Although the structure and dynamics of planktonic viruses in freshwater and seawater environments are relatively well documented, little is known about the occurrence and activity of these viruses in estuaries, especially in the tropics. Viral abundance, life strategies, and morphotype distribution were examined in the Bach Dang Estuary (Vietnam) during the dry season in 2009. The abundance of both viruses and their prokaryotic hosts decreased significantly from upstream to downstream, probably as the result of nutrient dilution and osmotic stress faced by the freshwater communities. The antibiotic mitomycin-C revealed that the fraction of lysogenic cells was substantially higher in the lower seawater part of the estuary (max 27.1%) than in the upper freshwater area where no inducible lysogens were observed. The question of whether there is a massive, continuous induction of marine lysogens caused by the mixing with freshwater is considered. Conversely, the production of lytic viruses declined as salinity increased, indicating a spatial succession of viral life strategies in this tropical estuary. Icosahedral tailless viruses with capsids smaller than 60 nm dominated the viral assemblage throughout the estuary (63.0% to 72.1% of the total viral counts), and their distribution was positively correlated with that of viral lytic production. Interestingly, the gamma-proteobacteria explained a significant portion of the variance in the <60 nm and 60 to 90 nm tailless viruses (92% and 80%, respectively), and in the Myoviridae (73%). Also, 60% of the variance of the tailless larger viruses (>90 nm) was explained by the beta-proteobacteria. Overall, these results support the view that the environment, through selection mechanisms, probably shapes the structure of the prokaryotic community. This might be in turn a source of selection for the virioplankton community via specific affiliation favoring particular morphotypes and life strategies.

The aim of this study was to examine the resistome characteristics of Salmonella spp. Contamination found in raw retail beef, pork, and chicken samples collected in Hanoi, Vietnam. Approximately 28% (25/90) of samples tested carried Salmonella bacteria. A total of 13/25 (52%) of these Salmonella bacteria were resistant to at least one antibiotic and 9/25 (36%) of the isolates were found to be multidrug resistant. RNA‐seq analysis detected the expression of 107 antibiotic resistance genes (e.g., 22 β‐lactam, 46 aminoglycosides, 8 quinolones, 7 chloramphenicol, 6 tetracycline, and 6 sulfonamide‐trimethoprim resistance genes, and 12 other antimicrobial resistance genes). The parC (S80R and novel mutations A628S) and gyrA (S83F and D87G) mutations contributed to ciprofloxacin resistance in Salmonella Indiana. The findings illustrate the significant potential for multiple‐antibiotic resistant Salmonella in raw retail meats from Hanoi markets, and also provide abundant data to better understand the multidrug resistant Salmonella resistome. Practical Applications Studying the antibiotic resistance characteristics of Salmonella will provide important information for the prevention, control of diseases as well as food contamination control and regulations on the use of antibiotics in treatment and animal husbandry in order to limit antibiotic resistance of bacteria. Studying the expression genome of Salmonella, especially antibiotic resistance genes in multi‐antibiotic resistant Salmonella isolates, provides insight into the molecular epidemiology of antibiotic resistance genes. More importantly, it is possible to detect new mutations in antibiotic resistance genes that cause antibiotic resistance in Salmonella. In addition, studying the expression genome could help to identify new gene groups that can cause antibiotic resistance in this bacterium.

Tuberculosis (TB) is the most common mycobacterial infection in developing countries, requiring a rapid, accurate, and well-differentiated detection/diagnosis. For the rapid detection and discrimination of Mycobacterium tuberculosis complex (MTC) from nontuberculous mycobacteria (NTM), a novel, simple, and primer-combined single-step multiplex PCR using three primer pairs (6110F-6110R, 1081F-1081R, and 23SF-23SR; annealing on each of IS6110, IS1081, and 23S rDNA targets), hereafter referred to as a triplex PCR, has been developed and evaluated. The expected product for IS6110 is 416 bp, for IS1081 is 300 bp, and for 23S rDNA is 206 bp by single PCR, which was used to verify the specificity of primers and the identity of MTC using DNA extracted from the M. tuberculosis H37Rv reference strain (ATCC, USA) and other mycobacteria other than tuberculosis (MOTT) templates. The triplex PCR assay showed 100% specificity and 96% sensitivity; the limit of detection for mycobacteria was ~100 fg; and it failed to amplify any target from DNA of MOTT (50 samples tested). Of 307 blinded clinical samples, overall 205 positive M. tuberculosis samples were detected by single PCR, 142 by conventional culture, and 90 by AFB smear methods. Remarkably, the triplex PCR could subsequently detect 55 positive M. tuberculosis from 165 culture-negative and 115 from 217 AFB smear-negative samples. The triplex PCR, targeting three regions in the M. tuberculosis genome, has proved to be an efficient tool for increasing positive detection/ discrimination of this bacterium from clinical samples.

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Background: The over using of antibiotics in hospitals, communities and agriculture has raised drug resistance in Vietnam.Objective: The study was to identify the multi antimicrobial resistance gene expression associated with extensively drug resistance phenotype in Klebsiella pneumonia (K.pneumoniae) isolated from clinical samples in the Military Hospital 103 in Vietnam.Material and Method: Seventeen extensively drug resistant (XDR) strains were identified and measured antibiotic susceptibility by using Vitek 2 Compact System. Genes related to the antimicrobial resistant were screened using in-house multiplex PCR at Vietnam Institute of Genome Research.Results: K.pneumoniae showed resistance to almost fifteen antibiotics with very high rates of over 70%, only sensitive to colistin 100%. There is a correlation between carpabenem resistance and XDR status in the K.pnemoniae group. Most of the K.pneumoniae isolates harbored the widely distributed ESBL gene groups. All the isolates carried more than 3