Dataset Information

Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands.

ABSTRACT: Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.

SUBMITTER: Naing SY

PROVIDER: S-EPMC8875366 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature

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Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands.

Naing Soe Yu SY Hordijk Joost J Duim Birgitta B Broens Els M EM van der Graaf-van Bloois Linda L Rossen John W JW Robben Joris H JH Leendertse Masja M Wagenaar Jaap A JA Zomer Aldert L AL

Pathogens (Basel, Switzerland) 20220120 2

Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), enviro ...[more]

PMID: 35215067

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Project description:BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAB) is a major public health concern globally. Often studied in the context of hospital outbreaks, little is known about the persistence and evolutionary dynamics of endemic CRAB populations.MethodsA three-month cross-sectional observational study was conducted in a 28-bed intensive care unit (ICU) in Hangzhou, China. A total of 5068 samples were collected from the hospital environment (n = 3985), patients (n = 964) and staff (n = 119). CRAB isolates were obtained from 10.5% of these samples (n = 532). All of these isolates, plus an additional 19 from clinical infections, were characterised through whole-genome sequencing.FindingsThe ICU CRAB population was dominated by OXA-23-producing global clone 2 isolates (99.3% of all isolates) that could be divided into 20 distinct clusters, defined through genome sequencing. CRAB was persistently present in the ICU, driven by regular introductions of distinct clusters. The hospital environment was heavily contaminated, with CRAB isolated from bed units on 183/335 (54.6%) sampling occasions but from patients on only 72/299 (24.1%) occasions. CRAB was spread to adjacent bed units and rooms, and following re-location of patients within the ICU. We also observed three horizontal gene transfer events between CRAB strains in the ICU, involving three different plasmids.InterpretationThe epidemiology of CRAB in this setting contrasted with previously described clonal outbreaks in high-income countries, highlighting the importance of environmental CRAB reservoirs in ICU epidemiology and the unique challenges in containing the spread of CRAB in ICUs where this important multidrug-resistant pathogen is endemic.FundingThis work was undertaken as part of the DETECTIVE research project funded by the Medical Research Council (MR/S013660/1), National Natural Science Foundation of China (81861138054, 32011530116, 31970128, 31770142), Zhejiang Province Medical Platform Backbone Talent Plan (2020RC075), and the National Key Research and Development Program of China grant (2018YFE0102100). W.v.S was also supported by a Wolfson Research Merit Award (WM160092).

Project description:This study was conducted in order to assess the acquisition rate of Acinetobacter baumannii by newborn screening, on admission and during the discharge process of neonatal intensive care unit. (NICU). Furthermore, we investigated risk factors for potential colonization and molecular epidemiology of isolated resistant bacteria. This prospective study was conducted in the neonatal unit of Hassan II University Hospital of Fez from February 2013 to July 2015. During this period, all consecutive admitted neonates were screened for A. baumannii intestinal carriage, on admission and during the discharge process. Bacteriological and molecular tests were evaluated according to the international standards. This study examines the screening on admission of 455 newborns, 59% of whom were male. The average gestational age and birth weight were 35.2 weeks and 2612.1 g respectively. In total, 277 patients were included in the acquisition study on admission. The prevalence of multi-drug resistant (MDR) A. baumannii strain carriage was 6.5%, while the acquisition rate during the hospital recovery was 13.7%. In this study, 68 MDR A. baumannii isolates were collected. The resistance rates to different antibiotic classes including, Ceftazidime, Gentamycin and Ciprofloxacin varied between 92 and 100%. Moreover, 13% of MDR A. baumannii isolates were carbapenemase producers and 88% harbored blaOXA-23 gene. On admission, three risk factors were significantly associated with A. baumannii colonization: age (OR, 2.803; IC95%, 1.191-6.596; P = 0.01), gender (OR, 0.382; IC95%, 0.158-0.921; P = 0.03) and the delivery birth at the Maternity of University Hospital (MUH), (OR, 0.196; IC95%, 0.071-0.540; P = 0.002). However during hospitalization, the only risk factor associated with acquisition of A. baumannii was the respiratory distress (OR, 2.270; IC95%, 1.055-4.881; P = 0.03). A high intestinal carriage rate of A. baumannii and multiple antibiotic resistance were found in our NICU. Thus, the spread of MDR A. baumannii should be monitored by an active surveillance strategy.

