Evolutionary epidemiology of Streptococcus iniae: Linking mutation rate dynamics with adaptation to novel immunological landscapes

Streptococcus iniae in aquaculture: a review of pathogenesis, virulence, and antibiotic resistance

One of the main challenges in aquaculture is pathogenic bacterial control. Streptococcus iniae stands out for its ability to cause high mortality rates in populations of commercially important fish populations and its recent recognition as an emerging zoonotic pathogen. The rise in identifying over 80 strains some displaying antibiotic resistance coupled with the emerging occurrence of infections in marine mammal species and wild fish underscores the urgent need of understanding pathogenesis, virulence and drug resistance mechanisms of this bacterium. This understanding is crucial to ensure effective control strategies. In this context, the present review conducts a bibliometric analysis to examine research trends related to S. iniae, extending into the mechanisms of infection, virulence, drug resistance and control strategies, whose relevance is highlighted on vaccines and probiotics to strengthen the host immune system. Despite the advances in this field, the need for developing more efficient identification methods is evident, since they constitute the basis for accurate diagnosis and treatment.

Intrapartum antibiotic prophylaxis selects for mutators in group B streptococci among persistently colonized patients

Through vaginal colonization, GBS causes severe pregnancy outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced early-onset disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence in the vaginal tract, whole-genome sequencing was performed on 97 isolates from 58 patients before (prenatal) and after (postpartum) IAP/childbirth. Core-gene mutation analysis identified 7,025 mutations between the paired isolates. Three postpartum isolates accounted for 98% of mutations and were classified as "mutators" because of point mutations within DNA repair systems. In vitro assays revealed stronger biofilms in two mutators. These findings suggest that antibiotics select for mutations that promote survival in vivo, which increases the likelihood of transmission to neonates. They also demonstrate how mutators can provide a reservoir of beneficial mutations that enhance fitness and genetic diversity in the GBS population.

Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis

Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.

The mef(A)/msr(D)-carrying streptococcal prophage Φ1207.3 encodes an SOS-like system, induced by UV-C light, responsible for increased survival and increased mutation rate

Bacterial SOS response is an inducible system of DNA repair and mutagenesis. Streptococci lack a canonical SOS response, but an SOS-like response was reported in some species. The mef(A)-msr(D)-carrying prophage Ф1207.3 of Streptococcus pyogenes contains a region, spanning orf6 to orf11, showing homology to characterized streptococcal SOS-like cassettes. Genome-wide homology search showed the presence of the whole Φ1207.3 SOS-like cassette in three S. pyogenes prophages, while parts of it were found in other bacterial species. To investigate whether this cassette confers an SOS-mutagenesis phenotype, we constructed Streptococcus pneumoniae R6 isogenic derivative strains: (i) FR172, streptomycin resistant, (ii) FR173, carrying Φ1207.3, and (iii) FR174, carrying a recombinant Φ1207.3, where the SOS-like cassette was deleted. These strains were used in survival and mutation rate assays using a UV-C LED instrument, for which we designed and 3D-printed a customized equipment, constituted of an instrument support and swappable-autoclavable mini-plates and lids. Upon exposure to UV fluences ranging from 0 to 6,400 J/m2 at four different wavelengths, 255, 265, 275, and 285 nm, we found that the presence of Φ1207.3 SOS-like cassette increases bacterial survival up to 34-fold. Mutation rate was determined by measuring rifampicin resistance acquisition upon exposure to UV fluence of 50 J/m2 at the four wavelengths by fluctuation test. The presence of Φ1207.3 SOS-like cassette resulted in a significant increase in the mutation rate (up to 18-fold) at every wavelength. In conclusion, we demonstrated that Φ1207.3 carries a functional SOS-like cassette responsible for an increased survival and increased mutation rate in S. pneumoniae. IMPORTANCE Bacterial mutation rate is generally low, but stress conditions and DNA damage can induce stress response systems, which allow for improved survival and continuous replication. The SOS response is a DNA repair mechanism activated by some bacteria in response to stressful conditions, which leads to a temporary hypermutable phenotype and is usually absent in streptococcal genomes. Here, using a reproducible and controlled UV irradiation system, we demonstrated that the SOS-like gene cassette of prophage Φ1207.3 is functional, responsible for a temporary hypermutable phenotype, and enhances bacterial survival to UV irradiation. Prophage Φ1207.3 also carries erythromycin resistance genes and can lysogenize different pathogenic bacteria, constituting an example of a mobile genetic element which can confer multiple phenotypes to its host.

