scholarly journals Genomic Epidemiology of Candida auris in Qatar Reveals Hospital Transmission Dynamics and a South Asian Origin

2021 ◽  
Vol 7 (3) ◽  
pp. 240
Author(s):  
Husam Salah ◽  
Sathyavathi Sundararaju ◽  
Lamya Dalil ◽  
Sarah Salameh ◽  
Walid Al-Wali ◽  
...  
Keyword(s):  
South Asian ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Candida Auris ◽  
Single Nucleotide ◽  
Genomic Epidemiology ◽  
East Region ◽  
Middle East Region

Candida auris is an emerging, multidrug-resistant fungal pathogen that has become a public health threat with an increasing incidence of infections worldwide. Candida auris spreads easily among patients within and between hospitals. Infections and outbreaks caused by C. auris have been reported in the Middle East region including Oman, Kuwait, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. Pathogen whole genome sequencing (WGS) was used to determine the epidemiology and drug resistance mutations of C. auris in Qatar. Forty-four samples isolated from patients in three hospitals and the hospital environment were sequenced by Illumina NextSeq. Core genome single nucleotide polymorphisms (SNPs) revealed that all isolates belonged to the South Asian lineage with genetic heterogeneity that suggests previous acquisition from foreign healthcare. The genetic variability among the outbreak isolates in the two hospitals (A and B) was low. Four environmental isolates clustered with the related clinical isolates, and epidemiologically linked isolates clustered together, suggesting that the ongoing transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Prominent mutations Y132F and K143R in ERG11 linked to increased fluconazole resistance were detected.

scholarly journals Molecular epidemiology of Candida auris in Qatar using whole genome sequence data

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Husam Salah ◽  
Sathyavathi Sundararaju ◽  
Lamya Dalil ◽  
Patrick Tang ◽  
Walid Al-Wali ◽  
...  
Keyword(s):  
Sequence Data ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Resistance Mutations ◽  
Candida Auris ◽  
East Region ◽  
Echinocandin Resistance ◽  
Middle East Region

Candida auris is an emerging, multidrug resistant fungal pathogen that has become a public health threat worldwide. Candida auris spreads easily among patients within and between hospitals, and the incidence of infections has increased substantially in the last decade. Multiple C. auris outbreaks have been reported worldwide including India, USA and United Kingdom. Infections and outbreaks caused by C. auris have also been reported in the Middle East region including Kuwait, Oman, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. This study uses whole genome sequencing (WGS) data to determine the epidemiology and the drug resistance mutations from C. auris in Qatar. Forty samples isolated from the patients and the hospital environment were sequenced by Illumina Nextseq. Core genome SNPs revealed that all isolates belonged to the Indian lineage, which could be originated from the expatriate labour from South Asia. The genetic variability among the isolates was low but comprised of more than one genetic cluster. The environmental isolates were identical to the clinical isolates, and the isolates from patients of different hospitals/outbreaks clustered together, suggesting the transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Mutations associated with azole and echinocandin resistance were discussed.

Importation, Mitigation, and Genomic Epidemiology of Candida auris at a Large Teaching Hospital

2017 ◽  
Vol 39 (1) ◽  
pp. 53-57 ◽  
Author(s):  
Emil P. Lesho ◽  
Melissa Z. Bronstein ◽  
Patrick McGann ◽  
Jason Stam ◽  
Yoon Kwak ◽  
...  
Keyword(s):  
New York ◽  
Teaching Hospital ◽  
Index Case ◽  
Index Patient ◽  
Multidrug Resistant ◽  
Multidisciplinary Teams ◽  
Nucleotide Polymorphisms ◽  
Case Patient ◽  
Candida Auris ◽  
Genomic Epidemiology

