Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

Surleac, Marius; Barbu, Ilda Czobor; Paraschiv, Simona; Popa, Luis Ovidiu; Gheorghe, Irina; Măruţescu, Luminiţa; Popa, Marcela; Sârbu, Ionela; Tălăpan, Daniela; Niţă, Mihai; Iancu, Alina Viorica; Arbune, Manuela; Manole, Alina; Nicolescu, S; Săndulescu, Oana; Streinu-Cercel, Adrian; Oțelea, Dan; Chifiriuc, Mariana Carmen

doi:10.1371/journal.pone.0228079

Cited by 60 publications

(35 citation statements)

References 54 publications

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“…However, it is unclear as to where this selection is predominantly operating. There have been a number of studies comparing wastewater and local clinical samples, and it is reasonably assumed that the microbial composition of hospital wastewater closely mirrors that of the hospital itself [14,[48][49][50]. However, an alternative is that resistance is both acquired and maintained directly within drain-associated biofilms, possibly driven by sub-lethal concentrations of antibiotics in these environments.…”

Section: Discussionmentioning

confidence: 99%

A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England

et al. 2021

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Klebsiella species occupy a wide range of environmental and animal niches, and occasionally cause opportunistic infections that are resistant to multiple antibiotics. In particular, Klebsiella pneumoniae (Kpne) has gained notoriety as a major nosocomial pathogen, due principally to the rise in non-susceptibility to carbapenems and other beta-lactam antibiotics. Whilst it has been proposed that the urban water cycle facilitates transmission of pathogens between clinical settings and the environment, the level of risk posed by resistant Klebsiella strains in hospital wastewater remains unclear. We used whole genome sequencing (WGS) to compare Klebsiella species in contemporaneous samples of wastewater from an English hospital and influent to the associated wastewater treatment plant (WWTP). As we aimed to characterize representative samples of Klebsiella communities, we did not actively select for antibiotic resistance (other than for ampicillin), nor for specific Klebsiella species. Two species, Kpne and K. ( Raoultella ) ornithinolytica (Korn), were of equal dominance in the hospital wastewater, and four other Klebsiella species were present in low abundance in this sample. In contrast, despite being the species most closely associated with healthcare settings, Kpne was the dominant species within the WWTP influent. In total, 29 % of all isolates harboured the bla OXA-48 gene on a pOXA-48-like plasmid, and these isolates were almost exclusively recovered from the hospital wastewater. This gene was far more common in Korn (68 % of isolates) than in Kpne (3.4 % of isolates). In general plasmid-borne, but not chromosomal, resistance genes were significantly enriched in the hospital wastewater sample. These data implicate hospital wastewater as an important reservoir for antibiotic-resistant Klebsiella , and point to an unsuspected role of species within the Raoultella group in the maintenance and dissemination of plasmid-borne bla OXA-48. This article contains data hosted by Microreact.

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Section: Discussionmentioning

confidence: 99%

A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England

et al. 2021

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“…WGS has also been implemented for comparative analysis from contrasting environments. Carbapenem resistant and ESBL-producing K. pneumoniae was found to carry a higher diversity of carbapenemases genes in wastewater isolates while antiseptic-resistance gene qacE was exclusive to clinical samples (Surleac et al, 2020).…”

Section: Resistome Surveillance Through Whole-genome Sequencingmentioning

confidence: 97%

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

et al. 2020

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A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.

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“…in the treated wastewater of a hospital (Gomi et al, 2018), of OXA-48 producing K. pneumoniae from hospital sewage (Zurfluh et al, 2017), or of the presence of the same clone in the hospital sewage and receiving river (Suzuki et al, 2020) raises concerns. Since its first detection in Székely et al (2013), OXA-48 was the most frequently encountered carbapenemase in Romania (Lixandru et al, 2015;Grundmann et al, 2017;Popescu et al, 2017;Baicus et al, 2018;Surleac et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Previous data from our research team (Surleac et al, 2020) showed that MDR, carbapenemase and ESBL-producing K. pneumoniae isolated from clinics, hospital wastewater, and urban WWTPs in different regions of the country exhibit multiple antibiotic and antiseptic resistance, as well as virulence genes, the ST101 clone being the most frequently encountered in all sampling sites. The K. pneumoniae ST101 clone seems to be well established in Romanian hospitals (Dortet et al, 2015;Czobor et al, 2016) and wastewaters (Surleac et al, 2020), this determining us to investigate its possible transmission from hospital to wastewater, aiming to comparatively characterize the K. pneumoniae ST101 isolated from an infectious diseases hospital and its wastewaters.…”

Section: Introductionmentioning

confidence: 87%

“…Out of a total of 101 carbapenem resistant K. pneumoniae strains, 78 isolated from wastewater and 23 from inpatients, some of them previously characterized for their antibiotic susceptibility profiles (Surleac et al, 2020), 31 were initially selected for the present study, based on their sampling location and MDR phenotype, as defined by Magiorakos et al, 2012 (Supplementary Table 3). For all the 31 strains, the MLST profile was inferred from WGS data (Surleac et al, 2020). The MLST profiles revealed by WGS data analyses highlighted that the K. pneumoniae ST101 subtype was the most prevalent (n = 11, 36%) in all three sampling points (Supplementary Figure 2).…”

Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

Cited by 60 publications

References 54 publications

A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England

A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

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