2461. Community-Acquired in Name Only: A Cluster of Carbapenem-Resistant Acinetobacter baumannii in a Burn Intensive Care Unit

Abstract Background Detection of nosocomial outbreaks often relies on epidemiological definitions of community and nosocomial acquisition. We report a cluster of three carbapenem-resistant Acinetobacter baumannii (CRAB) infections linked to a single source patient with infections occurring within 2 days of admission to a burn intensive care unit (ICU). The epidemiological investigation was supplemented by whole-genome sequencing (WGS) of clinical and environmental isolates. Methods Study participants included burn ICU patients identified with infections caused by CRAB. A detailed review of patient demographic and clinical data was conducted. Clinical A. baumannii isolates were assessed by antimicrobial susceptibility testing and WGS. Review of infection control practices on the affected unit was followed by environmental sampling. A. baumannii isolates obtained through environmental sampling were assessed for carbapenem resistance and then underwent WGS for comparison to the clinical isolates. Results Three cases of CRAB infection in the affected unit spanning a period of 3 months were linked to a preceding source patient, with CRAB isolates from the four patients differing by 5–7 single nucleotide variations. All case patients had been admitted to the same room within 2 days before development of CRAB infection. Environmental sampling performed while the third case patient occupied the room identified highly contaminated areas, and environmental CRAB isolates linked the patient isolates. The contaminated areas were subsequently re-sampled after enhanced terminal cleaning of the room. No additional CRAB was isolated, but other pathogenic organisms were recovered. Conclusion We report a cluster of three infections caused by highly resistant A. baumannii that occurred in a burn intensive care unit over a period of 3 months, linked to a single source patient. Three case patients developed infections classified as community-acquired using standard epidemiological definitions, however, whole-genome sequencing revealed clonality. An extensive investigation identified the role of environmental reservoirs. Burn patients may be particularly vulnerable to early-onset nosocomial infection from environmental contamination. Disclosures All authors: No reported disclosures.

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Molecular dissection of Carbapenem-resistant Acinetobacter baumannii circulating in Indian hospitals using Whole Genome Sequencing

10.1101/2021.07.30.454432 ◽

2021 ◽

Author(s):

Steffimol Rose ◽

Varun Shamanna ◽

Anthony Underwood ◽

Geetha Nagaraj ◽

Akshatha Prasanna ◽

...

Keyword(s):

Molecular Epidemiology ◽

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Clonal Complex ◽

Carbapenem Resistance ◽

Evolutionary Divergence ◽

Whole Genome ◽

Northern India ◽

Carbapenem Resistant

Objectives: Carbapenem-resistant Acinetobacter baumannii (CRAB) has acquired worldwide recognition as a serious nosocomial infection. It poses a concern to hospitalized patients because of the limited therapeutic options available. Thus, we investigated the molecular epidemiology and antibiotic resistance profiles of A. baumannii isolates in India. Materials and Methods: We characterized 306 retrospective A. baumannii clinical isolates collected from 18 centers across 10 states and 1 Union Territory of India between 2015 and 2019. Molecular epidemiology, and carbapenem resistance were studied by Whole Genome Sequencing. Results: A total of 105 different Sequence Types (STs) were identified including 48 reported STs and 57 Novel STs. 99 isolates were classified into Clonal Complex 451 (CC451) among which ST848 and ST1956 were the common STs. Carbapenemase resistance was confirmed in all the isolates with the presence of intrinsic bla OXA -51-like genes, and the acquired bla OXA-23 and bla NDM-1 genes. Conclusion: Most of the isolates were grouped under clonal complex 451. ST1053 caused an outbreak in Northern India during 2018 and 2019. Novel MLST alleles and STs were also detected, underlining an evolutionary divergence in India. The carbapenem-resistance was dominated by OXA-type carbapenemases and further surveillance of these carbapenem-resistant A. baumannii and antimicrobial stewardship should be strengthened.

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Control of Acinetobacter baumannii outbreak in the neonatal intensive care unit in Latvia: whole-genome sequencing powered investigation and closure of the ward

Antimicrobial Resistance and Infection Control ◽

10.1186/s13756-019-0537-z ◽

2019 ◽

Vol 8 (1) ◽

Cited By ~ 1

Author(s):

A. Gramatniece ◽

I. Silamikelis ◽

Ie. Zahare ◽

V. Urtans ◽

Ir. Zahare ◽

...

