Comparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution

Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55 ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity. Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies’ taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.

Pathological Diagnosis and Genomic Characterization of ICP4 Gene of lnfectious Laryngotracheitis Virus (ILTV) Isolates in Clinically Infected Chicken in Tamil Nadu, India

Background: Infectious laryngotracheitis (ILT) is an economically important viral respiratory disease in poultry. Recently, re-emergence of Infectious laryngotracheitis virus (ILTV) has been reported in several countries including India. The current study aimed to evaluate the poultry flocks of Tamil Nadu with circulating GaHV-1 and to elucidate the origin of the virus involved in the outbreak. Methods: In this study, a molecular based survey on the overall occurrence of natural cases of Infectious laryngo-tracheitis in poultry flocks from Tamil Nadu, India were performed. Pathological findings in respiratory and secondary lymphoid organs like caecal tonsils and harderian gland was carried out. The PCR technique targeting Infected Cell Protein-4 (ICP4) gene along with molecular characterization was performed. Result: The overall prevalence rate in the outbreak was 42.86% with highest incidence in layer flocks (62.85%) than the broiler flocks (22.85%). The highest susceptible age groups were between 20-30 weeks old. Tracheal pathology revealed epithelial sloughing, syncytial cell formation, eosinophilic intranuclear inclusion bodies and heterophilic exudation microscopically. Partial genome sequencing and phylogenetic analysis of ICP4 gene revealed high genetic homology between field isolates and the virulent strains from Turkey, Germany, China and Brazil. In the present study, along with pathological findings, a rapid and sensitive PCR assay was used for detection of ILT virus specific ICP4 gene in commercial poultry farms in the region.

Sow Vaccination Against Virulent Glaesserella Parasuis Shapes the Nasal Microbiota of Their Offspring

Glaesserella parasuis is the etiological agent of Glässer’s disease, a common pathology in the pork industry with higher prevalence in the postweaning period. Vaccination is one of the strategies to control this disease. Here, we investigated the effect that sow vaccination against virulent strains of G. parasuis had in the nasal microbiota of their offspring. Nasal swabs from fifteen days-old piglets from vaccinated (vs-P, N=11) and unvaccinated sows (cs-P, N=11) were obtained and DNA was extracted for 16S amplicon sequencing. Microbiota composition was different, with lower diversity in vs-P, and a strong clustering of the groups in beta diversity analysis. Among the 1,509 sequences associated to either study group, all the sequences classified as G. parasuis (N=10) had lower relative abundance in the vs-P group. A list of 32 inferred metabolic pathways were statistically different between groups. A distinctive structure of the two microbial networks was detected, with modules in the cs-P not conserved in the vs-P network. In conclusion, vaccination of the sows had a large effect in the microbiota composition of their offspring that went beyond the effect on the targeted pathogen. The mechanisms underneath these changes may include alteration of the microbiota network due to the elimination of the targeted pathogen and/or immunological changes.

Virulence Factors and Prevalence of Udder´s Pathogens in Dairy Cows during the Peripartal Period

Data presented in this study described the prevalence of udder pathogens and presence of virulence factors in staphylococci isolated from mastitis in dairy cows. The practical part of study was realized in five different dairy herds of Slovak spotted cattle breed located in Eastern Slovakia with conventional (non-organic) farming. At the beginning of lactation (during first two months after calving) were comprehensively investigated 960 cows from monitored herds. The comprehensive examination included clinical examination, sensory analysis of milk from fore stripping of each udder quarter, followed by assessment of the California mastitis test (CMT) and laboratory analyses of bacteria pathogens. Screening the health status of the mammary gland revealed that 314 cows (32.7%) had positive CMT score (1-3) for one or more quarters. Out of 230 infected milk samples, representing 24.0% of all dairy cows examined, were the most commonly isolated staphylococci (59.1% of positive findings), followed by E. coli (11.3%), streptococci Str. uberis (9.1%), Str. agalactiae (3.4%), and enterococci (6.1%). From 136 isolates of coagulase negative stafylococci (98 isolates) and S. aureus (38 isolates) were detected some virulence factors such as production of hemolysins (lysines ß and δ), gelatinase, biofilm, and hydrolyze of DNA. Isolated S. aureus, S. chromogenes and S. warneri had the most numerous representation of detected virulence factors, as demonstrated by the increased incidence of clinical forms of mastitis compared to less virulent strains.

