Table_1_Genetic characterization of multidrug-resistant Escherichia coli harboring colistin-resistant gene isolated from food animals in food supply chain.xlsx

Colistin is widely used for the prophylaxis and treatment of infectious disease in humans and livestock. However, the global food chain may actively promote the dissemination of colistin-resistant bacteria in the world. Mobile colistin-resistant (mcr) genes have spread globally, in both communities and hospitals. This study sought to genomically characterize mcr-mediated colistin resistance in 16 Escherichia coli strains isolated from retail meat samples using whole genome sequencing with short-read and long-read platforms. To assess colistin resistance and the transferability of mcr genes, antimicrobial susceptibility testing and conjugation experiments were conducted. Among the 16 isolates, 11 contained mcr-1, whereas three carried mcr-3 and two contained mcr-1 and mcr-3. All isolates had minimum inhibitory concentration (MIC) for colistin in the range 1–64 μg/mL. Notably, 15 out of the 16 isolates demonstrated successful transfer of mcr genes via conjugation, indicative of their presence on plasmids. In contrast, the KK3 strain did not exhibit such transferability. Replicon types of mcr-1-containing plasmids included IncI2 and IncX4, while IncFIB, IncFII, and IncP1 contained mcr-3. Another single strain carried mcr-1.1 on IncX4 and mcr-3.5 on IncP1. Notably, one isolate contained mcr-1.1 located on a chromosome and carrying mcr-3.1 on the IncFIB plasmid. The chromosomal location of the mcr gene may ensure a steady spread of resistance in the absence of selective pressure. Retail meat products may act as critical reservoirs of plasmid-mediated colistin resistance that has been transmitted to humans.</p

Additional file 1: Table S1. of First human case report of sepsis due to infection with Streptococcus suis serotype 31 in Thailand

Primer sets used for PCR and sequencing of cps locus of the unencapsulated S. suis serotype 31 strain 43640. (DOCX 25 kb

Additional file 2: Table S2. of First human case report of sepsis due to infection with Streptococcus suis serotype 31 in Thailand

Primer sets used for PCR and sequencing of cpsA and cpsB of the encapsulated S. suis serotype 31 isolated from pigs in this study. (DOCX 18 kb

MOESM1 of Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada

Additional file 1. Presence/absence of GZ1 genes in genomes of 34 S. suis serotype 9 strains and intermediately virulent serotype 2 strain 89-1591 identified in CGA. The presence or absence of a gene was coded as binary data with gene presence as 1 and gene absence as 0

MOESM1 of Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada

Additional file 1. Presence/absence of GZ1 genes in genomes of 34 S. suis serotype 9 strains and intermediately virulent serotype 2 strain 89-1591 identified in CGA. The presence or absence of a gene was coded as binary data with gene presence as 1 and gene absence as 0

MOESM2 of Genomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada

Additional file 2. Complete list of non-core virulence-associated genes present in S. suis serotype 9 strains tested. The presence or absence of a gene was coded as binary data with gene presence as “+” and absence as “−”. Complete genome of GZ0565 was used as reference for BFP66_RS01095, BFP66_RS1875, BFP66_RS7730, BFP66_RS8445, BFP66_RS9410 and Ag like protein (BFP66_04530). Complete genome of GZ1 was used as reference for other virulence genes

Clinical Specimen-Direct LAMP: A Useful Tool for the Surveillance of <i>bla</i>_OXA-23-Positive Carbapenem-Resistant <i>Acinetobacter baumannii</i>

<div><p>Healthcare-associated infections are a leading cause of morbidity and mortality worldwide. Treatment is increasingly complicated by the escalating incidence of antimicrobial resistance. Among drug-resistant pathogens, carbapenem-resistant <i>Acinetobacter baumannii</i> (CRAb) is of increasing concern because of the limited applicable therapies and its expanding global distribution in developed countries and newly industrialized countries. Therefore, a rapid detection method that can be used even in resource-poor countries is urgently required to control this global public health threat. Conventional techniques, such as bacterial culture and polymerase chain reaction (PCR), are insufficient to combat this threat because they are time-consuming and laborious. In this study, we developed a loop-mediated isothermal amplification (LAMP) method for detecting <i>bla</i>_OXA-23-positive CRAb, the most prevalent form of CRAb in Asia, especially in Thailand, and confirmed its efficacy as a surveillance tool in a clinical setting. Clinical samples of sputum and rectal swabs were collected from patients in a hospital in Bangkok and used for LAMP assays. After boiling and centrifugation, the supernatants were used directly in the assay. In parallel, a culture method was used for comparison purposes to evaluate the specificity and sensitivity of LAMP. As a first step, a total of 120 sputum samples were collected. The sensitivity of LAMP was 88.6% (39/44), and its specificity was 92.1% (70/76) using the culture method as the “gold standard”. When surveillance samples including sputum and rectal swabs were analyzed with the LAMP assay, its sensitivity was 100.0%. This method enables the direct analysis of clinical specimens and provides results within 40 minutes of sample collection, making it a useful tool for surveillance even in resource-poor countries.</p></div

Genotypes of carbapenem-resistant <i>A</i>. <i>baumannii</i> (CRAb) isolates from hospital patients in Bangkok.

<p>Total^a: Total number of isolates with each resistance gene</p><p>%^b: The proportion of isolates with each resistance gene</p><p>Genotypes of carbapenem-resistant <i>A</i>. <i>baumannii</i> (CRAb) isolates from hospital patients in Bangkok.</p

Real-time turbidity assays under various conditions using a turbidimeter.

<p>(A) To determine the optimal reaction conditions, a LAMP assay was performed on extracted bacterial DNA at temperatures ranging from 62°C to 67°C. At 65°C, the reaction finished within the shortest period of time, and the negative control remained transparent after 60 minutes of incubation. (B) To determine the detection limit, the extracted DNA templates were serially diluted 10 times (from 2 pg to 2×10⁻⁶ pg) and used in the LAMP assay. The turbidity was evaluated with a turbidimeter every 5 minutes.</p

LAMP primers used for <i>bla</i>_oxa-23 and the ITS sequence.

<p>F3: outer forward primer; B3: backward inner primer; LF/LB: loop primersouter backward primer; FIP: forward inner primer; BIP:</p><p>LAMP primers used for <i>bla</i>_oxa-23 and the ITS sequence.</p