OBJECTIVECandida auris (CA) is an emerging multidrug-resistant pathogen associated with increased mortality. The environment may play a role, but transmission dynamics remain poorly understood. We sought to limit environmental and patient CA contamination following a sustained unsuspected exposure.DESIGNQuasi-experimental observation.SETTINGA 528-bed teaching hospital.PATIENTSThe index case patient and 17 collocated ward mates.INTERVENTIONImmediately after confirmation of CA in the bloodstream and urine of a patient admitted 6 days previously, active surveillance, enhanced transmission-based precautions, environmental cleaning with peracetic acid-hydrogen peroxide and ultraviolet light, and patient relocation were undertaken. Pre-existing agreements and foundational relationships among internal multidisciplinary teams and external partners were leveraged to bolster detection and mitigation efforts and to provide genomic epidemiology.RESULTSCandida auris was isolated from 3 of 132 surface samples on days 8, 9, and 15 of ward occupancy, and from no patient samples (0 of 48). Environmental and patient isolates were genetically identical (4–8 single-nucleotide polymorphisms [SNPs]) and most closely related to the 2013 India CA-6684 strain (~200 SNPs), supporting the epidemiological hypothesis that the source of environmental contamination was the index case patient, who probably acquired the South Asian strain from another New York hospital. All isolates contained a mutation associated with azole resistance (K163R) found in the India 2105 VPCI strain but not in CA-6684. The index patient remained colonized until death. No surfaces were CA-positive 1 month later.CONCLUSIONCompared to previous descriptions, CA dissemination was minimal. Immediate access to rapid CA diagnostics facilitates early containment strategies and outbreak investigations.Infect Control Hosp Epidemiol 2018;39:53–57

scholarly journals Two Candida auris Cases in Germany with No Recent Contact to Foreign Healthcare—Epidemiological and Microbiological Investigations

2021 ◽  
Vol 7 (5) ◽  
pp. 380
Author(s):  
Joerg Steinmann ◽  
Thomas Schrauzer ◽  
Lisa Kirchhoff ◽  
Jacques F. Meis ◽  
Peter-Michael Rath
Keyword(s):  
South Asian ◽  
Multidrug Resistant ◽  
Health Care Facilities ◽  
Candida Auris ◽  
Contact Precautions ◽  
Asian Clade ◽  
Care Facilities ◽  
Long Time ◽  
European Health ◽  
Healthcare Associated

Candida auris has become a global fungal public health threat. This multidrug-resistant yeast is associated with nosocomial intra- and interhospital transmissions causing healthcare-associated infections. Here, we report on two C. auris cases from Germany. The two patients stayed in Germany for a long time before C. auris was detected during their hospitalization. The patients were isolated in single rooms with contact precautions. No nosocomial transmissions were detected within the hospital. Both C. auris isolates exhibited high minimum inhibitory concentrations (MICs) of fluconazole and one isolate additionally high MICs against the echinocandins. Microsatellite genotyping showed that both strains belong to the South Asian clade. These two cases are examples for appropriate in-hospital care and infection control without further nosocomial spread. Awareness for this emerging, multidrug-resistant pathogen is justified and systematic surveillance in European health care facilities should be performed.

scholarly journals Emergence of Resistance Mutations in Salmonella enterica Serovar Typhi Against Fluoroquinolones

2017 ◽  
Vol 4 (4) ◽  
Author(s):  
Takashi Matono ◽  
Masatomo Morita ◽  
Koji Yahara ◽  
Ken-ichi Lee ◽  
Hidemasa Izumiya ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Evolutionary Process ◽  
Resistance Mechanisms ◽  
Single Mutation ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Single Nucleotide ◽  
Salmonella Enterica Serovar Typhi ◽  
Resistant Strains ◽  
Emergence Of Resistance

