Allelic diversity uncovers protein domains contributing to the emergence of antimicrobial resistance.

Antimicrobial resistance (AMR) remains a major threat to global health. To date, tractable approaches that decipher how AMR emerges within a bacterial population remain limited. Here, we developed a framework that exploits genetic diversity from environmental bacterial populations to decode emergent phenotypes such as AMR. OmpU is a porin that can make up to 60% of the outer membrane of Vibrio cholerae, the cholera pathogen. This porin is directly associated with the emergence of toxigenic clades and confers resistance to numerous host antimicrobials. In this study, we examined naturally occurring allelic variants of OmpU in environmental V. cholerae and established associations that connected genotypic variation with phenotypic outcome. We covered the landscape of gene variability and found that the porin forms two major phylogenetic clusters with striking genetic diversity. We generated 14 isogenic mutant strains, each encoding a unique ompU allele, and found that divergent genotypes lead to convergent antimicrobial resistance profiles. We identified and characterized functional domains in OmpU unique to variants conferring AMR-associated phenotypes. Specifically, we identified four conserved domains that are linked with resistance to bile and host-derived antimicrobial peptides. Mutant strains for these domains exhibit differential susceptibility patterns to these and other antimicrobials. Interestingly, a mutant strain in which we exchanged the four domains of the clinical allele for those of a sensitive strain exhibits a resistance profile closer to a porin deletion mutant. Finally, using phenotypic microarrays, we uncovered novel functions of OmpU and their connection with allelic variability. Our findings highlight the suitability of our approach towards dissecting the specific protein domains associated with the emergence of AMR and can be naturally extended to other bacterial pathogens and biological processes.

Vibrio floridensis sp. nov., a novel species closely related to the human pathogen Vibrio vulnificus isolated from a cyanobacterial bloom.

A Gram-stain-negative, rod-shaped bacterial strain, designated Vibrio floridensis IRLE0018 (=NRRL B-65642=NCTC 14661), was isolated from a cyanobacterial bloom along the Indian River Lagoon (IRL), a large and highly biodiverse estuary in eastern Florida (USA). The results of phylogenetic, biochemical, and phenotypic analyses indicate that this isolate is distinct from species of the genus Vibrio with validly published names and is the closest relative to the emergent human pathogen, Vibrio vulnificus. Here, we present the complete genome sequence of V. floridensis strain IRLE0018 (4 535 135 bp). On the basis of the established average nucleotide identity (ANI) values for the determination of different species (ANI <95 %), strain IRLE0018, with an ANI of approximately 92 % compared with its closest relative, V. vulnificus, represents a novel species within the genus Vibrio. To our knowledge, this represents the first time this species has been described. The results of genomic analyses of V. floridensis IRLE0018 indicate the presence of antibiotic resistance genes and several known virulence factors, however, its pathogenicity profile (e.g. survival in serum, phagocytosis avoidance) reveals limited virulence potential of this species in contrast to V. vulnificus.

Molecular mechanisms and drivers of pathogen emergence.

Pathogen emergence (PE) is a complex phenomenon with major public health implications. Over the past decades, numerous underlying mechanisms facilitating the emergence of pathogenic bacteria have been elucidated. In this review, we highlight the diverse molecular and environmental drivers associated with PE, with an emphasis on the interplay of canonical gene transfer mechanisms and the increasingly appreciated role of genetic variations, providing a more coherent picture of this process. Given the interactive and multifactorial nature of PE, we contend that the development of approaches that embrace the integration of these factors is indispensable in order to truly comprehend this complex phenomenon and develop strategies to mitigate this threat.

Ecological diversification reveals routes of pathogen emergence in endemic Vibrio vulnificus populations.

Pathogen emergence is a complex phenomenon that, despite its public health relevance, remains poorly understood. Vibrio vulnificus, an emergent human pathogen, can cause a deadly septicaemia with over 50% mortality rate. To date, the ecological drivers that lead to the emergence of clinical strains and the unique genetic traits that allow these clones to colonize the human host remain mostly unknown. We recently surveyed a large estuary in eastern Florida, where outbreaks of the disease frequently occur, and found endemic populations of the bacterium. We established two sampling sites and observed strong correlations between location and pathogenic potential. One site is significantly enriched with strains that belong to one phylogenomic cluster (C1) in which the majority of clinical strains belong. Interestingly, strains isolated from this site exhibit phenotypic traits associated with clinical outcomes, whereas strains from the second site belong to a cluster that rarely causes disease in humans (C2). Analyses of C1 genomes indicate unique genetic markers in the form of clinical-associated alleles with a potential role in virulence. Finally, metagenomic and physicochemical analyses of the sampling sites indicate that this marked cluster distribution and genetic traits are strongly associated with distinct biotic and abiotic factors (e.g., salinity, nutrients, or biodiversity), revealing how ecosystems generate selective pressures that facilitate the emergence of specific strains with pathogenic potential in a population. This knowledge can be applied to assess the risk of pathogen emergence from environmental sources and integrated toward the development of novel strategies for the prevention of future outbreaks.

JMM Profile: Vibrio cholerae: an opportunist of human crises.

Vibrio cholerae O1 is the aetiological agent of the severe diarrhoeal disease cholera. Annually, there are an estimated 1-4 million cholera cases worldwide and over 140 000 deaths. The primary mode of disease transmission is through the consumption of water or food contaminated with the bacterium. Although cholera patients can be treated effectively using rehydration therapy, the disease remains a major scourge in areas with limited access to clean water and proper sanitation. Its continued prevalence highlights the failure of socioeconomic policies leading to wealth disparities, fragile and dated public infrastructure, and lack of appropriate health surveillance.

Antimicrobial polymer modifications to reduce microbial bioburden on endotracheal tubes and ventilator associated pneumonia.

Hospital associated infections (HAIs), infections acquired by patients during care in a hospital, remain a prevalent issue in the healthcare field. These infections often occur with the use of indwelling medical devices, such as endotracheal tubes (ETTs), that can result in ventilator-associated pneumonia (VAP). When examining the various routes of infection, VAP is associated with the highest incidence, rate of morbidity, and economic burden. Although ETTs are essential for the survival of patients requiring mechanical ventilation, their use comes with complications. The presence of an ETT in the airway impairs physiological host defense mechanisms for clearance of pathogens and provides a platform for oropharynx microorganism transport to the sterile tracheobronchial network. Antibiotics are administered to treat lower respiratory infections; however, they are not always effective and consequently can result in increased antibiotic resistance. Prophylactic approaches by altering the surface of ETTs to prevent the establishment and growth of bacteria have exhibited promising results. In addition, passive surface modifications that prevent bacterial establishment and growth, or active coatings that possess a bactericidal effect have also proven effective. In this review we aim to highlight the importance of preventing biofilm establishment on indwelling medical devices, focusing on ETTs. We will investigate successful antimicrobial modifications to ETTs and the future avenues that will ultimately decrease HAIs and improve patient care. STATEMENT OF SIGNIFICANCE: Infections that occur with indwelling medicals devices remain a constant concern in the medical field and can result in hospital-acquired infections. Specifically, ventilator associated pneumonia (VAP) occurs with the use of an endotracheal tube (ETT). Infections often require use of antibiotics and can result in patient mortality. Our review includes a summary of the recent collective work of antimicrobial ETT modifications and potential avenues for further investigations in an effort to reduce VAP associated with ETTs. Polymer modifications with antibacterial nature have been developed and tested; however, a focus on ETTs is lacking and clinical availability of new antimicrobial ETT devices is limited. Our collective work shows the successful and prospective applications to the surfaces of ETTs that can support researchers and physicians to create safer medical devices.