five unique genotypes, which clustered into two major genetic groups. The cyp51A gene mutations TR34/L98H and TR34/L98H/S297T were the most frequently found mutations, and the G54V mutation was reported for the first time in China. The geographic origin of the triazole-resistant isolates appeared to concentrate in eastern and south-eastern areas, which suggests that routine antifungal susceptibility testing in these areas should be performed for all clinically relevant A. fumigatus isolates to guide antifungal therapy and for epidemiological purposes.

The Cryptococcus species complex contains two closely related basidiomycetous yeasts: Cryptococcus neoformans and C. gattii, which cause cryptococcosis in humans and other animals. The species and varieties are characterized, by different clinical, epidemiological, biochemical and molecular features. The currently used identification methods are either time-consuming or not anymore commercially available. However, a rapid, sensitive and robust assay for the detection of these pathogens is vital for early diagnosis and appropriate treatment decisions. To overcome those limitations, four padlock probes targeting species-specific single nucleotide polymorphisms at the internal transcribed spacers (ITSs) of the RNA gene locus were developed and applied during isothermal hyperbranched rolling circle amplification (HRCA). The probes were tested against 99 samples, including 94 clinical cryptococcal cultures, three closely related Cryptococcus species, and two clinical specimens. The use of the padlock probes and the combination of probe signal amplification by HRCA provided a quick and sensitive assay for the accurate identification of C. neoformans var. grubii, C. neoformans var. neoformans and C. gattii. HRCA was also useful to detect hybrids, when they were heterozygous at the ITS locus. The HRCA results were in agreement with previous genotyping data based on PCR fingerprinting, amplified fragment length polymorphism and ITS sequencing.

The Cryptococcus species complex contains two sibling taxa, Cryptococcus neoformans and Cryptococcus gattii. Both species are basidiomycetous yeasts and major pathogens of humans and other mammals. Genotyping methods have identified major haploid molecular types of C. neoformans (VNI, VNII, VNB and VNIV) and of C. gattii (VGI, VGII, VGIII and VGIV). To investigate the phylogenetic relationships among these haploid genotypes, we selected 73 strains from 2000 globally collected isolates investigated in our previous typing studies, representing each of these genotypes and carried out multigene sequence analyses using four genetically unlinked nuclear loci, ACT1, IDE, PLB1 and URA5. The separate or combined sequence analyses of all four loci revealed seven clades with significant support for each molecular type. However, three strains of each species revealed some incongruence between the original molecular type and the sequence-based type obtained here. The topology of the individual gene trees was identical for each clade of C. neoformans but incongruent for the clades of C. gattii indicating recent recombination events within C. gattii. There was strong evidence of recombination in the global VGII population. Both parsimony and likelihood analyses supported three major clades of C. neoformans (VNI/VNB, VNII and VNIV) and four major clades of C. gattii (VGI, VGII, VGIII and VGIV). The sequence variation between VGI, VGIII and VGIV was similar to that between VNI/VNB and VNII. MATa was for the first time identified for VGIV. The VNIV and VGII clades are basal to the C. neoformans or the C. gattii clade, respectively. Divergence times among the seven haploid monophyletic lineages in the Cryptococcus species complex were estimated by applying the hypothesis of the molecular clock. The genetic variation found among all of these haploid monophyletic lineages indicates that they warrant varietal status.