Gene pool transmission of multidrug resistance among <i>Campylobacter</i> from livestock, sewage and human disease

Mourkas, Evangelos; Florez‐Cuadrado, Diego; Pascoe, Ben; Calland, Jessica K.; Bayliss, Sion C.; Mageiros, Leonardos; Méric, Guillaume; Hitchings, Matthew D.; Quesada, Alberto; Porrero, Concepción; Ugarte‐Ruiz, María; Gutiérrez‐Fernández, José; Domı́nguez, Lucas; Sheppard, Samuel K.

doi:10.1111/1462-2920.14760

Cited by 73 publications

(101 citation statements)

References 102 publications

(167 reference statements)

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“…The rapid evolution and diversification of C. jejuni within only a single year has also been facilitated by frequent recombination and HGT, which has been often observed in previous studies of C. jejuni (70)(71)(72). We present different lines of evidence to demonstrate the contribution of these processes in shaping the genomic structure of the New Hampshire population.…”

Section: Reticulated Evolution Due To Frequent Recombination In New Hsupporting

confidence: 49%

Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017

Park

Li²,

Zhang³

et al. 2020

J Clin Microbiol

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Campylobacter jejuni is one of the leading causes of bacterial gastroenteritis worldwide. In the United States, New Hampshire was one of the 18 states that reported cases in the 2016 to 2018 multistate outbreak of multidrug-resistant C. jejuni. Here, we aimed to elucidate the baseline diversity of the wider New Hampshire C. jejuni population during the outbreak. We used genome sequences of 52 clinical isolates sampled in New Hampshire in 2017, including 1 of the 2 isolates from the outbreak. Results revealed a remarkably diverse population composed of at least 28 sequence types, which are mostly represented by 1 or a few strains. A comparison of our isolates with 249 clinical C. jejuni from other states showed frequent phylogenetic intermingling, suggesting a lack of geographical structure and minimal local diversification within the state. Multiple independent acquisitions of resistance genes from 5 classes of antibiotics characterize the population, with 47/52 (90.4%) of the genomes carrying at least 1 horizontally acquired resistance gene. Frequently recombining genes include those associated with heptose biosynthesis, colonization, and stress resistance. We conclude that the diversity of clinical C. jejuni in New Hampshire in 2017 was driven mainly by the coexistence of phylogenetically diverse antibiotic-resistant lineages, widespread geographical mixing, and frequent recombination. This study provides an important baseline census of the standing pangenomic variation and drug resistance to aid the development of a statewide database for epidemiological studies and clinical decision making. Continued genomic surveillance will be necessary to accurately assess how the population of C. jejuni changes over the long term.

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Section: Reticulated Evolution Due To Frequent Recombination In New Hsupporting

confidence: 49%

Genomic Epidemiology and Evolution of Diverse Lineages of Clinical Campylobacter jejuni Cocirculating in New Hampshire, USA, 2017

Park

Li²,

Zhang³

et al. 2020

J Clin Microbiol

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“…For instance, the ability to produce alkaline phosphatase is encoded by a single gene (Torriani-Gorini, Yagil, & Silver, 1994). Furthermore, as suggested by Young (2016), simple traits are more likely to be carried on phages, plasmids, or transposons, further facilitating modification of microbial genomes at or below the species level through horizontal gene transfer or HGT (Mourkas et al, 2019;Polz, Hunt, Preheim, & Weinreich, 2006). On the contrary, complex traits that involve multiple functional genes tend to be conserved at a high rank in the phylogeny (Martiny et al, 2015).…”

Section: Toward a Trait-based Approach Of Microbial Functional Divementioning

confidence: 99%

Microbial functional diversity: From concepts to applications

Escalas

Hale

Voordeckers

et al. 2019

Ecology and Evolution

176

110

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Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

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“…A recent study by Mourkas and colleagues in Environmental Microbiology addresses this topic, providing a basis for understanding the interaction between different AMR gene pools and the potential source/sink contribution of livestock, humans and sewage effluents in the Campylobacter resistome. In their report, the authors highlight the existence of multiple HGT events within Campylobacter strains from the gut microbiome, evidenced by the existence of genetic islands (GIs) that contain clusters of genes for resistance to multiple drug classes and that are shared among isolates from multiple sources (livestock, humans and sewage) (Mourkas, et al , 2019).…”

Section: Figurementioning

confidence: 99%