Abundance of Colistin-Resistance Genes in Retail Meats in Vietnam.

The degree of contamination of retail meat with colistin-resistant bacteria and its potential contribution to dissemination within communities remains to be determined. Thus, we aimed to elucidate the contamination status of colistin-resistance genes, indicative of colistin-resistant bacteria, in retail meats in Vietnam. In total, 46 chicken and 49 pork meats from stores in Vietnam and Japan were examined. Multiplex real-time polymerase chain reaction with TaqMan probes was performed for detecting mcr-1, mcr-3, and Escherichia coli 16S rRNA. Colistin-resistant bacteria in meats were isolated using selective media. The minimum inhibitory concentrations of colistin were determined using the broth microdilution method. The results showed that 70.7% of chicken meats in Vietnam were contaminated with both mcr-1 and mcr-3. Meanwhile, mcr-1 and mcr-3 were detected in 15.9% and 40.9% of pork meat, respectively. Only mcr-3 was detected in 40% of chicken in Japan. In addition, mcr-1-harboring E. coli and mcr-3-harboring Aeromonas were isolated from chicken meats in Vietnam. Some of these isolates showed colistin resistance. These results showed that most retail meats were highly contaminated with colistin-resistance genes. Notably, our results suggest that mcr-3 is more prevalent in the contaminated samples compared with mcr-1.

Comparative genome analysis of colistin-resistant Escherichia coli harboring mcr isolated from rural community residents in Ecuador and Vietnam.

The spread of colistin-resistant bacteria among rural community residents of low- and middle-income countries is a major threat to community health. Although the mechanism of the spread of colistin-resistant bacteria in communities is unknown, geographic and regional characteristics may influence it. To elucidate the spread mechanism of colistin-resistant bacteria, we analyzed the genomes of colistin-resistant Escherichia coli isolated from Vietnam and Ecuador residents, which are geographically and socially different. Stool specimens of 139 and 98 healthy residents from Ecuador and Vietnam rural communities, respectively, were analyzed for colistin-resistant E. coli with mcr. Its prevalence in the residents of all the communities assessed was high and approximately equal in both countries: 71.8% in Ecuador and 69.4% in Vietnam. A phylogenetic tree analysis revealed that the sequence type of colistin-resistant E. coli was diverse and the major sequence types were different between the two countries. The location of mcr in the isolates showed that the proportion of chromosomal mcr was 35.1% and 8.5% in the Vietnam and Ecuador isolates, respectively. Most of these chromosomal mcr genes (75%-76%) had an intact mcr-transposon Tn6330. Contrastingly, the replicon types of the mcr-carrying-plasmids were diverse in both countries, but almost all belonged to IncI2 in Ecuador and IncX1/X4 in Vietnam. Approximately 26%-45% of these mcr-plasmids had other resistance genes, which also varied between countries. These results suggest that although the overall profile of the colistin-resistant E. coli isolates is diverse in these countries, the phylogenesis of the isolates and mcr-carrying plasmids has regional characteristics. Although the contributing factors are not clear, it is obvious that the overall profile of colistin-resistant bacteria dissemination varies between countries. Such different epidemic patterns are important for establishing country-specific countermeasures against colistin-resistant bacteria.

Horizontal transfer of a plasmid possessing mcr-1 marked with a single nucleotide mutation between Escherichia coli isolates from community residents.

OBJECTIVES: The widespread dissemination of phenotypic colistin-resistant (COR) bacteria in the community threatens public health. The horizontal gene transfer of the mobile colistin resistance gene via plasmids is thought to be one of the main mechanisms for dissemination. However, genotypic evidence to prove this in community settings is limited. This study used genome analysis to demonstrate the direct horizontal colistin resistance gene transfer via plasmids in isolates from the community. RESULTS: A total of 19 isolates of COR Escherichia coli from stool specimens of 23 residents from seven households in the Vietnamese community were assessed in this study. The whole-genome sequence data of isolates were acquired using a combination of DNBSEQ short-reads and Nanopore long-read sequencing. Analysis of genomic data was performed using online tools such as Geneious. Analysis of the genomic information of COR E. coli isolates revealed that the isolates from two residents of different households had a similar IncP1 plasmid possessing mcr-1.1, marked with a single nucleotide mutation at the same position. The study provided direct evidence to prove that mcr was horizontally transmitted among bacteria in community residents.

