Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand

Genomic analysis and virulence of human Streptococcus suis serotype 14

PURPOSE

Streptococcus suis serotype 14 is the second most prevalent serotype being highly prevalent in Southeast Asia. This study aimed to characterize genetic background, population structure, virulent genes, antimicrobial-resistant genes, and virulence of human S. suis serotype 14.

METHODS

Genomes of 11 S. suis serotype 14 were sequenced by short- and long-read sequencing platforms. The genomes were analyzed for genetic relationship, virulence-associated genes, and antimicrobial-resistant genes. Antimicrobial susceptibility was conducted and the virulence was tested based on cell assay.

RESULTS

All isolates belonged to clonal complex (CC) 1, with nine sequence type (ST) 105 isolates and each isolate of ST1 and ST237. They were susceptible to penicillin, whereas tetracycline and macrolide were resistance due to tetO and ermB. Genomic analysis revealed that the serotype 14-ST105 isolates were closely related to zoonotic serotype 14-ST105 isolates from Vietnam and the serotype 1-ST105 Thai strain. The serotype 14-ST1 isolate was closely related to pig-diseased serotype 1-ST1 isolates from UK and USA, whereas the serotype 14-ST237 isolate was related to serotype 1-ST237 strains recovered from healthy pig from Thailand. Of 150 virulence-associated genes, 13 were absent from the serotype 14 isolates, including atl1, atlAss, hhly3, nisK, nisR, pnuC, salK, salR, sp1, srtG, virB4, virD4, and zmp. The virulence of strain 32481, a representative S. suis serotype 14-ST105 isolate showed reduced adhesion and invasion of two epithelial cell lines (A549 and HeLa) when compared to the serotype 2-ST1 strain P1/7, whereas apoptosis was similar.

CONCLUSION

This study highlighted the pathogenic potential of virulent serotype 14-ST105 strains and the need for increased monitoring of S. suis serotypes other than for serotype 2.

Characterization of integrative and conjugative elements carrying erm(B) and tet(O) resistance determinants in streptococcus uberis isolates from bovine milk in Chiba prefecture, Japan: CompArative GEne cluster analysis toolbox with ICEfinder

OBJECTIVE

We aimed to characterize integrative and conjugative elements (ICEs) in antimicrobial resistant Streptococcs uberis isolates from bovine milk in Chiba, Japan, based on whole-genome sequence (WGS) data.

RESULTS

Of the 101 isolates, we found the 36 isolates harboring erm(B)-tet(O), showing resistance to macrolides-lincosamides-tetracyclines. The 22 isolates were randomly selected and subject to WGS determination. The genomes measured 1.991-2.517 Mbp, with G + C contents of 35.8-36.9%. We used ResFinder-ICEfinder (web-based applications) to search for the antimicrobial resistant genes and ICEs. ResFinder detected combined erm(B)-tet(O)-ant(6)-Ia at the identical contig in each WGS. ICEfinder detected ICEs belonging to the same contigs, which contained erm(B)-tet(O)-ant(6)-Ia complete or partial sequences. Detection of putative ICEs using comparative genomic analysis was performed with identification of other streptococcal ICE resembling S. uberis ICEs. Using comparative genomic analysis (a reference WGS in NZ01 strain), putative ICE base size in UB37 isolate was 77,386-bp that was identical in other 13 isolates. Another similar streptococcal ICE was S. suis ICEnsui78-tet(O)-erm(B) mobile element. For ICE characterization in S. uberis with WGSs, a comparative genomic analysis is required with use of ICEfinder and other annotation tools.

Streptococcus suis-Associated Meningitis in a Southern Region of Vietnam

Streptococcus suis is the most common and severe cause of meningitis in Vietnam, but the recent data about epidemiological characteristics and sequelae are still inadequate. We performed a retrospective study to describe the epidemiology, clinical characteristics, and outcomes of patients with S. suis-associated meningitis. A retrospective study was carried out by searching records from the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam, between January 2016 and January 2020. All data concerning epidemiological, clinical, and subclinical characteristics and treatment results were collected and analyzed. Over the study period, 153 cases were included in this study, with 95 cases occurring in the 2016-2017 period. The median age of all patients was 52 years (range, 29-90 years), and 70.6% of patients were male. Fifty-two patients (34%) were farmers, and the Mekong Delta was the region with the highest number of cases (60.1%). The most frequent manifestation of infection was fever (151/153, 98.7%), followed by hearing loss (64/153, 41.8%), and one patient (0.7%) died. All isolates remained susceptible to ceftriaxone, penicillin, vancomycin, and levofloxacin, whereas 99.2% of isolates were resistant to tetracycline. Occupational exposure to pigs and the consumption of contaminated food have been identified as primary risk factors associated with this zoonosis, and our study found no significant changes in epidemiological factors compared with past data. The Mekong Delta continues to be the most affected region for S. suis meningitis in southern Vietnam, with S. suis serotype 2 remaining the most relevant agent.