Knowledge, attitude and practice towards COVID-19 vaccination acceptance in West India

Background: After almost a year of the COVID-19 pandemic, economies around the world are opening up. However, with newer, more virulent strains being reported across the globe, the efficacy of vaccines has also come into question, and regulatory authorities are emphasising once again, the importance of mask use and social distancing. The aim of the study was to understand the knowledge, attitude and practice towards wearing of masks during this pandemic.Methods: This was a non-interventional, questionnaire based, cross sectional study conducted in urban slums in Mumbai, India. A validated questionnaire was administered to those who volunteered to be part of the study, during sero-survey in the slum area. Results: A total of 1342 participants were included in the study. An overwhelming 1232 (91.8%) knew that masks should cover both nose and mouth. Almost 72% claimed to wear their face masks more than 50% of the time when outside their homes, while 27.5% used them only when in crowded places. Interestingly only 3% said they did not wear masks at all. 86% subjects were of the opinion that cloth masks should be washed daily, and 5% said it should be washed once every two days. There was a significant association with the knowledge regarding proper usage and cleaning of mask, and age, gender and occupation.Conclusions: The knowledge and attitude towards wearing and care of masks reveals that there was a significant association between proper usage and cleaning of masks and age, occupation, literacy and income.

Control Strategies to Cope with Late Wilt of Maize

Control of maize late wilt disease (LWD) has been at the forefront of research efforts since the discovery of the disease in the 1960s. The disease has become a major economic restraint in highly affected areas such as Egypt and Israel, and is of constant concern in other counties. LWD causes dehydration and collapsing at a late stage of maize cultivation, starting from the male flowering phase. The disease causal agent, Magnaporthiopsis maydis, is a seed- and soil-borne phytoparasitic fungus, penetrating the roots at sprouting, colonizing the vascular system without external symptoms, and spreading upwards in the xylem, eventually blocking the water supply to the plant’s upperparts. Nowadays, the disease’s control relies mostly on identifying and developing resistant maize cultivars. Still, host resistance can be limited because M. maydis undergoes pathogenic variations, and virulent strains can eventually overcome the host immunity. This alarming status is driving researchers to continue to seek other control methods. The current review will summarize the various strategies tested over the years to minimize the disease damage. These options include agricultural (crop rotation, cover crop, no-till, flooding the land before sowing, and balanced soil fertility), physical (solar heating), allelochemical, biological, and chemical interventions. Some of these methods have shown promising success, while others have contributed to our understanding of the disease development and the environmental and host-related factors that have shaped its outcome. The most updated global knowledge about LWD control will be presented, and knowledge gaps and future aims will be discussed.

Multi-virulence and phenotypic spread of Campylobacter jejuni carried by chicken meat in Brazil

Campylobacter jejuni is the most incriminated pathogen in bacterial gastroenteritis, and therefore, characteristics of its epidemiology must be continuously investigated to support possible mitigating measures. This is particularly important when evaluating representative strains of the world's leading chicken meat exporter, Brazil. We evaluated a panel of 14 virulence genes in 359 strains of C. jejuni isolated from chilled broiler carcasses of Brazil. The genes were classified into five virulence categories (B: biofilm/motility; SS: secretion/cytotoxicity system; CI: invasion/colonization; GB: Guillain-Barré and AE: adaptation to stress). The percentage of strains with stress adaptation genes (86.07%) indicates the potential to adapt to unfavorable environmental conditions and hcp gene in 97.77%, indicates the ability to cause serious infections in humans. Genes related to GBS in 77.44% of strains are an additional concern, which must be monitored. The gene panel showed the presence of 124 virulence profiles. Individual analyzes by carcass, slaughter establishment, and municipalities where they were located showed high I.Var., of 0.82, 0.87 and 0.78, respectively. Georeferencing indicated state A as a hotspot for virulent strains. Higher levels of isolation and multi-virulence were identified in the summer, which in Brazil is hot and humid. Proteomics was able to discriminate the strains, but due to the high heterogeneity between them, it did not allow to explain their dissemination. Together, our results showed that the studied strains are a potential danger to public health and that there is an urgent need for their surveillance and the adoption of control measures, especially in state A.