Comparison of Phenotypic and Genotypic Patterns of Antimicrobial-Resistant Bacteroides fragilis Group Isolated from Healthy Individuals in Vietnam and Japan.

PURPOSE: Normal non-pathogenic flora can harm the host by acting as a reservoir of resistance determinants that are potentially transferable to human pathogens. This study aimed to assess the phenotypic and genotypic antimicrobial susceptibility patterns of the Bacteroides fragilis group (BFG) isolated from healthy individuals in Vietnam and Japan in order to elucidate the prevalence of antimicrobial resistance in human flora in the two economically and geographically different countries. MATERIALS AND METHODS: BFG was isolated from fecal samples of 80 healthy individuals in Vietnam (n=51) and Japan (n=29). Isolated strains were identified using MALDI-TOF MS, and the minimum inhibitory concentration (MIC) of 18 antibiotics was determined using the agar dilution method. Additionally, 20 antimicrobial resistance genes were detected using standard PCR. RESULTS: A total of 139 BFG strains belonging to 11 BFG species were isolated from the two countries, with diversity in the prevalence of each species. B. fragilis was not the predominant species. Isolations from Vietnam and Japan showed some similarities in terms of MIC50 values, MIC90 values, and the percentage of resistant strains. However, isolations from Vietnam showed significantly higher resistance to piperacillin, cefmetazole, clindamycin, tetracycline, and minocycline. ErmB, tet36, tetM, nim, catA, and qnrA were not found in either country. CepA was more common in B. fragilis than in non-fragilis Bacteroides. In contrast, cfiA, ermG, mefA, msrSA, tetX, tetX1, bexA, qnrB, and qnrS were found only in non-fragilis Bacteroides. There were differences in the prevalence of ermG, linA, mefA, msrSA, and qnrS between isolates from Vietnam and Japan. CONCLUSION: This study is the first report on the antimicrobial susceptibility patterns in the BFG isolated from healthy individuals in Vietnam and Japan. Compared to isolations from Japan, isolations from Vietnam showed significantly higher resistance to antimicrobial agents. The distribution of various antibiotic resistance genes also differed between the two countries.

High Prevalence of Colistin-Resistant Escherichia coli with Chromosomally Carried mcr-1 in Healthy Residents in Vietnam.

The wide distribution of colistin-resistant bacteria in developing countries has become a common phenomenon. To understand the mechanisms underlying their distribution, we studied the mcr genetic background of colistin-resistant Escherichia coli isolates from the fecal microbiota of healthy human residents from a community in Vietnam with a high prevalence of colistin-resistant E. coli with mcr Fifty-seven colistin-resistant isolates were obtained from 98 residents; one isolate was collected from each individual and analyzed for mcr We found that 36.8% of the isolates carried chromosomal mcr-1 Further, 63.2% and 1.8% of the isolates carried mcr-1 on the plasmid and the plasmid/chromosome, respectively. Whole-genome sequencing of genetically unrelated isolates showed that the majority (6 of 7) of the isolates had the chromosomal mcr-1 in a complete ancestral mcr-1 transposon Tn6330, ISApl1-mcr-1-PAP2-ISApl1, which was inserted at various positions on the chromosomes. In addition, the majority (87.5%) of Tn6330 of mcr-1-carrying plasmids (n = 8) lacked both upstream and downstream ISApl1 transposons. The results obtained in this study indicate that plasmid-to-chromosomal transfer of mcr-1 may have occurred recently in the fecal microbiota of the residents. Additionally, Tn6330 on the chromosome may lose ISApl1 from the transposon during multiplication to gain a more stable mcr-1 state on the chromosome. Stabilization of resistance by the chromosomal incorporation of mcr-1 would be an additional challenge in combating the dissemination of resistant bacteria.IMPORTANCE Elucidation of the mechanism of the wide dissemination of colistin-resistant bacteria in communities of developing countries is an urgent public health issue. In this study, we investigated the genetic background of the colistin resistance gene mcr in E. coli isolates from the fecal microbiota of healthy human residents living in a community in Vietnam with a high prevalence of colistin-resistant E. coli Our study revealed for the first time, a surprisingly high percentage (36.8%) of colistin-resistant E. coli carrying chromosomal mcr-1, the emergence of which may have occurred recently, in the fecal microbiota of the community residents. The mcr-1 transposon on the chromosome may develop into a more stable genotype by the loss of insertion sequences (ISs). Our results are valuable in understanding the mechanism underlying the increasing prevalence of colistin-resistant bacteria within a community.