Fulminant Streptococcus suis Infection Causing Myocardial Damage and Toxic Shock-Like Syndrome: A Case Report

There have been no prior reports of direct myocardial damage caused by Streptococcus suis (S. suis), and understanding the clinical course of myocardial involvement is crucial for early diagnosis and initiation of treatment for this infection. A male pig farmer presented as an outpatient with a fever and sore throat, but within hours, his cardiac function declined, and his general condition deteriorated. Despite receiving comprehensive treatment, he succumbed to complications associated with toxic shock-like syndrome (TSLS). Blood cultures identified S. suis, and myocardial pathology revealed the presence of this bacterium in necrotic areas. This case marks the first reported instance of myocardial damage accompanied by TSLS due to S. suis, highlighting the significance of this infection.

Genomic epidemiology in Streptococcus suis: Moving beyond traditional typing techniques

Streptococcus suis is a bacterial gram-positive pathogen that causes invasive infections in swine and is also a zoonotic disease agent. Traditional molecular typing techniques such as ribotyping, multilocus sequence typing, pulse-field gel electrophoresis, or randomly amplified polymorphic DNA have been used to investigate S. suis population structure, evolution, and genetic relationships and support epidemiological and virulence investigations. However, these traditional typing techniques do not fully reveal the genetically heterogeneous nature of S. suis strains. The high-resolution provided by whole-genome sequencing (WGS), which is now more affordable and more commonly available in research and clinical settings, has unlocked the exploration of S. suis genetics at full resolution, permitting the determination of population structure, genetic diversity, identification of virulent clades, genetic markers, and other bacterial features of interest. This approach will likely become the new gold standard for S. suis strain typing as WGS instruments become more widely available and traditional typing techniques are gradually replaced.

Translocation across a human enteroid monolayer by zoonotic Streptococcus suis correlates with the presence of Gb3-positive cells

Streptococcus suis is a zoonotic pathogen that can cause meningitis and septicaemia. The consumption of undercooked pig products is an important risk factor for zoonotic infections, suggesting an oral route of infection. In a human enteroid model, we show that the zoonotic CC1 genotype has a 40% higher translocation frequency than the non-zoonotic CC16 genotype. Translocation occurred without increasing the permeability or disrupting the adherens junctions and tight junctions of the epithelial monolayer. The translocation of zoonotic S. suis was correlated with the presence of Gb3-positive cells, a human glycolipid receptor found on Paneth cells and targeted by multiple enteric pathogens. The virulence factors Streptococcal adhesin Protein and suilysin, known to interact with Gb3, were not essential for translocation in our epithelial model. Thus, the ability to translocate across an enteroid monolayer correlates with S. suis core genome composition and the presence of Gb3-positive cells in the intestinal epithelium.

Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France

Streptococcus suis is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes (n=217) was found in the genomes. Apart from the frequently reported erm(B) and tet(O) genes, more recently described AMR genes were identified [vga(F)/sprA, vat(D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.

Molecular Epidemiology of Underreported Emerging Zoonotic Pathogen Streptococcus suis in Europe

Streptococcus suis, a zoonotic bacterial pathogen circulated through swine, can cause severe infections in humans. Because human S. suis infections are not notifiable in most countries, incidence is underestimated. We aimed to increase insight into the molecular epidemiology of human S. suis infections in Europe. To procure data, we surveyed 7 reference laboratories and performed a systematic review of the scientific literature. We identified 236 cases of human S. suis infection from those sources and an additional 87 by scanning gray literature. We performed whole-genome sequencing to type 46 zoonotic S. suis isolates and combined them with 28 publicly available genomes in a core-genome phylogeny. Clonal complex (CC) 1 isolates accounted for 87% of typed human infections; CC20, CC25, CC87, and CC94 also caused infections. Emergence of diverse zoonotic clades and notable severity of illness in humans support classifying S. suis infection as a notifiable condition.

Prevalence of Streptococcus suis serotype 2 isolated from pigs: A systematic review and meta-analysis

Background and Aim

Among Streptococcus suis serotypes, S. suis serotype 2 is the most significant serotype that causes serious diseases in pigs and humans worldwide. The present study aimed to estimate the global prevalence of S. suis serotype 2 isolated from pigs, determine its trend, and explore the factors associated with this serotype.

Materials and Methods

We retrieved relevant published studies from PubMed, Scopus, and the Web of Science. The retrieved citations were screened for possible inclusion. Relevant data were then extracted from the included studies. The random-effects model was used for all meta-analyses. A subgroup meta-analysis was used to assess the heterogeneity of the prevalence for four characteristics (continents, sampling organs, reporting unit, and pig's health status). A cumulative meta-analysis was performed to determine the cumulative prevalence over time. Meta-regression analysis was used to determine the trend of pooled prevalence of S. suis serotype 2 over time.

