PL10 Using pathogen population genomics to study the evolution, spread, and antibiotic resistance of STIs

Escherichia coli is a commensal species of the lower intestine, but also a major pathogen causing intestinal and extra-intestinal infections. Most studies on genomic evolution of E. coli used isolates from infections, and/or focused on antibiotic resistance, but neglected the evolution of virulence. Here instead, we whole-genome sequenced a collection of 436 E. coli isolated from fecal samples of healthy adult volunteers in France between 1980 and 2010. These isolates were distributed among 159 sequence types (STs), the five most frequent being ST10 (15.6%), ST73 (5.5%) and ST95 (4.8%), ST69 (3.7%) and ST59 (3.7%), and 230 O:H serotypes. ST and serotype diversity increased over time. Comparison with 912 E. coli bacteremia isolates from similar region and time showed a greater diversity in commensal isolates. The O1, O2, O6 and O25-groups used in bioconjugate O-antigen vaccine were found in only 63% of the four main STs associated with a high risk of bacteremia (ST69, ST73, ST95 and ST131). In commensals, STs associated with a high risk of bacteremia increased in frequency. Both extra-intestinal virulence-associated genes and resistance to antibiotics increased in frequency. Evolution of virulence genes was driven by both clonal expansion of STs with more virulence genes, and increases in frequency within STs, whereas the evolution of resistance was dominated by increases in frequency within STs. This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over a 30-year period and suggests that the efficacy of O-antigen vaccines would be threatened by serotype replacement.

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Vaccination can drive an increase in frequencies of antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1718712115 ◽

2018 ◽

Vol 115 (12) ◽

pp. 3102-3107 ◽

Cited By ~ 17

Author(s):

Uri Obolski ◽

José Lourenço ◽

Craig Thompson ◽

Robin Thompson ◽

Andrea Gori ◽

...

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Population Structure ◽

Streptococcus Pneumoniae ◽

Bacterial Pathogen ◽

Epidemiological Studies ◽

Theoretical Framework ◽

Health Concern ◽

Public Health Concern ◽

Pathogen Population

The bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis, and septicemia. Available vaccines target only a subset of serotypes, so vaccination is often accompanied by a rise in the frequency of nonvaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among nonvaccine serotypes. Building on previous multilocus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation of serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in a rapid increase in the frequency of preexisting resistant variants of nonvaccine serotypes due to the removal of competition from vaccine serotypes.

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Vaccination can drive an increase in frequencies of antibiotic resistance among non-vaccine serotypes of Streptococcus pneumoniae

10.1101/135863 ◽

2017 ◽

Cited By ~ 1

Author(s):

Uri Obolski ◽

José Lourenço ◽

Sunetra Gupta

Keyword(s):

Public Health ◽

Antibiotic Resistance ◽

Streptococcus Pneumoniae ◽

Bacterial Pathogen ◽

Epidemiological Studies ◽

Health Concern ◽

Public Health Concern ◽

Pathogen Population ◽

Vaccine Serotypes ◽

Pneumococcal Carriage

AbstractThe bacterial pathogen Streptococcus pneumoniae is a major public health concern, being responsible for more than 1.5 million deaths annually through pneumonia, meningitis and septicemia. In spite of vaccination efforts, pneumococcal carriage and disease remain high, since available vaccines target only a subset of serotypes and vaccination is often accompanied by a rise in non-vaccine serotypes. Epidemiological studies suggest that such a change in serotype frequencies is often coupled with an increase of antibiotic resistance among non-vaccine serotypes. Building on previous multi-locus models for bacterial pathogen population structure, we have developed a theoretical framework incorporating variation in serotype and antibiotic resistance to examine how their associations may be affected by vaccination. Using this framework, we find that vaccination can result in rapid increase in frequency of pre-existing resistant variants of non-vaccine serotypes due to the removal of competition from vaccine serotypes.

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Origin of OXA-23 Variant OXA-239 from a Recently Emerged Lineage of Acinetobacter baumannii International Clone V

mSphere ◽

10.1128/msphere.00801-19 ◽

2020 ◽

Vol 5 (1) ◽

Cited By ~ 9

Author(s):

Lucia Graña-Miraglia ◽

Benjamin A. Evans ◽

Luis E. López-Jácome ◽

Melissa Hernández-Durán ◽

Claudia Adriana Colín-Castro ◽

...

Keyword(s):

Antibiotic Resistance ◽

Latin America ◽

Resistance Genes ◽

Population Genomics ◽

Antibiotic Resistance Genes ◽

Developed Countries ◽

Content Type ◽

Recent Emergence ◽

Whole Genomes ◽

The World

ABSTRACT Over the last few decades, carbapenemase-producing Acinetobacter baumannii has become a major cause of nosocomial infections all over the world. However, the genome identity of lineages of this species in Latin America has not been studied as much as in developed countries. Here, through a population genomics approach considering the whole genomes of 148 isolates (almost 40 from Mexico and Honduras), we describe the recent emergence of the lineage sequence type 758 (ST758), which belongs to the international clone V and has spread out to Canada, Mexico, Honduras, and Colombia. Notably, this lineage was found to coexist with other A. baumannii lineages in hospitals in Mexico and Honduras. Isolates from this lineage show considerable variation in antibiotic resistance profiles, but most of them are resistant to carbapenems. Moreover, we found a variety of acquired oxacillinase (OXA) families within this lineage and tracked the very recent inception, and subsequent horizontal transmission, of the OXA-239 carbapenemase. This work highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes. IMPORTANCE A. baumannii is a major cause of nosocomial infections all over the world. Although many isolates from developed countries have been studied in terms of their genome sequence, isolates from Latin America have been much less studied. In this study, using a population genomics approach considering the whole genomes of 148 isolates, we describe the recent emergence of the lineage ST758 endemic to Latin America and the inception of the OXA-239 carbapenemase. Our study highlights the urgent need to investigate recently emerged lineages of this species in Latin America and elsewhere, as these might harbor novel antibiotic resistance genes.

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