Short Variable Regions flaA Gene (SVR-flaA) Diversity and Virulence Profile of Multidrug-Resistant Campylobacter from Poultry and Poultry Meat in India.

Human gastrointestinal infections caused by Campylobacter species is the second most important foodborne illness after salmonellosis worldwide. Poultry represent one of the main sources of Campylobacter organisms. In the present study, the short variable region of flagellin gene (SVR-flaA) typing was carried out to determine the variation among the circulating strains of Campylobacter jejuni and Campylobacter coli. The C. jejuni and C. coli isolated from poultry and poultry meat were screened for the presence of virulence determinants like cadF, flaA, cdtB, and wlaN gene. The screening for wlaN gene is crucial in view of the fact that most patients with Guillian Barre's (GB) syndrome with a preceding history of diarrheal illness have been found to harbor wlaN gene-positive C jejuni strains. Out of the 200 samples comprising poultry meat and cloacal swabs, 21.5% of samples were found to harbor Campylobacter spp. of which 2.5% were Campylobacter jejuni, and 19% were confirmed as Campylobacter coli. The cadF, flaA, cdtB virulence genes were detected in all the Campylobacter spp. isolated in the present study. The presence of the wlaN gene in the Campylobacter jejuni isolated in the present study may pose a public health threat with long-term human health implications. The SVR-flaA typing of twelve Campylobacter isolates obtained in the present study revealed that Campylobacter coli flaA sequence OL471375 is a new strain with a novel allele type 1,675 and peptide sequence 5 which stands deposited in pubMLST database for Campylobacter. The other flaA-SVR gene sequences identified in this study were OL471369, OL471370, OL471371, OL471372, OL471373, and OL471374. Among twelve Campylobacter spp., three distinct DdeI-RFLP patterns were observed, each varying in size from 100 to 1,000 base pairs. Antimicrobial profiling of the Campylobacter spp. isolated in the present study revealed that 50% of the strains were multidrug resistant. All the Campylobacter spp. were resistant to ciprofloxacin (CIP), ampicillin (AMP), penicillin (PEN), and nalidixic acid (NAL) whereas 57.1% of strains were resistant to tetracycline (TET) and erythromycin (ERY) 28% to amoxicillin (AMX) and enrofloxacin (ENO), 85% to amikacin (AMK). The high degree of resistance to fluoroquinolones observed in the present study is crucial in view of fluoroquinolones being drugs of choice for the treatment of human Campylobacter infections.

Scavenger receptor B1 facilitates the endocytosis of Escherichia coli via TLR4 signaling in mammary gland infection.

SCARB1 belongs to class B of Scavenger receptors (SRs) that are known to be involved in binding and endocytosis of various pathogens. SRs have emerging role in regulating innate immunity and host-pathogen interactions by acting in co-ordination with Toll-like receptors.Query Little is known about the function of SCARB1 in milk-derived mammary epithelial cells (MECs). This study reports the role of SCARB1 in infection and its potential association in TLR4 signaling on bacterial challenge in Goat mammary epithelial cells (GMECs). The novelty in the establishment of MEC culture lies in the method that aims to enhance the viability of the cells with intact characteristics upto a higher passage number. We represent MEC culture to be used as a potential infection model for deeper understanding of animal physiology especially around the mammary gland. On E.coli challenge the expression of SCARB1 was significant in induced GMECs at 6 h. Endoribonuclease-esiRNA based silencing of SCARB1 affects the expression of TLR4 and its pathways i.e. MyD88 and TRIF pathways on infection. Knockdown also affected the endocytosis of E.coli in GMECs demonstrating that E.coli uses SCARB1 function to gain entry in cells. Furthermore, we predict 3 unique protein structures of uncharacterized SCARB1 (Capra hircus) protein. Overall, we highlight SCARB1 as a main participant in host defence and its function in antibacterial advances to check mammary gland infections. Video Abstract.

Comparative RNA-Seq analysis reveals insights in Salmonella disease resistance of chicken; and database development as resource for gene expression in poultry.