Results

Of 600 articles retrieved, 36 studies comprising a total sample size of 6939 isolates or samples from 16 countries of four continents were included for meta-analysis. The pooled prevalence of S. suis serotype 2 isolated from pigs was 13.6% (95% confidence interval [CI], 10.7%-17.1%), with high heterogeneity among the included studies (Cochran's Q, 431.6; p < 0.001; I2 = 91.9%; Table-1). No statistical significance was observed among subgroups of the four characteristics examined. However, the pooled prevalence of S. suis serotype 2 was as high as 16.0% (95% CI, 12.5%-20.3%; n = 16) in diseased pigs compared with 9.9% (95% CI, 5.6%-17.0%; n = 15) in healthy pigs. The pooled prevalence of S. suis serotype 2 isolated from pigs did not significantly decrease over time [regression coefficient = -0.020 (95% CI, 0.046-0.006, p = 0.139)]. The pooled prevalence of S. suis serotype 2 isolated from pigs fluctuated slightly between 13.2% and 17.8% from 2007 to 2023, although the pooled prevalence gradually decreased from 30.6% in 1987 to over 20% in 2003.

Conclusion

The global prevalence of S. suis serotype 2 isolated from pigs was estimated to be 13.6% (approximately 10% in healthy pigs and around 16% in diseased pigs). S. suis serotype 2 isolated from pigs did not change significantly over time. These results indicate that S. suis serotype 2 remains a problem for the pig industry and poses a threat to human health.

Screening of Streptococcus suis in swine workers of selected states in Peninsular Malaysia

Background and Aim

Streptococcus suis is a zoonotic pathogen that is highly associated with contact between live pigs and raw pig material. In view of the recent reports of human infections in Malaysia, epidemiological data on the status of S. suis in the human population, especially among people working closely with pigs and/or raw pork, should be provided. The aim of this study was to detect S. suis among individuals working in the swine industry in several major pig production areas in Peninsular Malaysia.

Materials and Methods

Demographic information, exposure determinants, and oral swabs were collected from swine personnel, including farmers, butchers, and veterinarians. Oral swabs were subjected to bacterial isolation and conventional polymerase chain reaction (PCR) assays for S. suis detection.

Results

The study included 40 participants working in the swine industry, with a predominant representation of males (62.5%) and Malaysian Chinese individuals (60.0%) who consumed pork (92.5%). Notably, none of the participants reported consuming raw or partially cooked pork. In spite of their occupational exposure risk, none of the oral swabs showed positive results for S. suis infection.

Conclusion

To the best of our knowledge, this is the first report and detection study of S. suis using oral swabs obtained from swine personnel in Peninsular Malaysia.

Diversity and evolution of an abundant ICEclc family of integrative and conjugative elements in Pseudomonas aeruginosa

IMPORTANCE

Microbial populations swiftly adapt to changing environments through horizontal gene transfer. While the mechanisms of gene transfer are well known, the impact of environmental conditions on the selection of transferred gene functions remains less clear. We investigated ICEs, specifically the ICEclc-type, in Pseudomonas aeruginosa clinical isolates. Our findings revealed co-evolution between ICEs and their hosts, with ICE transfers occurring within strains. Gene functions carried by ICEs are positively selected, including potential virulence factors and heavy metal resistance. Comparison to publicly available P. aeruginosa genomes unveiled widespread antibiotic-resistance determinants within ICEclc clades. Thus, the ubiquitous ICEclc family significantly contributes to P. aeruginosa's adaptation and fitness in diverse environments.

Human Streptococcus suis Infections in Thailand: Epidemiology, Clinical Features, Genotypes, and Susceptibility

Streptococcus suis is a zoonotic pathogen causing substantial economic losses to the pig industry, as well as being a human health burden due to infections worldwide, especially in Southeast Asia. In Thailand, there was high cumulative incidence in humans during 1987-2021, mostly in males. At least five large outbreaks have been documented after the largest outbreak in China in 2005, which was related to the consumption of raw pork or dishes containing pig's blood. The major clinical features are sepsis or meningitis, with hearing loss a major complication of S. suis disease. Thai human S. suis isolates have shown diversity in serotypes and sequence types (STs), with serotype 2 and STs 1 and 104 being major genotypes. β-Lactam antibiotics can be used in empirical treatment for human S. suis infections; however, intermediate resistance to penicillin has been reported. Reducing S. suis incidence in Thailand requires a multidimensional approach, with combined efforts from the government and public health sectors through policy, regulations, education, and active surveillance.