Abstract Background Little is known about the evolutionary process and emergence time of resistance mutations to fluoroquinolone in Salmonella enterica serovar Typhi. Methods We analyzed S. Typhi isolates collected from returned travelers between 2001 and 2016. Based on ciprofloxacin susceptibility, isolates were categorized as highly resistant (minimum inhibitory concentration [MIC] ≥ 4 μg/mL [CIPHR]), resistant (MIC = 1–2 μg/mL [CIPR]), intermediate susceptible (MIC = 0.12–0.5 μg/mL [CIPI]), and susceptible (MIC ≤ 0.06 μg/mL [CIPS]). Results A total of 107 isolates (33 CIPHR, 14 CIPR, 30 CIPI, and 30 CIPS) were analyzed by whole-genome sequencing; 2461 single nucleotide polymorphisms (SNPs) were identified. CIPS had no mutations in the gyrA or parC genes, while each CIPI had 1 of 3 single mutations in gyrA (encoding Ser83Phe [63.3%], Ser83Tyr [33.3%], or Asp87Asn [3.3%]). CIPHR had the same 3 mutations: 2 SNPs in gyrA (encoding Ser83Phe and Asp87Asn) and a third in parC (encoding Ser80Ile). CIPHR shared a common ancestor with CIPR and CIPI isolates harboring a single mutation in gyrA encoding Ser83Phe, suggesting that CIPHR emerged 16 to 23 years ago. Conclusions Three SNPs—2 in gyrA and 1 in parC—are present in S. Typhi strains highly resistant to fluoroquinolone, which were found to have evolved in 1993–2000, approximately 10 years after the beginning of the ciprofloxacin era. Highly resistant strains with survival advantages arose from strains harboring a single mutation in gyrA encoding Ser83Phe. Judicious use of fluoroquinolones is warranted to prevent acceleration of such resistance mechanisms in the future.

Whole genome sequence of first Candida auris strain, isolated in Russia

2019 ◽  
Vol 58 (3) ◽  
pp. 414-416 ◽  
Author(s):  
Ivan M Pchelin ◽  
Daniil V Azarov ◽  
Maria A Churina ◽  
Igor A Ryabinin ◽  
Irina V Vibornova ◽  
...  
Keyword(s):  
South Asian ◽  
Genome Sequence ◽  
Draft Genome ◽  
Multidrug Resistant ◽  
Whole Genome Sequence ◽  
Candida Auris ◽  
Fluconazole Resistance ◽  
Russian Strain ◽  
Resistant Strains ◽  
Original Species

Abstract Candida auris is an emergent yeast pathogen, easily transmissible between patients and with high percent of multidrug resistant strains. Here we present a draft genome sequence of the first known Russian strain of C. auris, isolated from a case of candidemia. The strain clustered within South Asian C. auris clade and seemingly represented an independent event of dissemination from the original species range. Observed fluconazole resistance was probably due to F105L and K143R mutations in ERG11.

scholarly journals 2267. Epidemiology of Candida auris Candidemia in a Teaching Hospital in North of Oman: One-Year Survival

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S776-S776
Author(s):  
Arash Eatemadi ◽  
Aiman Al Wahibi ◽  
Hilal Al shibli ◽  
Ali Al reesi
Keyword(s):  
Public Health ◽  
Teaching Hospital ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Fungal Treatment ◽  
Candida Auris ◽  
Coagulase Negative Staphylococci ◽  
Central Public Health ◽  
Antibiotic Susceptibility Test ◽  
Recent Emergence

