Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing.

Tarka Raj Bhatta,Anthony Chamings,Soren Alexandersen

doi:10.3390/v13081608

Abstract

Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.

Highlights

Porcine enteric diseases like diarrhoea or other intestinal problems and poor growth performance are some of the major problems in pig herds causing huge economic losses around the world [1,2,3,4,5,6,7,8]
The method was able to identify and quantify a relatively high abundance of the bacterium Lawsonia intracellularis, which was initially suspected by the veterinarian and subsequently identified by the histopathologist and could be consistent with the clinical disease, poor growth, and lesions observed [25,26,27]
It could detect the presence of several species of Brachyspira and Campylobacter, which may have been involved in the diarrhoea [28,29,30,31] and demonstrated that Salmonella was not present in the samples similar to the microbiological testing

Summary

Introduction

It has been suggested that various etiological agents acting either individually or synergistically including viruses, bacteria, and parasites are responsible for clinical consequences such as diarrhoea and poor growth in pigs [9,10]. Viruses, including picornaviruses such as porcine sapelovirus (PSV), porcine enteroviruses (PEV), and porcine teschoviruses (PTV), have been identified in association with various disorders, including diarrhoea, polioencephalomyelitis, respiratory distress, dullness, skin lesions, pyrexia, and flaccid paralysis [11,12,13,14,15]. Porcine circovirus type 2 (PCV2) has been associated with a number of diseases/clinical syndromes together called porcine circovirus associated diseases (PCVAD) [19], including postweaning multisystemic wasting syndrome (PMWS)

Methods

Results

Conclusion