Salmonella, one of the major infectious diseases in poultry, causes considerable economic losses in terms of mortality and morbidity, especially in countries that lack effective vaccination programs. Besides being resistant to diseases, indigenous chicken breeds are also a potential source of animal protein in developing countries. For understanding the disease resistance, an indigenous chicken line Kashmir faverolla, and commercial broiler were selected. RNA-seq was performed after challenging the chicken with Salmonella Typhimurium. Comparative differential expression results showed that following infection, a total of 3153 genes and 1787 genes were differentially expressed in the liver and spleen, respectively. The genes that were differentially expressed included interleukins, cytokines, NOS2, Avß-defensins, toll-like receptors, and other immune-related gene families. Most of the genes and signaling pathways involved in the innate and adaptive immune responses against bacterial infection were significantly enriched in the Kashmir faverolla. Pathway analysis revealed that most of the enriched pathways were MAPK signaling pathway, NOD-like receptor signaling pathway, TLR signaling pathway, PPAR signaling pathway, endocytosis, etc. Surprisingly some immune-related genes like TLRs were upregulated in the susceptible chicken breed. On postmortem examination, the resistant birds showed small lesions in the liver compared to large necrotic lesions in susceptible birds. The pathological manifestations and RNA sequencing results suggest a balancing link between resistance and infection tolerance in Kashmir faverolla. Here we also developed an online Poultry Infection Database (https://skuastk.org/pif/index.html), the first publicly available gene expression resource for disease resistance in chickens. The available database not only shows the data for gene expression in chicken tissues but also provides quick search, visualization and download capacity.

Clostridium perfringens from fresh water fish of Kashmir Himalaya and their aquatic environment: Toxinotyping and phylogenetic analysis.

Clostridium perfringens is a common anaerobic foodborne pathogen known to produce >20 toxins. In nature, this bacterium has 7 different toxinotypes (A-G) based on the presence of its 6 main toxins. The present study examined the occurrence of different toxinotypes of this bacterium in the ichthyofauna and aquatic environments of Kashmir Himalayan lakes, India. A total of 510 samples (210 water; 150 each of common carp and snow trout) were collected from 3 different lacustrine habitats (Dal, Anchar and Nigeen Lakes) of the region. By performing 16S rRNA PCR test, it was observed that all 210 water samples and 80 (26.66%) of 300 fish samples tested for this specific bacterial species were positive. Then by using multiplex-PCR targeting six virulence genes of C. perfringens, it was confirmed that all the 290 isolates from water and fish samples were positive for Toxinotype A, as only cpa toxin gene was amplified. Phylogenetic analysis of the amplified gene and its amino-acid sequences revealed 95%-98% homology with analogous sequences of this bacterial strain reported from China, Egypt and India. The study documents the existence of C. perfringens toxinotype A in the ichthyofauna of Kashmiri Himalayan lakes, entailing that fish can likely act as transmission medium for C. perfringens food poisoning to humans via food.

Expression of lncRNAs in response to bacterial infections of goat mammary epithelial cells reveals insights into mammary gland diseases.

Mastitis or inflammation of the mammary gland is a highly economic and deadly alarming disease for the dairy sector as well as policymakers caused by microbial infection. Transcriptomic and proteomic approaches have been widely employed to identify the underlying molecular mechanisms of bacterial infections in the mammary gland. Numerous differentially expressed mRNAs, miRNAs, and proteins together with their associated signaling pathways have been identified during bacterial infection, paving the way for analysis of their biological functions. Long noncoding RNAs (lncRNAs) are important regulators of multiple biological processes. However, little is known regarding their role in bacterial infection in mammary epithelial cells. Hence, RNA-sequencing was performed by infecting primary mammary epithelial cells (pMECs) with both gram-negative (E. coli) and gram-positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control. Additionally, potential targets of the lncRNAs were predicted in cis- and trans-configuration. KEGG analysis revealed that DE lncRNAs were associated with at least 15 immune-related pathways. Therefore, our study revealed that bacterial challenge triggers the expression of lncRNAs associated with immune response and defense mechanisms in goat mammary epithelial cells.