Concurrent infections of Streptococcus iniae and Aeromonas veronii in farmed Giant snakehead (Channa micropeltes)

The giant snakehead, Channa micropeltes, is an increasingly important economic freshwater fish in Thailand and other regions of Asia. Presently, giant snakehead are cultured under intensive aquaculture conditions, leading to high stress and conditions favouring disease. In this study, we reported a disease outbreak in farmed giant snakehead with a cumulative mortality of 52.5%, continuing for 2 months. The affected fish exhibited signs of lethargy, anorexia and haemorrhage of the skin and eyes. Further bacterial isolations revealed two different types of colonies on tryptic soy agar: small white, punctate colonies of gram-positive cocci and cream-coloured, round and convex colonies of rod-shaped gram-negative bacteria. Additional biochemical and species-specific PCR analysis based on 16S rRNA confirmed the isolates as Streptococcus iniae and Aeromonas veronii. Multilocus sequence analysis (MLSA) placed the S. iniae isolate into a large clade of strains from clinically infected fish worldwide. Gross necropsy findings showed liver congestion, pericarditis and white nodules in the kidney and liver. Histologically, the affected fish showed focal to multifocal granulomas with inflammatory cell infiltration in kidney and liver, enlarged blood vessels with mild congestion within the meninges of the brain and severe necrotizing and suppurative pericarditis with myocardial infarction. Antibiotic susceptibility tests revealed that S. iniae was sensitive to amoxicillin, erythromycin, enrofloxacin, oxytetracycline, doxycycline and resistant to sulfamethoxazole-trimethoprim, while the A. veronii was susceptible to erythromycin, enrofloxacin, oxytetracycline, doxycycline, sulfamethoxazole-trimethoprim and resistant to amoxicillin. Conclusively, our findings highlighted the natural concurrent bacterial infections in cultured giant snakehead, which support the implementation of appropriate treatment and control strategies.

Biofilm formation of pathogenic bacteria isolated from aquatic animals

Bacterial biofilm formation is one of the dynamic processes, which facilitates bacteria cells to attach to a surface and accumulate as a colony. With the help of biofilm formation, pathogenic bacteria can survive by adapting to their external environment. These bacterial colonies have several resistance properties with a higher survival rate in the environment. Especially, pathogenic bacteria can grow as biofilms and can be protected from antimicrobial compounds and other substances. In aquaculture, biofilm formation by pathogenic bacteria has emerged with an increased infection rate in aquatic animals. Studies show that Vibrio anguillarum, V. parahaemolyticus, V. alginolyticus, V. harveyi, V. campbellii, V. fischeri, Aeromonas hydrophila, A. salmonicida, Yersinia ruckeri, Flavobacterium columnare, F. psychrophilum, Piscirickettsia salmonis, Edwardsiella tarda, E. ictaluri, E. piscicida, Streptococcus parauberis, and S. iniae can survive in the environment by transforming their planktonic form to biofilm form. Therefore, the present review was intended to highlight the principles behind biofilm formation, major biofilm-forming pathogenic bacteria found in aquaculture systems, gene expression of those bacterial biofilms and possible controlling methods. In addition, the possibility of these pathogenic bacteria can be a serious threat to aquaculture systems.

Streptococcosis a Re-Emerging Disease in Aquaculture: Significance and Phytotherapy

Simple Summary

Streptococcosis is an economical important bacterial disease that can seriously cause huge losses in the global aquaculture sector. In recent years studies have focused on to use extracts or essences of medicinal herbs and plants to control or treat the disease outbreaks and, in most cases the results were promising. The essential oils of the herbs or plants are more effective than the extracts and, the extracts examined have moderate efficacy in term of increasing fish survival against fish streptococcosis that could be due to the enhancement of fish immunity by the herb bio-compounds. The lack of dosage optimization, toxicity and bioavailability assays of a specific herb/plant or its bioactive compound in fish organs make it difficult to judge the validation of clinical efficacy of a particular herb/plant against fish streptococcosis, and thus, required further investigations.

Abstract

Streptococcosis, particularly that caused by S. iniae and S. agalactiae, is a major re-emerging bacterial disease seriously affecting the global sustainability of aquaculture development. Despite a wide spread of the disease in aquaculture, few studies have been directed at assessing the in vitro antagonistic activity and in vivo efficacy of medicinal herbs and other plants against streptococcal agents. Most in vitro studies of plant extractives against S. iniae and S. agalactiae have found antibacterial activity, but essential oils, especially those containing eugenol, carvacrol or thymol, are more effective. Although essential oils have shown better anti-streptococcal activity in in vitro assays, in vivo bioassays require more attention. The extracts examined under in vivo conditions show moderate efficacy, increasing the survival rate of infected fish, probably through the enhancement of immunity before challenge bioassays. The available data, however, lack dosage optimization, toxicity and bioavailability assays of a specific plant or its bioactive compound in fish organs; hence, it is difficult to judge the validation of clinical efficacy for the prevention or treatment of fish streptococcosis. Despite the known bioactive compounds of many tested plants, few data are available on their mode of action towards streptococcal agents. This review addresses the efficacy of medicinal plants to fish streptococcosis and discusses the current gaps.

