Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species

Saralegui, Claudia; Ponce-Alonso, Manuel; Pérez-Viso, Blanca; Alegre, Laura Moles; Escribano, Esperanza; Lázaro-Perona, Fernando; Lanza, Val F.; Pipaón, Miguel Sáenz de; Rodríguez, Juan M.; Baquero, Fernando; Campo, R. del

doi:10.3389/fmicb.2020.00451

Cited by 25 publications

(31 citation statements)

References 54 publications

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“…nematodiphila (Sne) and S. ureilytica (Sur), has not yet been well elucidated even in the above-mentioned comparative genome analyses [16–18, 22].…”

Section: Introductionmentioning

confidence: 99%

“…Starting from the first whole-genome sequence (WGS) determination and detailed genomic comparison of two Sma strains (Db11, an isolate from an insect source; and SM39, a multidrug-resistant clinical isolate) [15], both of which were used as representative strains of Sma in this study, several comparative genome analyses have been reported. They included a large-scale genomic analysis of multidrug-resistant (MDR) clones in the UK and Ireland [9] and more recently published studies that analysed many publicly available WGSs [16][17][18]. The results of three recent studies indicated the presence of clinical isolate-enriched lineages, but WGSs of environmental isolates were limited in the database.…”

Section: Introductionmentioning

confidence: 99%

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Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex

et al. 2022

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Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the ‘ S. marcescens complex’), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila , S. marcescens sensu stricto, S. ureilytica and S. surfactantfaciens, respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.

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“…nematodiphila (Sne) and S. ureilytica (Sur), has not yet been well elucidated even in the above-mentioned comparative genome analyses [16–18, 22].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex

et al. 2022

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“…It is found in the environment (including soil, water, sludge and compost), plants, insects, and clinical specimens from humans and animals. In humans, it is a cause of opportunistic and nosocomial infections, with increasing concerns for neonatal units of hospital [ 1 ]. S .…”

Section: Introductionmentioning

confidence: 99%

Healthcare-associated infections caused by chlorhexidine-tolerant Serratia marcescens carrying a promiscuous IncHI2 multi-drug resistance plasmid in a veterinary hospital

et al. 2022

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The bacterium Serratia marcescens can cause opportunistic infections in humans and in animals. In veterinary settings, the diversity, reservoirs and modes of transmission of this pathogen are poorly understood. The phenotypes and genotypes of Serratia spp. isolated from dogs, cats, horses, a bird and a rabbit examined at an Australian veterinary hospital between 2008 and 2019 were characterised. The isolates were identified as S. marcescens (n = 15) or S. ureilytica (n = 3) and were placed into four distinct phylogenetic groups. Nine quasi-clonal isolates associated with post-surgical complications in different patients displayed high levels of resistance to the antimicrobials fluoroquinolones, cephalosporins, aminoglycosides, and to the disinfectant chlorhexidine. A Serratia sp. with a similar resistance profile was also isolated from chlorhexidine solutions used across the Hospital, suggesting that these infections had a nosocomial origin. A genomic island encoding a homolog of the Pseudomonas MexCD-OprJ biocide efflux system was detected in the chlorhexidine-tolerant Serratia. The nine multi-drug resistant Serratia isolates also possessed a Ser-83-Ile mutation in GyrA conferring fluoroquinolone resistance, and carried a large IncHI2 conjugative plasmid encoding antimicrobial and heavy metal resistances. This replicon was highly similar to a plasmid previously detected in a strain of Enterobacter hormaechei recovered from the Hospital environment. IncHI2 plasmids are commonly found in Enterobacteriaceae, but are rarely present in Serratia spp., suggesting that this plasmid was acquired from another organism. A chlorhexidine-tolerant Serratia isolate which lacked the IncHI2 plasmid was used in mating experiments to demonstrate the transfer of multi-drug resistance from a E. hormaechei donor. This study illustrates the importance of environmental surveillance of biocide-resistance in veterinary hospitals.

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“…The first is a beta lactamase with high similarity to bla‐C in Mycobacterium (>98% AA similarity), potentially responsible for the observed instances of (intermediate) phenotypic resistance to beta‐lactam antibiotics (Table 2). The second are genes with high (~80% AA) similarity to oqxB ; an efflux pump conferring resistance to fluoroquinolones and benzalkonium chloride and are prevalent in S. marcescens clinical isolates (Saralegui et al ., 2020). Most interestingly is the identification of blaSPR‐1 , a metallo‐β‐lactamase (MBL), which confer carbapenem resistance originally characterized in S. proteamaculans (Vella et al ., 2013) (~80% AA similarity).…”

Section: Resultsmentioning

confidence: 99%

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

Ferraresso

Lawton

Bayliss

et al. 2020

Environmental Microbiology

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Soil biomes are vast, exceptionally diverse and crucial to the health of ecosystems and societies. Soils also contain an appreciable, but understudied, diversity of opportunistic human pathogens. With climate change and other forms of environmental degradation potentially increasing exposure risks to soilborne pathogens, it is necessary to gain a better understanding of their ecological drivers. Here we use the Galleria mellonella insect virulence model to selectively isolate pathogenic bacteria from soils in Cornwall (UK). We find a high prevalence of pathogenic soil bacteria with two genera, Providencia and Serratia, being especially common. Providencia alcalifaciens, P. rustigianii, Serratia liquefaciens and S. plymuthica strains were studied in more detail using phenotypic virulence and antibiotic resistance assays and whole-genome sequencing. Both genera displayed low levels of antibiotic resistance and antibiotic resistance gene carriage. However, Serratia isolates were found to carry the recently characterized metallo-β-lactamase blaSPR-1 that, although not conferring high levels of resistance in these strains, poses a potential risk of horizontal transfer to other pathogens where it could be fully functional. The Galleria assay can be a useful approach to uncover the distribution and identity of pathogenic bacteria in the environment, as well as uncover resistance genes with an environmental origin.

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Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species

Cited by 25 publications

References 54 publications

Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex

Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex

Healthcare-associated infections caused by chlorhexidine-tolerant Serratia marcescens carrying a promiscuous IncHI2 multi-drug resistance plasmid in a veterinary hospital

Determining the prevalence, identity and possible origin of bacterial pathogens in soil

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