Genetic investigation within Lactococcus garvieae revealed two genomic lineages

Prevalence, Virulence, and Antibiotics Gene Profiles in Lactococcus garvieae Isolated from Cows with Clinical Mastitis in China

Lactococcus garvieae (L. garvieae) is a pathogenic gram-positive, catalase-negative (GPCN) bacterium that causes bovine mastitis. A total of 49 L. garvieae isolates were identified from 1441 clinical mastitis (CM) samples. The pathogenic effects of L. garvieae were studied with two infection models: bovine mammary epithelial cells cultured in vitro and murine mammary infections in vivo. The overall farm prevalence was 15.5% (13/84 farms in 9/19 provinces) and sample prevalence was 3.40% (49/1441). Post-treatment somatic cell count (SCC) post L. garvieae infection was significantly higher than the other GPCN pathogens isolated, and the bacteriological cure fraction was 41.94% (13/31) after intramammary antibiotic treatment. All L. garvieae isolates were resistant to rifaximin, 12.24% of isolates were resistant to cephalexin, and 10.20% (5/49) were multidrug-resistant (MDR). The most prevalent virulence genes were Hemolysin 1 (hly1)(100%), Hemolysin 2 (hly2) (97.96%), NADH oxidase (NADHO) (100%), Superoxide dismutase (SOD) (100%), Adhesin Pav (Pav) (100%), Adhesin PsaA (PsaA) (100%), Enolase (eno) (100%), Adhesin cluster 1(AC1) (100%), Adhesin cluster 2 (AC2) (100%), and several exopolysaccharides. L. garvieae rapidly adhered to bovine mammary epithelial cells, resulting in an elevated lactate dehydrogenase release. Edema and congestion were observed in challenged murine mammary glands and bacteria were consistently isolated at 12, 24, 48, 72, and 120 h after infection. We concluded that L. garvieae had good adaptive ability in the bovine and murine mammary cells and tissue. Given the resistance profile, penicillin and ampicillin are potential treatments for CM cases caused by L. garvieae.

Isolation and characterization of Lactococcus garvieae from rainbow trout, Onchorhyncus mykiss, from California, USA

Lactococcus garvieae is an emergent bacterial pathogen of salmonid fish in North America that causes acute infections particularly at water temperatures above 15°C. During 2020, L. garvieae was detected in rainbow trout, Onchorhyncus mykiss, cultured in Southern California and the Eastern Sierras. Infected fish exhibited high mortalities and nonspecific clinical signs of lethargy, erratic swimming, dark skin pigmentation, and exophthalmia. Macroscopic changes included external and internal hemorrhages, mainly in the eyes, liver, coelomic fat, intestine, and brain. Histological examination revealed splenitis, branchitis, panophthalmitis, hepatitis, enteritis, and coelomitis, with variable degrees of tissue damage among evaluated fish. Pure colonies of L. garvieae were isolated from infected trout and specific PCR primers for L. garvieae confirmed the preliminary diagnosis. Multilocus sequence analysis showed that the strains recovered from diseased trout represent a novel genetic group. Isolates were able to form biofilms within 24 h that increased their resistance to disinfection by hydrogen peroxide. Laboratory challenge methods for inducing lactococcosis in steelhead trout, O. mykiss, were evaluated by intracoelomic injection with serial dilutions of L. garvieae. The median lethal dose 21 days post challenge was ∼20 colony-forming units/fish. Experimentally infected trout presented similar clinical signs, gross changes, and microscopic lesions as those with natural disease, fulfilling Koch's postulates and demonstrating the high virulence of the recovered strains.

Genomic relatedness of a canine Lactococcus garvieae to human, animal and environmental isolates