Molecular Investigation of Recurrent Streptococcus iniae Epizootics Affecting Coral Reef Fish on an Oceanic Island Suggests at Least Two Distinct Emergence Events

Streptococcus iniae is an emerging zoonotic pathogen of increasing concern for aquaculture and has caused several epizootics in reef fishes from the Caribbean, the Red Sea and the Indian Ocean. To study the population structure, introduction pathways and evolution of S. iniae over recurring epizootics on Reunion Island, we developed and validated a Multi Locus Sequence Typing (MLST) panel using genomic data obtained from 89 isolates sampled during epizootics occurring over the past 40years in Australia, Asia, the United States, Israel and Reunion Island. We selected eight housekeeping loci, which resulted in the greatest variation across the main S. iniae phylogenetic clades highlighted by the whole genomic dataset. We then applied the developed MLST to investigate the origin of S. iniae responsible for four epizootics on Reunion Island, first in inland aquaculture and then on the reefs from 1996 to 2014. Results suggest at least two independent S. iniae emergence events occurred on the island. Molecular data support that the first epizootic resulted from an introduction, with inland freshwater aquaculture facilities acting as a stepping-stone. Such an event may have been facilitated by the ecological flexibility of S. iniae, able to survive in both fresh and marine waters and the ability of the pathogen to infect multiple host species. By contrast, the second epizootic was associated with a distinct ST of cosmopolitan distribution that may have emerged as a result of environment disturbance. This novel tool will be effective at investigating recurrent epizootics occurring within a given environment or country that is despite the fact that S. iniae appears to have low genetic diversity within its lineage.

Streptococcal Infections in Marine Mammals

Marine mammals are sentinels for the marine ecosystem and threatened by numerous factors including infectious diseases. One of the most frequently isolated bacteria are beta-hemolytic streptococci. However, knowledge on ecology and epidemiology of streptococcal species in marine mammals is very limited. This review summarizes published reports on streptococcal species, which have been detected in marine mammals. Furthermore, we discuss streptococcal transmission between and adaptation to their marine mammalian hosts. We conclude that streptococci colonize and/or infect marine mammals very frequently, but in many cases, streptococci isolated from marine mammals have not been further identified. How these bacteria disseminate and adapt to their specific niches can only be speculated due to the lack of respective research. Considering the relevance of pathogenic streptococci for marine mammals as part of the marine ecosystem, it seems that they have been neglected and should receive scientific interest in the future.

Multilocus sequence analysis of diverse Streptococcus iniae isolates indicates an underlying genetic basis for phenotypic heterogeneity

Streptococcus iniae is a Gram-positive, opportunistically zoonotic bacterium infective to a wide variety of farmed and wild fish species worldwide. Outbreaks in wild fish can have detrimental environmental and cultural impacts, and mortality events in aquaculture can result in significant economic losses. As an emerging or re-emerging pathogen of global significance, understanding the coalescing factors contributing to piscine streptococcosis is crucial for developing strategies to control infections. Intraspecific antigenic and genetic variability of S. iniae has made development of autogenous vaccines a challenge, particularly where the diversity of locally endemic S. iniae strains is unknown. This study genetically and phenotypically characterized 11 S. iniae isolates from diseased wild and farmed fish from North America, Central America, and the Caribbean. A multilocus sequence analysis (MLSA) scheme was developed to phylogenetically compare these isolates to 84 other strains of Streptococcus spp. relevant to aquaculture. MLSA generated phylogenies comparable to established genotyping methods, and isolates formed distinct clades related to phenotype and host species. The endothelial Oreochromis mossambicus bulbus arteriosus cell line and whole blood from rainbow trout Oncorhynchus mykiss, Nile tilapia Oreochromis niloticus, and white sturgeon Acipenser transmontanus were used to investigate the persistence and virulence of the 11 isolates using in vitro assays. In vivo challenges using an O. niloticus model were used to evaluate virulence by the intragastric route of infection. Isolates showed significant differences (p < 0.05) in virulence and persistence, with some correlation to genogroup, establishing a basis for further work uncovering genetic factors leading to increased pathogenicity.