Is the any standard procedure or protocol followed for the identification of cause of new disease outbreak(or new pathogen)? Is it different for different countries?
Pathogen identification procedure is not necessarily standardised due to differences in resources available to each country but there are certainly several characterised and accepted approaches used to identify a disease causing pathogen. The predominant techniques used to identify pathogens relies upon conventional clinical microbiology-based approaches, which has been highlighted in the comments above. However these conventional techniques such as standard culture and susceptibility tests have many drawbacks such as time-consuption and lack of scalability in addition to lack of direct characterisation of virulence factors. Most pathogen (except prions) logically carry a unique DNA or RNA signatures that differentiate it from other organisms, which provides the basis for disease causing pathogen characterisation. According to this page there are two approaches used to detect a pathogen, once sampling has taken place.
1) qPCR based pathogen detection: allowing sensitive and real-time detection of genetic signatures, which is not currently matched by sensors such as immune-assay techniques (lagging in detection time, logistics and costing) and optical techniques (lacking specificity).
2) Microarray based pathogen detection: allowing combination of nucleic acid amplification (offered by PCR based techniques) combined with massive screening capability of microarray technology, resulting in high level of sensitivity, specificity, and throughput.
These techniques are obviously combined with powerful software technologies required to sieve through the data and allow for easing of experimental burden, minimising assay development as well as operational costs. Now clearly these techniques including sensors and conventional microbiology are used concurrently/synergistically to more efficiently identify a disease causing pathogen and strategies a treatment/preventative measure. This review nicely illustrates the molecular basis for pathogen identification and discusses general considerations (in this case for fungus detection) such as DNA extraction methods, sampling preparations and strategies and goes on to highlight some other sequencing independent methods such as FISH and macroarray.
This paper writes about sequencing based strategies and using the BLAST (NCBI) tool and talks about identification of variant strains of known species, identification of non-cultivatable pathogens and more importantly related to this question, identification of new species using (rDNA) phylogenetic trees of bacterial 16S gene and the fungal 18S gene, commonly used for this type of analysis. This is done in order to determine the phylogenetic position of a the suspected new species compared to a closely known related species, which is useful when there is a <98% of the sequence similarity with known species.
I was first thinking of voting to close the question because it was too broad, but in reconsideration I think the answer of showing why it is too broad would constitute a proper answer in this case.
First of all, the term disease is one of the most general terms for a problem in medicine. The only term that could be higher up is "medical condition." It could be an infectious disease, genetic disease, induced disease (think chemicals, tobacco, etc), or [insert organ here, ie heart] disease (which are not necessarily genetic). There are attempts to distinguish between "diseases" and "disorders," but the difference is not always clear. The term "disorder" is growing in usage and scope because it is seen as having fewer negative connotations than disease (think disease of the mind vs. disorder of the mind).
Thus each field has it's own ways of identifying new diseases. As a general trend new diseases are found now by identifying greater specificity within a previously general disease. For example, a person could be said to have an "adrenal cancer," but now we would want to know if they have an adrenocortical carcinoma. In an infectious setting, we could think of all the particular pneumonia being specified out of interstitial lung diseases.
Diseases caused by external agents (pathogens, toxins, etc) can sometimes be more uniquely novel, in that they can change into something unpredicted (new compound or virus made by man for example). Perhaps you meant to ask if there were standard ways for identifying new viruses or microbes?