Genome sequence of Dichelobacter nodosus JKS-07B isolate from J&K, India associated with virulent footrot of sheep.

INTRODUCTION: Virulent footrot of sheep caused by Dichelobacter nodosus is associated with tremendous economic losses due to recurrent treatment costs and increased culling rates. This organism being a fastidious anaerobe is difficult to isolate on ordinary media that does not support its growth. The D. nodosus serogroup B isolate described in the present study has been used in the preparation of the whole-cell killed vaccine against footrot in India. D. nodosus serogroup B is the predominant serogroup involved in virulent footrot (lesion score 4) in India as well as in many sheep-rearing countries of the globe. METHODS: Genomic DNA was extracted using wizard Genomic DNA purification kit. The whole genome of the D. nodosus strain B was sequenced using an Illumina HiSeq 2500 platform and annotated according to functional gene categories. Annotations were performed using in-house developed Perl scripts using Nr/Nt database, uniprot, Pfam, KEGG, Panther DB, and GO database. RESULT: The assembled genome size is 1.311,533 Mb and GC content is 44.38. A total of 1215 protein-coding genes, 44tRNA and 7 rRNA were identified. The genome shows 98.63% sequence homology with the reference genome. However, 21 new genes have been identified in this genome. The information will provide insights into the various genes and regulators necessary for D. nodosus growth and survival. DISCUSSION: The genome information of this serogroup B of D. nodosus isolate involved in 85-90% cases of virulent footrot of sheep in India provides further insights for improvement of the killed vaccine (B serogroup) developed recently in India. For the development of an efficacious vaccine against virulent footrot, it is essential to know the serological diversity as well as the virulent status of the strains of the D. nodosus. This serogroup isolate is a potential vaccine candidate to mitigate ovine footrot in India as the majority of virulent footrot cases belong to serogroup B of D. nodosus.

Methicillin resistance genes and in vitro biofilm formation among Staphylococcus aureus isolates from bovine mastitis in India.

INTRODUCTION: Biofilms, an assemblage of microbial cells irreversibly associated with a surface and enclosed in a matrix of polysaccharide material pose serious health challenges, resulting in high economic losses. The emergence of methicillin-resistant S. aureus (MRSA) infections and ability to form biofilms in dairy animals is of emerging concern for livestock and public health owing to their association with serious infections. The present study was undertaken to examine the presence of methicillin resistance genes among the biofilm forming Staphylococcus aureus strains isolated from cases of acute and subacute bovine mastitis. A total of 150 mastitic milk samples referred to Veterinary Clinical Complex, Shuhama (Aulesteng) SKUAST-K were screened in present study. The methicillin resistant Staphylococcus aureus isolates were also screened for in vitro biofilm forming ability. RESULTS: A total of 80 (53.33%) S. aureus isolates were recovered from cases of bovine mastitis of which 20 (25%) were methicillin (mecA) gene positive. Of the 20 mecA positive isolates, 20% were positive for SCCmec I, 35% for SCCmec IV and 45% for SCCmec V subtypes. In vitro antibiotic sensitivity testing of MRSA revealed complete resistance towards methicillin and other pencillin group of antibiotics. CONCLUSION: A significant correlation was observed between in vitro biofilm formation and presence of methicillin resistance gene in S aureus isolates recovered from acute and subacute mastitis. The Staphylococcus aureus isolates positive for methicillin resistance gene (mecA) were either strong or moderate biofilm formers.

Draft genome sequence of Dichelobacter nodosus JKS-07 serogroup E from India.