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Neonatal Intensive Care ◽

Whole Genome

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Whole-Genome Sequencing for Investigating a Health Care-Associated Outbreak of Carbapenem-Resistant Acinetobacter baumannii

Diagnostics ◽

10.3390/diagnostics11020201 ◽

2021 ◽

Vol 11 (2) ◽

pp. 201

Author(s):

Sang Mee Hwang ◽

Hee Won Cho ◽

Tae Yeul Kim ◽

Jeong Su Park ◽

Jongtak Jung ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Snp Analysis ◽

Whole Genome ◽

Phylogenetic Tree Analysis ◽

Web Based ◽

Hospital Outbreak ◽

Carbapenem Resistant ◽

Bioinformatics Tools

Carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in hospital settings challenge the treatment of patients and infection control. Understanding the relatedness of clinical isolates is important in distinguishing outbreak isolates from sporadic cases. This study investigated 11 CRAB isolates from a hospital outbreak by whole-genome sequencing (WGS), utilizing various bioinformatics tools for outbreak analysis. The results of multilocus sequence typing (MLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic tree analysis by WGS through web-based tools were compared, and repetitive element polymerase chain reaction (rep-PCR) typing was performed. Through the WGS of 11 A. baumannii isolates, three clonal lineages were identified from the outbreak. The coexistence of blaOXA-23, blaOXA-66, blaADC-25, and armA with additional aminoglycoside-inactivating enzymes, predicted to confer multidrug resistance, was identified in all isolates. The MLST Oxford scheme identified three types (ST191, ST369, and ST451), and, through whole-genome MLST and whole-genome SNP analyses, different clones were found to exist within the MLST types. wgSNP showed the highest discriminatory power with the lowest similarities among the isolates. Using the various bioinformatics tools for WGS, CRAB outbreak analysis was applicable and identified three discrete clusters differentiating the separate epidemiologic relationships among the isolates.

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Extensively drug-resistant Acinetobacter baumannii isolated from intensive care units in northern Italy: a genomic approach to characterize new sequence types

Future Microbiology ◽

10.2217/fmb-2019-0083 ◽

2019 ◽

Vol 14 (15) ◽

pp. 1281-1292 ◽

Cited By ~ 2

Author(s):

Giovanni Lorenzin ◽

Erika Scaltriti ◽

Franco Gargiulo ◽

Francesca Caccuri ◽

Giorgio Piccinelli ◽

...

Keyword(s):

Intensive Care ◽

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Intensive Care Units ◽

Genome Sequencing ◽

Multilocus Sequence Typing ◽

Whole Genome ◽

Drug Resistant ◽

Extensively Drug Resistant ◽

Sequence Types

Aim: This study aims to characterize clinical strains of Acinetobacter baumannii with an extensively drug-resistant phenotype. Methods: VITEK® 2, Etest® method and broth microdilution method for colistin were used. PCR analysis and multilocus sequence typing Pasteur scheme were performed to identify bla-OXA genes and genetic relatedness, respectively. Whole-genome sequencing analysis was used to characterize three isolates. Results: All the isolates were susceptible only to polymyxins. blaOXA-23-like gene was the only acquired carbapenemase gene in 88.2% of the isolates. Multilocus sequence typing identified various sequence types: ST2, ST19, ST195, ST577 and ST632. Two new sequence types, namely, ST1279 and ST1280, were detected by whole-genome sequencing. Conclusion: This study showed that carbapenem-resistant A. baumannii isolates causing infections in intensive care units almost exclusively produce OXA-23, underlining their frequent spread in Italy.

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Data on Whole-Genome Sequencing Are Insufficient to Rule Out Patient-to-Patient Transmission as a Significant Source of Staphylococcus aureus Acquisition in an Intensive Care Unit

Clinical Infectious Diseases ◽

10.1093/cid/ciu368 ◽

2014 ◽

Vol 59 (5) ◽

pp. 752-752 ◽

Cited By ~ 1

Author(s):

J. P. Mills ◽

D. R. Linkin ◽

Keyword(s):

Intensive Care Unit ◽

Staphylococcus Aureus ◽

Intensive Care ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Significant Source ◽

Whole Genome ◽

Rule Out

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Using whole-genome sequencing and a pentaplex real-time PCR to characterize third-generation cephalosporin-resistant Enterobacteriaceae from Southeast Queensland, Australia

10.1101/2020.02.20.958728 ◽

2020 ◽

Author(s):

AG Stewart ◽

EP Price ◽

K Schabacker ◽

M Birikmen ◽

PNA Harris ◽

...