Abstract Background Recent emergence of Candida auris as a multidrug resistant fungal pathogen, is a serious concerns for public health. However, there is a paucity of reported cases from Oman. Literature search resulted in finding only 7 cases from Oman, reporting C. auris infections in the articles first published in 2017. However, the rate of isolatin is increasing. Methods In this study, we included the results of all positive blood cultures of C. auris in Suhar teaching hospital from May 2018 (date of first detection) till end of April 2019. Further confirmation of the species was performed by MALDI-TOF and antibiotic susceptibility test (AST) by Vitek 2 in central public health laboratory (CPHL) of Oman. Results We detected 13 patients (9 females, 4 males). The mean age was 58.61% years (28–76 years). All candidemic patients had serious underlying conditions, including prolonged hospital stay or extensive and prolonged antimicrobial exposure or medical comorbidities (8 of 13). The time from hospital admission to onset of C. auris candidemia was 8–49 days, with a median of approximately 27 days. The most common isolated co- pathogen from blood culture was K. pneumonia (without regard to Coagulase-negative staphylococci). As average, every patient received 4.8 kind of different antibiotics in mean 88 doses before candidemia developed and piperacillin–tazobactam was the most common used antibiotics. AST was done just for 5 patients and revealed high-level resistance to fluconazole and Amphotricin B while, Echinocandins (anidulafungin, caspofungin) were fully sensitive and voricunazole had intermediate sensitivity. Mean duration of anti-fungal treatment was 12.5 days (5 – 26 days). 8 patients treated by Echinocandins (4/8 died), 4 by Fluconazole (3/4 died) and one without treatment discharged. 30-day all-cause mortality was 61.5%. Conclusion In Oman, C. auris has been reported from many hospitals. Resistance to several antifungal agents and persistence in the hospital environment make this organism a potential menace for the treating physician and the infection control personnel. In our hospital, every candidemic patient should be treated with Echinocandins and assumed to be resistant to Fluconazole until proven otherwise according to results of AST. Disclosures All authors: No reported disclosures.

scholarly journals Genomic Investigation Reveals Contaminated Detergent as the Source of an Extended-Spectrum-β-Lactamase-Producing Klebsiella michiganensis Outbreak in a Neonatal Unit

2020 ◽  
Vol 58 (5) ◽  
Author(s):  
Paul Chapman ◽  
Brian M. Forde ◽  
Leah W. Roberts ◽  
Haakon Bergh ◽  
Debra Vesey ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Klebsiella Oxytoca ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Nucleotide Polymorphism ◽  
Taxonomic Assignment ◽  
Single Nucleotide ◽  
Content Type ◽  
Extended Spectrum ◽  
Antimicrobial Resistance Genes

ABSTRACT Klebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which the sources of transmission may be challenging to elucidate. We describe the use of whole-genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates. Ceftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read sequencing (Illumina) and long-read sequencing (MinION; Oxford Nanopore Technologies) were used to confirm species taxonomy, to identify antimicrobial resistance genes, and to determine phylogenetic relationships using single-nucleotide polymorphism profiling. A total of 21 organisms (10 patient-derived isolates and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from multiple detergent-dispensing bottles were either identical or closely related by single-nucleotide polymorphism comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk expression equipment. No new cases were identified once the detergent bottles were removed. Environmental reservoirs may be an important source in outbreaks of multidrug-resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.

scholarly journals LB1. Regional Assessment and Containment of Candida auris Transmission in Post-Acute Care Settings—Orange County, California, 2019

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S993-S993 ◽  
Author(s):  
Ellora Karmarkar ◽  
Ellora Karmarkar ◽  
Kathleen O’Donnell ◽  
Christopher Prestel ◽  
Kaitlin Forsberg ◽  
...  
Keyword(s):  
Acute Care ◽  
Orange County ◽  
Invasive Disease ◽  
Nucleotide Polymorphisms ◽  
Nursing Facilities ◽  
Candida Auris ◽  
Single Nucleotide ◽  
Skilled Nursing ◽  
And Control