Lactococcus (L.) garvieae is a zoonotic fish pathogen that can also cause bacteraemia and endocarditis in humans and has been isolated from healthy or diseased domestic animals. Nevertheless L. garvieae is more an opportunistic, than a primary pathogen since most affected humans have predisposing conditions and comorbidities. L. garvieae is also present in other animal species, most frequently cattle, but also sheep, goats, water buffaloes, and pigs, and much more rarely dogs, cats, horses, camel, turtle, snake and crocodile. The purpose of this study was to genomically (i) confirm the identification by MALDI-TOF MS® of a L. garvieae from the nasal discharge of a dog with chronic respiratory disorders and (ii) compare this canine isolate with human and animal L. garvieae isolates. According to the BLAST analysis after Whole Genome Sequencing, this canine isolate was more than 99% identical to 3 L. garvieae and belonged to a new Multi-Locus Sequence Type (ST45). MLST and whole genomes-based phylogenetic analysis were performed on the canine isolate and the 40 genomes available in Genbank. The canine L. garvieae was most closely related to an Australian camel and an Indian fish L. garvieae and more distantly to human L. garvieae. Twenty-five of the 29 putative virulence-associated genes searched for were detected, but not the 16 capsule-encoding genes. The heterogeneity of the L. garvieae species is reflected by the diversity of the MLSTypes and virulotypes identified and by the phylogenetic analysis.

First Identification and Characterization of Lactococcus garvieae Isolated from Rainbow Trout (Oncorhynchus mykiss) Cultured in Mexico

Lactococcosis is a hyperacute hemorrhagic septicemia disease caused by Lactococcus garvieae, which is an emerging pathogen in global fish farming. Between 2016 and 2018, rainbow trout (Oncorhynchus mykiss) from five farms that presented outbreaks were sampled as part of a Mexican surveillance program for the detection of fish diseases. Fourteen L. garvieae isolates were recovered from sampled fish, as confirmed by biochemical tests, 16S rRNA gene sequencing, and clinical and histological insights. The biochemical and protein profiles of the isolates obtained were homogeneous. Repetitive extragenic palindromic-(REP)-and enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) analyses established weak genetic heterogeneity. Rainbow trout challenged with two of the isolates used at different bacterial concentrations (10-2 and 10-4 CFU/mL) showed melanosis, and hemorrhages were observed in the fins, liver, kidney, and spleen. Isolates were obtained from all of the organs sampled, including from surviving fish, as either pure or mixed cultures. The present study is the first to confirm the presence of L. garvieae as the agent of severe lactococcosis outbreaks in the two primary Mexican states for trout farming.

Genomic analysis of Lactococcus garvieae isolates

Lactococcus garvieae is a well-known fish pathogen, and in recent years, a human pathogen of increasing clinical significance. However, not much is known about the variances in characteristics of strains isolated locally and overseas. This study aims at conducting comparative genomic analysis on local and overseas L. garvieae isolates, to further understand the phylogenetic and virulence variances between the two groups. The genomic DNA of 11 local L. garvieae isolates (fish 6, human 5) were sequenced, annotated and typed using multi-locus sequence typing (MLST). A total of six novel sequence types (STs) were found in the local isolates. Genotypic overlapping of the STs was observed between local fish and human isolates with overseas fish, food and human clinical isolates. Thereby, suggesting a possible transmission between fish or food and humans. Virulence genes (putative internalin and putative mucus adhesin) were found to be specific to genomic clusters (GC), GC2 and GC3. A higher incidence of resistance genes was also observed in local isolates (n=8, 72.72%) when compared to the overseas isolates (n=7, 41.18%). This study represents the first evidence of genetic variances amongst local and overseas isolates, and virulence characteristics specific to the phylogeny of L. garvieae.

Comparative genomic analysis of three lytic Lactococcus garvieae phages, novel phages with genome architecture linking the 936 phage species of Lactococcus lactis

To date, a number of bacteriophages that infect Lactococcus garvieae isolated from marine fish have been identified. However, the evolutionary insight between L. garvieae phages and other viral community have not yet been immersedly investigated. In this study, completed genomic sequence of phage PLgY-30 was obtained, a comparative analysis of three lytic phages, which have been using for phage typing and treatment of L. garvieae infecting marine fish, is conducted. The results revealed that the genomes of lytic phages specific for L. garvieae isolated from diseased marine fish share a high level of homology and almost all proteins are conserved. At genome level, no similarity was detected for either PLgY-30 or PLgY-16, while PLgW-1 shares only very limited homology (1%) with other sequences in Genbank database. In addition, the function of only 35% of ORFs in the PLgY-30 phage genomes could be predicted, demonstrating that it is novel phage. At protein level, lytic phage proteins shared a significant similarity to various proteins of global phage species isolated from dairy fermentation facilities that utilize L. lactis as a primary starter culture, called the 936 phage group. Genome organization and architecture of three lytic phages are also similar to that of the 936 phage group. To our knowledge, this is the first time lytic bacteriophages infecting L. garvieae from marine fish were characterized to genome level.