Project description:BackgroundAcinetobacter baumannii is an emerging pathogen capable of causing hospital-acquired infections (HAIs). It has the ability to survive on environmental surfaces for months, making transmission difficult to control. Our report describes the investigation and restriction of an outbreak of A.baumannii in the Neonatal Intensive Care Unit (NICU) using whole-genome sequencing (WGS) and multi-modal infection control measures.MethodsA prospective surveillance of HAIs was initiated in the NICU at the Pauls Stradins Clinical University Hospital (PSCUH) in Latvia on 1/9/2012 and identified an outbreak of A.baumannii. Case definitions for A.baumannii bloodstream infection (BSI) and colonization were implemented; surveillance cultures were obtained from all admitted patients to monitor the rate of colonization; an infection prevention and control team was formed and infection control interventions implemented. Environmental sampling of the NICU and Labour ward was performed. We employed WGS to differentiate phenotypically identical multidrug-resistant A.baumannii (MDRAB) strains from simultaneous intrahospital outbreaks in the adult Intensive Care Unit and NICU.ResultsBetween 1/9/2012 and 31/12/2017 the surveillance included 2157 neonates. A total of 17 neonates had A.baumannii BSI, with the highest rate of 30.0 cases per 1000 bed-days in November 2012. Rectal screening samples were positive for A.baumannii-complex in 182 neonates reaching 119.6 per 1000 bed-days in July 2015. All 298 environmental cultures were negative. Two phenotypically identical MDRAB isolates from the simultaneous intrahospital outbreaks were differentiated using WGS, ruling out an inter-ward transmission. Adherence to stringent infection control measures decreased BSI cases but colonization remained persistent. With several relapses, the outbreak was ongoing for four years. No new A.baumannii BSI cases were registered after total environmental decontamination in the NICU in July 2015. Colonization reappeared and persisted until in November 2016 when the ward was temporarily closed, relocated and renovated. No A.baumannii cases were registered after the renovation.ConclusionThe HAI surveillance system successfully detected and facilitated the control of the A.baumannii outbreak. Whole-genome sequencing was found to be a useful method for differentiation of phenotypically identical A.baumannii strains from the intrahospital outbreak. Only multi-modal infection control program, including closure, temporary relocation, and renovation of the ward, restricted the outbreak.

Project description:BackgroundAcinetobacter baumannii (A. baumannii) is a life-threatening and challenging pathogen. In addition, it accounts for numerous serious infections, particularly among immunocompromised patients. Resistance to nearly all clinically used antibiotics and their ability to spread this resistance is one of the most important concerns related to this bacterium.ObjectivesThis study describes different molecular mechanisms of two multidrug-resistant A. baumannii isolates obtained from endotracheal aspirates collected from the neonatal intensive care unit (NICU), Ain Shams University Hospital, Egypt.MethodsFollowing the identification of two isolates, they were examined for susceptibility to antimicrobial agents. This was followed by multilocus sequence typing as well as whole-genome sequence (WGS). Additionally, a Pathosystems Resources Integration Center (PATRIC) analysis was performed.ResultsTwo isolates, Ab119 and Ab123, exhibited resistance to all tested antibiotics except for tigecycline and colistin. The WGS analysis of antimicrobial resistance genes (AMR) indicated that both isolates shared beta-lactam, aminoglycoside, macrolides, and sulfonamide resistance genes. Furthermore, each strain revealed different resistance genes such as blaNDM-1, blaNDM-10, OXA-64, aph (3')-VI, Tet-B in Ab119 strain and blaOXA-68, blaPER-1, blaPER-7, Tet-39 in Ab123 strain. Multiple efflux pump genes were detected. Multilocus sequence typing indicated that both isolates belong to the same sequence type (ST931), which belongs to international clone (IC3). Both isolates exhibited the presence of multiple mobile genetic elements (MGEs), but no plasmid was detected in either of them.ConclusionsA low prevalence of the IC3 sequence type was identified among two A. baumannii isolates obtained from the NICU in Egypt, exhibiting a high resistance level. Healthcare workers must have knowledge regarding the prevalence of A. baumannii among different populations in order to administer suitable treatment, improve patient outcomes, and apply effective infection control practices.

Dataset Information

Genomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands.

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Genomic Investigation of Two <i>Acinetobacter baumannii</i> Outbreaks in a Veterinary Intensive Care Unit in The Netherlands.

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