Abstract Background Patients in long-term acute care hospitals (LTACHs) and skilled nursing facilities with ventilator units (VSNFs) are at high risk for Candida auris colonization; among patients colonized with this emerging pathogen, 5%–10% develop invasive disease with >45% mortality. In September 2018, a California LTACH-affiliated laboratory began enhanced C. auris surveillance by classifying species of Candida isolated from routine urine specimens. In February 2019, the first known Southern California case was detected in an Orange County (OC) LTACH; the patient had not traveled outside the region, indicating local acquisition. We performed point prevalence surveys (PPS) and infection prevention (IP) assessments at all OC LTACHs and VSNF subacute units to identify patients colonized with C. auris and control transmission. Methods During March–August 2019, we conducted PPS at facilities by collecting composite axilla and groin swabs for C. auris polymerase chain reaction testing and reflex culture from all patients who assented. Facilities with ≥1 C. auris-colonized patient repeated a PPS every 2 weeks to assess for new transmission. Isolate relatedness was assessed by whole-genome sequencing (WGS). We evaluated hand hygiene (HH) adherence, access to alcohol-based hand rubs (ABHR), and cleaning of high-touch surfaces to guide IP recommendations. Results The first PPS at all OC LTACHs (n = 3) and adult VSNFs (n = 14) identified 45 C. auris-colonized patients in 3 (100%) LTACHs and 6 (43%) VSNFs; after repeated PPS, the total count reached 124. Most patients (70%) were at 2 facilities (Table 1). Three of 124 patients developed candidemia. To date, isolates from 48 patients have completed WGS; all were highly related (<11 single-nucleotide polymorphisms) in the African clade. Of 9 facilities with C. auris, 5 had HH adherence < 50%, 3 had limited ABHR, and at 2, <60% of assessed high-touch surfaces were clean. We recommended regular HH and cleaning audits, and increased ABHR. Conclusion Our investigation, prompted by enhanced surveillance, identified C. auris at 9 OC facilities. WGS indicated a single introduction and local transmission. Early detection, followed by rapid county-wide investigation and IP support, enabled containment efforts for C. auris in OC. Disclosures All authors: No reported disclosures.

scholarly journals Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England

2015 ◽  
Vol 53 (10) ◽  
pp. 3141-3147 ◽  
Author(s):  
M. D. Cairns ◽  
M. D. Preston ◽  
T. D. Lawley ◽  
T. G. Clark ◽  
R. A. Stabler ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
De Novo ◽  
University Hospital ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Conjugative Transposon ◽  
Content Type ◽  
Genomic Epidemiology ◽  
Hospital Outbreak ◽  
Nosocomial Diarrhea

Clostridium difficileremains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulentC. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients withC. difficileinfection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates.De novoassembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages ofC. difficileRT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.

scholarly journals Screening for Candida auris in patients admitted to eight intensive care units in England, 2017 to 2018

2021 ◽  
Vol 26 (8) ◽  
Author(s):  
Ashley Sharp ◽  
Berit Muller-Pebody ◽  
Andre Charlett ◽  
Bharat Patel ◽  
Rebecca Gorton ◽  
...  
Keyword(s):  
Intensive Care ◽  
Intensive Care Units ◽  
Health Indicators ◽  
Multidrug Resistant ◽  
Hospital Environment ◽  
Candida Auris ◽  
Flight Mass Spectrometry ◽  
Upper Confidence Limit ◽  
National Cohort ◽  
Local Risk

Background Candida auris is an emerging multidrug-resistant fungal pathogen associated with bloodstream, wound and other infections, especially in critically ill patients. C. auris carriage is persistent and is difficult to eradicate from the hospital environment. Aim We aimed to pilot admission screening for C. auris in intensive care units (ICUs) in England to estimate prevalence in the ICU population and to inform public health guidance. Methods Between May 2017 and April 2018, we screened admissions to eight adult ICUs in hospitals with no previous cases of C. auris, in three major cities. Swabs were taken from the nose, throat, axilla, groin, perineum, rectum and catheter urine, then cultured and identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Patient records were linked to routine ICU data to describe and compare the demographic and health indicators of the screened cohort with a national cohort of ICU patients admitted between 2016 and 2017. Results All C. auris screens for 921 adults from 998 admissions were negative. The upper confidence limit of the pooled prevalence across all sites was 0.4%. Comparison of the screened cohort with the national cohort showed it was broadly similar to the national cohort with respect to demographics and co-morbidities. Conclusion These findings imply that C. auris colonisation among patients admitted to ICUs in England is currently rare. We would not currently recommend widespread screening for C. auris in ICUs in England. Hospitals should continue to screen high-risk individuals based on local risk assessment.

Sign in / Sign up

Export Citation Format

Share Document