Sand bedding as a reservoir for Lactococcus garvieae dissemination in dairy farms

Lactococcus garvieae is now recognized as a species with clinical significance for human and veterinary medicine. The aim of this study was to evaluate the presence of this pathogen in sand bedding and milk samples. Two farms in Minnesota with problems of clinical and subclinical mastitis due to streptococci-like organisms were selected. Twenty-four Lactococcus garvieae isolates from sand bedding and 18 isolates from quarter milk were comparatively studied using a genotypic approach. RAPD (random amplification of polymorphic DNA) PCR and REP (repetitive element palindromic) PCR experiments highlighted a similar electrophoretic profile. When genes belonging to the core genome of L. garvieae were tested through a MLRT (multilocus restriction typing), we again observed that all L. garvieae isolates coming from sand bedding and milk shared a common profile, distinguishable from previously studied representative L. garvieae strains. These data indicate that the L. garvieae isolated from sand bedding and milk originated from a few strains adapted to persist in the same habitat. This supports the hypothesis that sand bedding can represent a reservoir of L. garvieae strains and be a potential vehicle for their dissemination in dairy farms.

Characterization of prophages of Lactococcus garvieae

This report describes the morphological characterization and genome analysis of an induced prophage (PLg-TB25) from a dairy strain of Lactococcus garvieae. The phage belongs to the Siphoviridae family and its morphology is typical of other lactococcal phages. A general analysis of its genome did not reveal similarities with other lactococcal phage genomes, confirming its novelty. However, similarities were found between genes of its morphogenesis cluster and genes of Gram-positive bacteria, suggesting that this phage genome resulted from recombination events that took place in a heterogeneous microbial environment. An in silico search for other prophages in 16 L. garvieae genomes available in public databases, uncovered eight seemingly complete prophages in strains isolated from dairy and fish niches. Genome analyses of these prophages revealed three novel L. garvieae phages. The remaining prophages had homology to phages of Lactococcus lactis (P335 group) suggesting a close relationship between these lactococcal species. The similarity in GC content of L. garvieae prophages to the genomes of L. lactis phages further supports the hypothesis that these phages likely originated from the same ancestor.

The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens

Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.

A virulent phage infecting Lactococcus garvieae, with homology to Lactococcus lactis phages

A new virulent phage belonging to the Siphoviridae family and able to infect Lactococcus garvieae strains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only two L. garvieae strains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacterium Lactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness of L. garvieae phage GE1 to L. lactis phages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58 L. lactis strains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

Temperature-dependent expression of virulence genes in fish-pathogenic bacteria

Virulence gene expression in pathogenic bacteria is modulated by environmental parameters. A key factor in this expression is temperature. Its effect on virulence gene expression in bacteria infecting warm-blooded hosts is well documented. Transcription of virulence genes in these bacteria is induced upon a shift from low environmental to a higher host temperature (37°C). Interestingly, host temperatures usually correspond to the optimum for growth of these pathogenic bacteria. On the contrary, in ectothermic hosts such as fish, molluscs, and amphibians, infection processes generally occur at a temperature lower than that for the optimal growth of the bacteria. Therefore, regulation of virulence gene expression in response to temperature shift has to be modulated in a different way to that which is found in bacteria infecting warm-blooded hosts. The current understanding of virulence gene expression and its regulation in response to temperature in fish-pathogenic bacteria is limited, but constant extension of our knowledge base is essential to enable a rational approach to the problem of the bacterial fish diseases affecting the aquaculture industry. This is an interesting issue and progress needs to be made in order to diminish the economic losses caused by these diseases. The intention of this review is, for the first time, to compile the scattered results existing in the field in order to lay the groundwork for future research. This article is an overview of those relevant virulence genes that are expressed at temperatures lower than that for optimal bacterial growth in different fish-pathogenic bacteria as well as the principal mechanisms that could be involved in their regulation.

Next-generation sequencing as an approach to dairy starter selection

Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.