Whole-genome sequencing and comparative analysis of the genomes of Bacteroides thetaiotaomicron and Escherichia coli isolated from a healthy resident in Vietnam.

OBJECTIVES: The aim of this study was to report the draft genome sequences of two multidrug-resistant bacteria (Bacteroides thetaiotaomicron F9-2 and Escherichia coli 09-02E) isolated from stool samples of a healthy resident in Vietnam. METHODS: Genome sequences were determined using MiSeq and MinION platforms. Genome assembly was performed using Platanus Assembler v.1.2.4 and Canu v.1.7. The DDBJ Fast Annotation and Submission Tool were used for genome annotation. RESULTS: The genome of B. thetaiotaomicron F9-2 comprised 6 283 774 bp with a GC content of 42.7% and 4802 protein coding sequences (CDS), whereas the genome of E. coli 09-02E comprised 5 246 320 bp with a GC content of 50.6% and 4991 protein CDS. Both strains harboured common antimicrobial resistance genes, such as those for sulfonamides (sul2) and aminoglycosides (strA, strB). However, the sul2-strA-strB cassette was located on the chromosome of B. thetaiotaomicron F9-2, whereas it was located on a plasmid in E. coli 09-02E. These genes were flanked by different insertion sequences. CONCLUSION: Considering their diversities in the human gut resistome, these strains would be of considerable interest for detailed comparative genomic analysis. Notably, the same sul2 cassette was found in facultative and obligate anaerobic bacterial isolates (resident in humans). However, the different location of the cassette indicates a possible mechanism of gene transfer among gut microbes.

Prevalence Of mcr-1 Among Cefotaxime-Resistant Commensal Escherichia coli In Residents Of Vietnam.

PURPOSE: The dissemination of colistin-resistant bacteria harboring the colistin-resistance gene mcr-1 in developing countries has recently entered the spotlight as an emerging public health threat, which is attributed to the abuse of colistin use in these countries. However, the prevalence of these bacteria in developing countries has not been extensively investigated. Therefore, in the present study, we examined the prevalence of cefotaxime-resistant commensal Escherichia coli harboring mcr-1 among residents of a representative Vietnamese village and assessed the characteristics of these isolates. MATERIALS AND METHODS: The stool samples, one stool sample per resident, of 612 residents were cultured on MacConkey agar with cefotaxime. Resulting E. coli-like colonies were isolated and examined further for the presence of colistin-resistant extended-spectrum ß-lactamase (ESBL)-producing E. coli with mcr-1. Antibiotic susceptibility tests were performed, and clonal relationship among colistin-resistant isolates was assessed. RESULTS: Thirty-one of the 451 cefotaxime-resistant E. coli isolates were resistant to colistin and the majority possessed mcr-1, blaCTX-M , and/or blaTEM , except for two isolates that produced the AmpC ß-lactamase. All mcr-1 ESBL-producing E. coli isolates were multidrug-resistant (5-11 antibiotics). The isolates contained various plasmid replicon types, including the most prevalent types IncHI2 (54.8%), IncFIB (48.4%), and IncN (41.9%). In addition, 83.9% of the mcr-1 ESBL-E. coli isolates possessed a transposon ISApl1-mcr-1 segment. Furthermore, 77.4% of the mcr-1 ESBL-E. coli isolates belonged to phylogenetic group A. Pulsed-field gel electrophoresis analysis indicated limited clonal expansion of a specific strain. CONCLUSION: These results demonstrate the wide dissemination of colistin-resistant ESBL-E. coli harboring mcr-1 among commensal bacteria of rural residents in Vietnam, suggesting possible mobilization of the mcr-1 gene among ESBL-producing microbiota, which is a great public health concern.