OBJECTIVES: Dichelobacter nodosus is an anaerobic bacterium with fastidious growth requirements that is the principal cause of footrot associated with lameness in sheep and goats. In India, D. nodosus serogroups B and E have been recorded as major causes of footrot. Here we report the draft genome sequence of a D. nodosus serogroup E strain (JKS-07) from a case of virulent footrot in India. METHODS: The whole genome of the D. nodosus JKS-07 serogroup E was sequenced using an Illumina HiSeq 2500 platform and was annotated according to functional gene categories. De novo genome assembly and annotation were performed using Perl scripts developed in-house using the Nr/Nt and UniProt databases. RESULTS: The assembled genome is 1389350bp and contains 1301 genes. The genome has 45 tRNAs and 9 rRNAs. The draft genome sequence will provide insight into the various genes and regulators involved in D. nodosus growth and survival. CONCLUSION: Information on the genome of the D. nodosus serogroup E strain is important bearing in mind the fact that both serogroups B and E are associated with virulent footrot, either alone or frequently together. In order to develop an efficacious vaccine against virulent footrot, it is essential to know the serological diversity as well as the virulence status of the D. nodosus strains. Serogroups B and E are potential vaccine candidates to mitigate ovine footrot in India.

Gene expression and antibody response in chicken against Salmonella Typhimurium challenge.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a primary avian pathogen responsible for severe intestinal pathology in younger chickens and economic losses to poultry industry. Furthermore, S. Typhimurium is also able to cause infection in humans, characterized by acute gastrointestinal disease. A study was conducted to investigate antibody response and expression kinetics of interferon gamma (IFNγ), interleukin (IL-12, and IL-18) genes in broiler chicken at 0, 1, 3, 5, 7, 9, 11, 13, and 15 D post infection following experimental infection of S. Typhimurium. Immunological studies showed higher titres of IgG and IgM in the infected group as compared to the age-matched un-infected control group. The Real-Time PCR-based gene expression analysis revealed significant increase of IFNγ, IL-12, and IL-18 mRNA levels in the infected group as compared to their respective controls (P < 0.05). The present study shall help in understanding the immune responses in birds, thus allowing development of more effective vaccines and vaccination strategies.

Isolation, molecular characterization and prevalence of Clostridium perfringens in sheep and goats of Kashmir Himalayas, India.

AIM: The study was conducted to report the occurrence of the Clostridium perfringens in sheep and goats of the Kashmir valley for the 1st time and to characterize them molecularly with respect to toxin genes to determine the prevalence of the various toxinotypes. MATERIALS AND METHODS: A total of 177 samples (152 from sheep and 25 from goats) collected from healthy, diarrheic animals, and morbid material of animals suspected to have died of enterotoxaemia were screened for C. perfringens toxinotypes. The presumptive positive isolates were confirmed using 16S rRNA gene-based polymerase chain reaction (PCR). All the confirmed isolates were screened for six toxin genes, namely; cpa, cpb, etx, cpi, cpb2, and cpe using a multiplex PCR. RESULTS: The PCR amplification of 16S rRNA gene revealed that out of 177 samples collected, 125 (70.62%) were found positive for C. perfringens, of which 110 (72.36%) were from sheep and 15 (60%) were from goats. The highest prevalence of C. perfringens toxinotype D was observed in lambs (56.16%) and kids (46.16%) followed by 3.84% in adult sheep while it was absent in samples obtained from adult goats. The multiplex PCR revealed that 67 (60.90%) isolates from sheep and 8 (53.33%) isolates from goats belonged to toxinotype A, while 43 (39.09%) isolates from sheep and 7 (46.66%) isolates from goats were detected as toxinotype D. None of the isolates was found to be toxinotype B, C, or E. All the C. perfringens toxinotype A isolates from sheep were negative for both cpb2 and cpe genes, however, 27.90% toxinotype D isolates from sheep carried cpb2 gene, and 6.97% possessed cpe gene. In contrast, 12.50% C. perfringens toxinotype A isolates from goats harbored cpb2 and cpe genes while 14.28% isolates belonging to toxinotype D carried cpb2 and cpe genes, respectively. CONCLUSION: The high prevalence of C. perfringens was observed, even in day-old lambs. The toxinotypes A and D are prevalent in both sheep and goats. The severity of disease and mortality may be associated with the presence of minor toxins in both the detected toxinotypes.