Insertion sequence elements in Lactococcus garvieae

Insertion sequences are the simplest intracellular Mobile Genetic Elements which can occur in very high numbers in prokaryotic genomes, where they play an important evolutionary role by promoting genome plasticity. As such, the studies on the diversity and distribution of insertion sequences in genomes not yet investigated can contribute to improve the knowledge on a bacterial species and to identify new transposable elements. The present work describes the occurrence of insertion sequences in Lactococcus garvieae, an opportunistic emerging zoonotic and human pathogen, also associated with different food matrices. To date, no insertion elements have been described for L. garvieae in the IS element database. The analysis of the twelve published L. garvieae genomes identified 15 distinct insertion sequences that are members of the IS3, IS982, IS6, IS21 and IS256 families, including five new elements. Most of the insertion sequences in L. garvieae show substantial homology to the Lactococcus lactis elements, suggesting the movement of IS between these two species phylogenetically closely related. ISLL6 elements belonging to IS3 family were most abundant, with several copies distributed in 9 of the 12 genomes analyzed. An alignment analysis of two complete genomes carrying multi-copies of this insertion sequence indicates a possible involvement of ISLL6 in chromosomal rearrangement.

Lactococcus garvieae: where is it from? A first approach to explore the evolutionary history of this emerging pathogen

The population structure and diversity of Lactococcus garvieae, an emerging pathogen of increasing clinical significance, was determined at both gene and genome level. Selected lactococcal isolates of various origins were analyzed by a multi locus sequence typing (MLST). This gene-based analysis was compared to genomic characteristics, estimated through the complete genome sequences available in database. The MLST identified two branches containing the majority of the strains and two branches bearing one strain each. One strain was particularly differentiated from the other L. garvieae strains, showing a significant genetic distance. The genomic characteristics, correlated to the MLST-based phylogeny, indicated that this “separated strain” appeared first and could be considered the evolutionary intermediate between Lactococcus lactis and L. garvieae main clusters. A preliminary genome analysis of L. garvieae indicated a pan-genome constituted of about 4100 genes, which included 1341 core genes and 2760 genes belonging to the dispensable genome. A total of 1491 Clusters of Orthologous Genes (COGs) were found to be specific to the 11 L. garvieae genomes, with the genome of the “separated strain” showing the highest presence of unique genes.

Global transcriptome analysis of Lactococcus garvieae strains in response to temperature

Lactococcus garvieae is an important fish and an opportunistic human pathogen. The genomic sequences of several L. garvieae strains have been recently published, opening the possibility of global studies on the biology of this pathogen. In this study, a whole genome DNA microarray of two strains of L. garvieae was designed and validated. This DNA microarray was used to investigate the effects of growth temperature (18°C and 37°C) on the transcriptome of two clinical strains of L. garvieae that were isolated from fish (Lg8831) and from a human case of septicemia (Lg21881). The transcriptome profiles evidenced a strain-specific response to temperature, which was more evident at 18°C. Among the most significant findings, Lg8831 was found to up-regulate at 18°C several genes encoding different cold-shock and cold-induced proteins involved in an efficient adaptive response of this strain to low-temperature conditions. Another relevant result was the description, for the first time, of respiratory metabolism in L. garvieae, whose gene expression regulation was temperature-dependent in Lg21881. This study provides new insights about how environmental factors such as temperature can affect L. garvieae gene expression. These data could improve our understanding of the regulatory networks and adaptive biology of this important pathogen.

The complex microbiota of raw milk

Here, we review what is known about the microorganisms present in raw milk, including milk from cows, sheep, goats and humans. Milk, due to its high nutritional content, can support a rich microbiota. These microorganisms enter milk from a variety of sources and, once in milk, can play a number of roles, such as facilitating dairy fermentations (e.g. Lactococcus, Lactobacillus, Streptococcus, Propionibacterium and fungal populations), causing spoilage (e.g. Pseudomonas, Clostridium, Bacillus and other spore-forming or thermoduric microorganisms), promoting health (e.g. lactobacilli and bifidobacteria) or causing disease (e.g. Listeria, Salmonella, Escherichia coli, Campylobacter and mycotoxin-producing fungi). There is also concern that the presence of antibiotic residues in milk leads to the development of resistance, particularly among pathogenic bacteria. Here, we comprehensively review these topics, while comparing the approaches, both culture-dependent and culture-independent, which can be taken to investigate the microbial composition of milk.

Genome Sequences of Two Lactococcus garvieae Strains Isolated from Meat

Lactococcus garvieae is an important fish pathogen and an emerging opportunistic human pathogen, as well as a component of natural microbiota in dairy and meat products. We present the first report of genome sequences of L. garvieae I113 and Tac2 strains isolated from a meat source.