Genome analysis provides insight into hyper-virulence of Streptococcus suis LSM178, a human strain with a novel sequence type 1005

Streptococcus suis has been well-recognized as a zoonotic pathogen worldwide, and the diversity and unpredictable adaptive potential of sporadic human strains represent a great risk to the public health. In this study, S. suis LSM178, isolated from a patient in contact with pigs and raw pork, was assessed as a hyper-virulent strain and interpreted for the virulence based on its genetic information. The strain was more invasive for Caco-2 cells than two other S. suis strains, SC19 and P1/7. Sequence analysis designated LSM178 with serotype 2 and a novel sequence type 1005. Phylogenetic analysis showed that LSM178 clustered with highly virulent strains including all human strains and epidemic strains. Compared with other strains, these S. suis have the most and the same virulent factors and a type I-89 K pathogenicity island. Further, groups of genes were identified to distinguish these highly virulent strains from other generally virulent strains, emphasizing the key roles of genes modeling transcription, cell barrier, replication, recombination and repair on virulence regulation. Additionally, LSM178 contains a novel prophage conducive potentially to pathogenicity.

An atypical class of non-coding small RNAs is produced in rice leaves upon bacterial infection

Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant–microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20–22 nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences, with about half of them encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and xisRNA loci predominantly coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant–microbe interactions.

Efficiency of disinsection and deratization aimed at reducing epidemiologic risks in gorno-altaiskiy high-mountain natural plague focus

Our research aim was to estimate efficiency of emergency disinsection and deratization that were accomplished to reduce risks of diseases among population in Gorno-Altaiskiy high-mountain natural plague focus. The research was performed in 2016–2021 in Gorno-Altaiskiy high-mountain plague focus which is the northern part of Sailygem cross-border natural focus located both in Russia and Mongolia. Zoological, epizootologic, epidemiological and statistical research procedures as well as GIS-tools were applied to collect and analyze research data. Epidemiologic surveillance over plague in the focus has been accomplished since 1961. Prior to 2011 only rhamnoso-positive strains of the plague microbe with selective virulence were found here, belonging to the Central Asian subspecies Yersinia pestis altaica, circulating mainly in the population of the Ochotona pallassi. Given that, the focus was believed to have low epidemic potential. Since 2012 highly virulent strains of the basic plague microbe Yersinia pestis ssp. pestis started to occur in populations of Marmota baibacina and other carriers. As a result, starting from that period of time, epidemiologic status of the focus changed and it led to 3 cases of bubonic plague among humans in 2014–2016. Disinsection and deratization remained the major components in anti-epidemic activities aimed at non-specific plague prevention. In 2016–2021 fields disinsection covered a total square equal to 162.7 km2; disinsection in settlements, 127.3 thousand m2; deratization in settlements, 461.7 thousand m2. An approach involving disinsection only on land spots that were considered epidemically hazardous was first implemented; such land spots were around livestock breeders’ camps located within boundaries of detected epizooties. Efficiency of fields disinsection amounted to 94.6; disinsection in settlements, 100 %; deratization in settlements, 88.0 %. Population of plague vectors and carriers was controlled bearing in mind environmental aspects in regulating numbers of animals and compliance with environmental protection requirements. Deratization and disinsection, together with other activities aimed at plague prevention, provide epidemiologic welfare in the focus and reduce its epizootic activity.