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Uncovering The Spread of Drug-Resistant Bacteria Through Next-Generation Sequencing Based Surveillance: Transmission of Extended-Spectrum Β-Lactamase-Producing Enterobacteriaceae by A Contaminated Duodenoscope

ABSTRACT: Transmission of Extended-Spectrum Β-Lactamase-Producing Enterobacteriaceae by A Contaminated Duodenoscope

PROVIDER: PRJEB67940 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12175051_1.fastq.gz	Fastqsanger.gz
	ERR12175051_2.fastq.gz	Fastqsanger.gz
	ERR12175052_1.fastq.gz	Fastqsanger.gz
	ERR12175052_2.fastq.gz	Fastqsanger.gz
	ERR12175053_1.fastq.gz	Fastqsanger.gz

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Uncovering the spread of drug-resistant bacteria through next-generation sequencing based surveillance: transmission of extended-spectrum β-lactamase-producing Enterobacterales by a contaminated duodenoscope.

Project description:Contamination of duodenoscopes is a significant concern due to the transmission of multidrug-resistant organisms (MDROs) among patients who undergo endoscopic retrograde cholangiopancreatography (ERCP), resulting in outbreaks worldwide. In July 2020, it was determined that three different patients, all had undergone ERCP with the same duodenoscope, were infected. Two patients were infected with blaCTX-M-15 encoding Citrobacter freundii, one experiencing a bloodstream infection and the other a urinary tract infection, while another patient had a bloodstream infection caused by blaSHV-12 encoding Klebsiella pneumoniae. Molecular characterization of isolates was available as every ESBL-producing isolate undergoes Next-Generation Sequencing (NGS) for comprehensive genomic analysis in our center. After withdrawing the suspected duodenoscope, we initiated comprehensive epidemiological research, encompassing case investigations, along with a thorough duodenoscope investigation. Screening of patients who had undergone ERCP with the implicated duodenoscope, as well as a selection of hospitalized patients who had ERCP with a different duodenoscope during the outbreak period, led to the discovery of three additional cases of colonization in addition to the three infections initially detected. No microorganisms were detected in eight routine culture samples retrieved from the suspected duodenoscope. Only after destructive dismantling of the duodenoscope, the forceps elevator was found to be positive for blaSHV-12 encoding K. pneumoniae which was identical to the isolates detected in three patients. This study highlights the importance of using NGS to monitor the transmission of MDROs and demonstrates that standard cultures may fail to detect contaminated medical equipment such as duodenoscopes.

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Project description:The present study examines changes in global gene expression patterns and in virulence factor-associated genes in an extended spectrum beta-lactamase (ESBL)-producing UPEC (ESBL019) during the morphologic transitions induced by an ineffective antibiotic and in the presence of human primary bladder epithelial cells. The morphological shifts induced by ineffective antibiotics are associated with significant transcriptional virulence alterations in ESBL-producing UPEC, which may affect survival and persistence in the urinary tract.

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Project description:Maternal carriage and vertical transmission of extended-spectrum, beta-lactamase-producing Enterobacteriaceae (ESBL-E), such as Escherichia coli, hamper the treatment of infections, resulting in high morbidity. E. coli is the most frequent cause of early-onset neonatal sepsis (EOS) in preterm infants, where ESBL-E are more frequently isolated. In this prospective, case-controlled study, maternal rectovaginal ESBL-E colonization and vertical transmission to preterm infants were assessed in 160 women with preterm premature rupture of membranes (PPROM; 57.4%) or preterm labor (42.6%); additional cultures were obtained from the placenta, amnion, and umbilical cord during preterm labor. Maternal and neonatal ESBL-E-carriage rates were 17.5% and 12.9%, respectively, and the vertical-transmission rate was 50%. Maternal ESBL-E colonization among women with PPROM was 21.3%, and in women with premature labor it was 12.6%. No correlation was observed between maternal ESBL-E-colonization and previous hospitalization or antibiotic administration during pregnancy. However, a correlation was found between placental inflammation and maternal ESBL-E colonization (p = 0.007). ESBL-E-colonized infants were delivered at an earlier gestational age and were more likely to have complications. Thus, the high ESBL-E carriage rate in women with threatened preterm labor, without obvious risk factors for carriage, and a high vertical transmission rate, combined with a correlation between placental inflammation and ESBL-E carriage, support maternal-neonatal ESBL-E-colonization surveillance and active measures to prevent ESBL-E-related EOS.

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Project description:Eighty-four clinical isolates of the family Enterobacteriaceae, recovered from 1998 to 2000 in 15 hospitals in 10 Polish cities, were analyzed. All the isolates produced beta-lactamases with pIs of 8.4 and 5.4, and the pI 8.4 enzymes were demonstrated to hydrolyze cefotaxime but not ceftazidime in the in vitro bioassay. PCR analysis and DNA sequencing have revealed that in all cases the pI 8.4 beta-lactamase was probably the CTX-M-3 extended-spectrum beta-lactamase (ESBL) variant, which was originally identified in 1996 in Praski Hospital in Warsaw. In the majority of isolates, bla(CTX-M-3) genes resided within large conjugative plasmids with similar fingerprints, which, in the context of the high degree of diversity of the randomly amplified polymorphic DNA types of the isolates, suggested that horizontal transfer of plasmids was likely the main mechanism of CTX-M-3 spread. The dissemination of plasmids was probably preceded by the center-to-center transmission of several strains, as indicated by the identification by pulsed-field gel electrophoresis of closely related or possibly related Klebsiella pneumoniae, Escherichia coli, and Citrobacter freundii isolates in five different hospitals. CTX-M-3-producing organisms revealed a very high degree of diversity in beta-lactam resistance levels and patterns. This was attributed to several factors, such as the production of other beta-lactamases including additional ESBLs, possible quantitative variations in CTX-M-3 expression, segregation of AmpC derepressed mutants, and permeability alterations.

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