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Whole Genome Sequencing ◽

Real Time ◽

Genome Sequencing ◽

Real Time Pcr ◽

Generation Cephalosporin ◽

Whole Genome ◽

Third Generation ◽

Sensitivity Testing

AbstractThird-generation cephalosporin-resistant (3GC-R) Enterobacteriaceae represent a major threat to human health. Here, we captured 288 3GC-R Enterobacteriaceae clinical isolates from 258 patients presenting at a regional Australian hospital over a 14-month period. Alongside routine mass spectrometry speciation and antibiotic sensitivity testing, isolates were examined using a rapid (~40 min) pentaplex real-time PCR assay targeting the most common extended spectrum β-lactamases (ESBLs; CTX-M-1 and CTX-M-9 groups, plus TEM, SHV, and an internal 16S ribosomal DNA control). Additionally, AmpC CMY β-lactamase prevalence was examined using a singleplex PCR. A subset of isolates, including all 3GC-R isolates obtained from the intensive care unit, were subjected to whole-genome sequencing (WGS) to assess transmission dynamics, the presence of unidentified resistance determinants, and genotyping accuracy. Escherichia coli (80.2%) and Klebsiella pneumoniae (17.0%) were dominant, with Klebsiella oxytoca, Klebsiella aerogenes and Enterobacter cloacae infrequently identified. Ceftriaxone and cefoxitin resistance was identified in 97% and 24.5% of E. coli and K. pneumoniae isolates, respectively. Consistent with global findings in Enterobacteriaceae, the majority (98.3%) of isolates harbored at least one β-lactamase gene, with 144 (50%) encoding blaCTX-M-1 group, 92 (31.9%) blaCTX-M-9 group, 48 (16.7%) blaSHV, 133 (46.2%) blaTEM, and 34 (11.8%) blaCMY. WGS of β-lactamase negative or carbapenem-resistant isolates identified uncommon ESBLs and carbapenemases, including blaNDM and blaIMP, and confirmed all PCR-positive genotypes. No evidence of transmission among intensive care unit patients was identified. We demonstrate that our PCR assays enable the rapid and cost-effective identification of ESBLs in the hospital setting, which has important infection control and therapeutic implications.

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Use of whole-genome sequencing to detect an outbreak of Malassezia pachydermatis infection and colonization in a neonatal intensive care unit—California, 2015–2016

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2020.73 ◽

2020 ◽

Vol 41 (7) ◽

pp. 851-853 ◽

Cited By ~ 1

Author(s):

Nancy A. Chow ◽

Raymond Chinn ◽

Alice Pong ◽

Kerry Schultz ◽

Janice Kim ◽

...

Keyword(s):

Intensive Care Unit ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Neonatal Intensive Care ◽

Infection Prevention ◽

Whole Genome ◽

Prevention Measures ◽

Malassezia Pachydermatis

AbstractWhole-genome sequencing confirmed the presence of a Malassezia pachydermatis outbreak among neonates in a neonatal intensive care unit. This technology supports the importance of adhering to infection prevention measures.

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Whole-Genome Sequencing for Outbreak Investigations of Methicillin-Resistant Staphylococcus aureus in the Neonatal Intensive Care Unit: Time for Routine Practice?

Infection Control and Hospital Epidemiology ◽

10.1017/ice.2015.73 ◽

2015 ◽

Vol 36 (7) ◽

pp. 777-785 ◽

Cited By ~ 38

Author(s):

Taj Azarian ◽

Robert L. Cook ◽

Judith A. Johnson ◽

Nilmarie Guzman ◽

Yvette S. McCarter ◽

...

Keyword(s):

Intensive Care Unit ◽

Staphylococcus Aureus ◽

Phylogenetic Analysis ◽

Intensive Care ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Neonatal Intensive Care ◽

Whole Genome ◽

Genome Wide ◽

Typing Methods

BACKGROUNDInfants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates among a population sample that appears homogenous when evaluated using conventional typing methods.OBJECTIVETo investigate a putative MRSA outbreak in a NICU utilizing whole-genome sequencing and phylogenetic analysis to identify recent transmission events.DESIGNClinical and surveillance specimens collected during clinical care and outbreak investigation.PATIENTSA total of 17 neonates hospitalized in a 43-bed level III NICU in northeastern Florida from December 2010 to October 2011 were included in this study.METHODSWe assessed epidemiological data in conjunction with 4 typing methods: antibiograms, PFGE, spa types, and phylogenetic analysis of genome-wide SNPs.RESULTSAmong the 17 type USA300 isolates, 4 different spa types were identified using pulsed-field gel electrophoresis. Phylogenetic analysis identified 5 infants as belonging to 2 clusters of epidemiologically linked cases and excluded 10 unlinked cases from putative transmission events. The availability of these results during the initial investigation would have improved infection control interventions.CONCLUSIONWhole-genome sequencing and phylogenetic analysis are invaluable tools for epidemic investigation; they identify transmission events and exclude cases mistakenly implicated by traditional typing methods. When routinely applied to surveillance and investigation in the clinical setting, this approach may provide actionable intelligence for measured, appropriate, and effective interventions.Infect. Control Hosp. Epidemiol. 2015;36(7):777–785

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