Prevalence, antimicrobial resistance and genomic comparison of non-typhoidal salmonella isolated from pig farms with different levels of intensification in Yangon Region, Myanmar

In Myanmar, where backyard, semi-intensive, and intensive pig (Sus scrofa domesticus) farming coexist, there is limited understanding of the zoonotic risks and antimicrobial resistance (AMR) associated with these farming practices. This study was conducted to investigate the prevalence, AMR and genomic features of Salmonella in pig farms in the Yangon region and the impact of farm intensification to provide evidence to support risk-based future management approaches. Twenty-three farms with different production scales were sampled for two periods with three sampling-visit each. Antimicrobial susceptibility tests and whole-genome sequencing were performed on the isolates. The prevalence of Salmonella was 44.5% in samples collected from backyard farms, followed by intensive (39.5%) and semi-intensive farms (19.5%). The prevalence of multi-drug resistant isolates from intensive farms (45/84, 53.6%) was higher than those from backyard (32/171, 18.7%) and semi-intensive farms (25/161, 15.5%). Among 28 different serovars identified, S. Weltevreden (40; 14.5%), S. Kentucky (38; 13.8%), S. Stanley (35, 12.7%), S. Typhimurium (22; 8.0%) and S. Brancaster (20; 7.3%) were the most prevalent serovars and accounted for 56.3% of the genome sequenced strains. The diversity of Salmonella serovars was highest in semi-intensive and backyard farms (21 and 19 different serovars, respectively). The high prevalence of globally emerging S. Kentucky ST198 was detected on backyard farms. The invasive-infection linked typhoid-toxin gene (cdtB) was found in the backyard farm isolated S. Typhimurium, relatively enriched in virulence and AMR genes, presented an important target for future surveillance. While intensification, in terms of semi-intensive versus backyard production, maybe a mitigator for zoonotic risk through a lower prevalence of Salmonella, intensive production appears to enhance AMR-associated risks. Therefore, it remains crucial to closely monitor the AMR and virulence potential of this pathogen at all scales of production. The results underscored the complex relationship between intensification of animal production and the prevalence, diversity and AMR of Salmonella from pig farms in Myanmar

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

Streptococcus suis causes disease in pigs worldwide and is increasingly implicated in zoonotic disease in East and South-East Asia. To understand the genetic basis of disease in S. suis, we study the genomes of 375 isolates with detailed clinical phenotypes from pigs and humans from the United Kingdom and Vietnam. Here, we show that isolates associated with disease contain substantially fewer genes than non-clinical isolates, but are more likely to encode virulence factors. Human disease isolates are limited to a single-virulent population, originating in the 1920 s when pig production was intensified, but no consistent genomic differences between pig and human isolates are observed. There is little geographical clustering of different S. suis subpopulations, and the bacterium undergoes high rates of recombination, implying that an increase in virulence anywhere in the world could have a global impact over a short timescale.Peer reviewe

Provinces of Vietnam.

<p>Provinces (coloured) from which sampled pig originated are located in the south of Vietnam and surrounding Ho Chi Minh City.</p

Pulse field gel electrophoresis (PFGE) of <i>Streptococcus suis</i> serotype 2 strains isolated from tonsils of healthy pigs.

<p>Six <i>S. suis</i> serotype 2 strains isolated from patients with meningitis in southern Vietnam whose PFGE patterns represent the dominant PFGE patterns across <i>S. suis</i> serotype 2 strains isolated from humans (labeled A–F), were included for comparison purpose. A dendrogram was generated by Dice analysis (band tolerance, 1.3%) and cluster analysis with unweighted pair group method with arithmetic mean, using Bionumerics software (Applied Maths, Belgium). Bars indicate 95% confidence intervals. Columns: Cls: PFGE cluster; Pro: province of pig's origin or patients' residence; Date: date of tonsil collection or patients' admission; SH: slaughterhouse ID; WS: Whole sale seller ID; ST: sequence type, Res: tetracycline and erythromycin resistance gene detected by PCR and sequencing, ef: <i>epf</i> or <i>epf*</i> gene detected by PCR. CC: Cu Chi- HCMC; LA: Long An; HM: Hoc Mon – HCMC; HCM: Ho Chi Minh City; BD: Binh Duong; BTr: Ben Tre; DN: Dong Nai; BTh: Binh Thuan. O: amplicons of <i>tet</i>(O) gene detected. M: amplicons of <i>tet</i>(M) gene detected. B: amplicons of <i>erm</i>(B) gene detected. L: amplicons of <i>tet</i>(L) gene detected *: amplicons of mosaic tetracyclin resistance encoding gene <i>tet</i>(O/W/32/O) detected in these strains. #: no amplicons of <i>erm</i>(A), <i>erm</i>(B) or <i>mef</i>(A) were detected in these erythormycine resistant strains. 0: no amplicons of <i>epf</i> or <i>epf*</i> gene detected. 1: amplicons of <i>epf</i> gene detected. 2: amplicons of <i>epf</i>* gene detected.</p

Serotype distribution across <i>Streptococcus suis</i> strains isolated from pig tonsils.

<p>@ Serotyping was repeated three times; additional analysis of 7 representative strains by MLST and 16S rDNA sequencing confirmed that these strains are S. suis.</p><p>*Includes serotype 5, 8, 9,10, 11, 12, 13, 15, 19, 20, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33.</p><p>**Strains reacting with antisera against two or three different serotypes.</p><p>#23 strains were auto-agglutinating, 16 strains could not be assigned to any serotype after agglutination with polyvalent antisera, and 6 strains reacted negatively with all poly-valent antisera.</p

Sampling of tonsils and associated culture results.

<p>*Pigs sampled in slaughterhouse I originated from (number of samples): Ben Tre province (25), Binh Duong province (31), Dong Nai province (75); slaughterhouse II: Binh Duong province (55), Binh Thuan province (83), Ho Chi Minh City (Hoc Mon) (12), Long An province (30), Tien Giang province (34); slaughterhouse III: Binh Duong province (50), Ho Chi Minh City (Cu Chi) (84), Long An province (37).</p