Origins and environmental mobility of antibiotic resistance genes, virulence factors and bacteria in a tidal creek's watershed

In situ dynamics of Vibrio parahaemolyticus and Vibrio vulnificus in water, sediment and triploid Crassostrea virginica oysters cultivated in floating gear

AIMS

To understand spatial-temporal distribution of V. parahaemolyticus and V. vulnificus in triploid C. virginica in off-bottom aquaculture.

METHODS AND RESULTS

Oysters, sediments, and water were seasonally collected in Georgia, USA. V. parahaemolyticus and V. vulnificus were quantified with tlh/tdh/trh, and vvhA genes, respectively. No tdh/trh genes were detected. Highest concentrations of tlh gene were observed in summer sediments > oysters > water (10⁵ /g, 10⁴ /g, 10³ /ml). VvhA concentrations were similar in sediments and oysters but never exceeded ≥ 3x10¹ /ml in water. Concentrations of tlh and vvhA genes correlated to temperature and turbidity, respectively; which along with their different spatial distribution indicated different environmental drivers. In oysters, ratios of the tlh and vvhA to 16S rRNA gene have increased from 0 to 10^-1 and 10^-2 in summer, while these ratios in water and sediments were lower by 2-3 orders of magnitude.

CONCLUSIONS

Dynamics of tlh and vvhA concentrations and abundances suggested enrichment of V. parahaemolyticus and V. vulnificus by off-bottom triploid oysters in summer resulting in their abundance by far exceeding that in water.

SIGNIFICANCE AND IMPACT OF THE STUDY

This first report on enrichment of Vibrio pathogens in triploid oysters with no direct contact to sediments reveals a threat to human health suggesting their monitoring in triploid off-bottom C. virginica aquaculture.

Bacteriological and histopathological findings in cetaceans that stranded in the Philippines from 2017 to 2018

The relatively high frequency of marine mammal stranding events in the Philippines provide many research opportunities. A select set of stranders (n = 21) from 2017 to 2018 were sampled for bacteriology and histopathology. Pertinent tissues and bacteria were collected from individuals representing eight cetacean species (i.e. Feresa attenuata, Kogia breviceps, Globicephala macrorhynchus, Grampus griseus, Lagenodelphis hosei, Peponocephala electra, Stenella attenuata and Stenella longirostris) and were subjected to histopathological examination and antibiotic resistance screening, respectively. The antibiotic resistance profiles of 24 bacteria (belonging to genera Escherichia, Enterobacter, Klebsiella, Proteus, and Shigella) that were isolated from four cetaceans were determined using 18 antibiotics. All 24 isolates were resistant to at least one antibiotic class, and 79.17% were classified as multiple antibiotic resistant (MAR). The MAR index values of isolates ranged from 0.06 to 0.39 with all the isolates resistant to erythromycin (100%; n = 24) and susceptible to imipenem, doripenem, ciprofloxacin, chloramphenicol, and gentamicin (100%; n = 24). The resistance profiles of these bacteria show the extent of antimicrobial resistance in the marine environment, and may inform medical management decisions during rehabilitation of stranded cetaceans. Due to inadequate gross descriptions and limited data gathered by the responders during the stranding events, the significance of histopathological lesions in association with disease diagnosis in each cetacean stranding or mortality remained inconclusive; however, these histopathological findings may be indicative or contributory to the resulting debility and stress during their strandings. The findings of the study demonstrate the challenges faced by cetacean species in the wild, such as but not limited to, biological pollution through land-sea movement of effluents, fisheries interactions, and anthropogenic activities.

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis

Widespread use of antibiotics has enhanced the evolution of highly resilient pathogens and poses a severe risk to human health via coselection of antibiotic resistance genes (ARGs) and virulence factors (VFs). In this study, we rigorously evaluate the abundance relationship and physical linkage between ARGs and VFs by performing a comprehensive analysis of 9,070 bacterial genomes isolated from multiple species and hosts. The coexistence of ARGs and VFs was observed in bacteria across distinct phyla, pathogenicities, and habitats, especially among human-associated pathogens. The coexistence patterns of gene elements in different habitats and pathogenicity groups were similar, presumably due to frequent gene transfer. A shorter intergenic distance between mobile genetic elements and ARGs/VFs was detected in human/animal-associated bacteria, indicating a higher transfer potential. Increased accumulation of exogenous ARGs/VFs in human pathogens highlights the importance of gene acquisition in the evolution of human commensal bacteria. Overall, the findings provide insights into the genic features of combinations of ARG-VF and expand our understanding of ARG-VF coexistence in bacteria.IMPORTANCE Antibiotic resistance has become a serious global health concern. Despite numerous case studies, a comprehensive analysis of ARG and VF coexistence in bacteria is lacking. In this study, we explore the coexistence profiles of ARGs and VFs in diverse categories of bacteria by using a high-resolution bioinformatics approach. We also provide compelling evidence of unique ARG-VF gene pairs coexisting in specific bacterial genomes and reveal the potential risk associated with the coexistence of ARGs and VFs in organisms in both clinical settings and environments.

Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes

Human beings have used large amounts of antibiotics, not only in medical contexts but also, for example, as growth factors in agriculture and livestock, resulting in the contamination of the environment. Even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are affected as well. Therefore, both pathogenic and nonpathogenic bacteria have gradually become resistant to antibiotics. We tested whether there is still cooccurrence of resistance and virulence determinants. We performed a comparative study of environmental and human gut metagenomes from different individuals and from distinct human populations across the world. We found a great diversity of antibiotic resistance determinants (AR diversity [ARd]) and virulence factors (VF diversity [VFd]) in metagenomes. Importantly there is a correlation between ARd and VFd, even after correcting for protein family richness. In the human gut, there are less ARd and VFd than in more diversified environments, and yet correlations between the ARd and VFd are stronger. They can vary from very high in Malawi, where antibiotic consumption is unattended, to nonexistent in the uncontacted Amerindian population. We conclude that there is cooccurrence of resistance and virulence determinants in human gut microbiomes, suggesting a possible coselective mechanism.IMPORTANCE Every year, thousands of tons of antibiotics are used, not only in human and animal health but also as growth promoters in livestock. Consequently, during the last 75 years, antibiotic-resistant bacterial strains have been selected in human and environmental microbial communities. This implies that, even when pathogenic bacteria are the targets of antibiotics, hundreds of nonpathogenic bacterial species are also affected. Here, we performed a comparative study of environmental and human gut microbial communities issuing from different individuals and from distinct human populations across the world. We found that antibiotic resistance and pathogenicity are correlated and speculate that, by selecting for resistant bacteria, we may be selecting for more virulent strains as a side effect of antimicrobial therapy.

Persistence of bacterial pathogens, antibiotic resistance genes, and enterococci in tidal creek tributaries

Intertidal creeks form the primary hydrologic link between estuaries and land-based activities on barrier islands. Fecal indicators Enterococcus spp. (Entero1), pathogens Shigella spp. (ipaH), Salmonella spp. (invA), E. coli of EHEC/EPEC groups (eaeA), E. coli of EAEC, EIEC, and UPEC groups (set1B), E. coli of STEC group (stx1); and tetracycline resistance genes (tet(B), tet(C), tet(D), tet(E), tet(K), tet(Q), tet(W), and tet(X); TRG) were detected in the headwater of Oakdale Creek (Sapelo Island, GA) receiving runoffs from Hog Hammock village. Excavation of drainage ditches around the village caused a high increase in the incidence of the above determinants. Water samples were collected from the headwater, transferred to diffusion chambers, submersed in the headwater, saltmarsh, and mouth of the creek; and the determinants were monitored for 3 winter months. With some exceptions, their persistence decreased in order headwater > saltmarsh > mouth. Genes associated with Enterococcus spp. were the most persistent at all the sites, following in the headwater with determinants for Salmonella spp. and E. coli of EAEC, EIEC, and UPEC groups. In the mouth, the most persistent gene was eaeA indicating EHEC, EPEC, and STEC. Tet(B) and tet(C) persisted the longest in headwater and saltmarsh. No TRG persisted after 11 days in the mouth. Most determinants revealed correlations with temperature and pH, and inverse correlations with dissolved oxygen. Decay rates of the above determinants varied in the range of -0.02 to -0.81/day, and were up to 40 folds higher in the saltmarsh and mouth than in the headwater. Our data demonstrated that water parameters could to some extent predict a general trend in the fate of virulence and antibiotic resistance determinants in tidal creek tributaries but strongly suggested that their persistence in these tributaries cannot be predicted from that of enterococci, or extrapolated from one biological contaminant to another.

Bacterial isolates from the Arctic region (Pasvik River, Norway): assessment of biofilm production and antibiotic susceptibility profiles

Bacterial biofilm production is recognized as a strategy that helps aquatic bacteria in resisting to the presence of several kinds of pollutants, including antibiotics, in the bulk environment. The Pasvik River, located between Norway, Russia and Finland, is a sub-Arctic site polluted by wastes from metallurgic and mining activities. In order to study whether and to what extent bacteria are able to produce biofilms, and to assess whether this physiological characteristic influences their resistance to antibiotics, an investigation was performed on bacteria isolated from water and sediment collected along the Pasvik River course during two surveys (May and July). Bacterial strains were screened for their biofilm production and profiles of susceptibility to antibiotics. Results showed that biofilm formation was a widespread characteristic of the isolates. Most of them were also resistant to several antibiotics, such as ampicillin (100% of the isolates) as well as cefazolin, cefoxitin, ceftriaxone, mezlocillin, nitrofurantoin and sisomicin (90% of the total strains). This study shows a significant association between biofilm formation and antibiotic resistance at inner stations both in water and in sediments in May only. This suggests that in Pasvik River colder temperature may stimulate bacterial aggregation into biofilm and simultaneously decrease bacterial susceptibility to antibiotics; since the occurrence of antibiotic resistance has frequently been linked to the presence of pollutants, this result could represent a strategy of bacterial survival under altered environmental conditions.

The prevalence of antibiotic-resistant bacteria (ARB) in waters of the Lower Ballona Creek Watershed, Los Angeles County, California

Screening for the prevalence of antibiotic-resistant bacteria (ARB) was done at the Ballona Creek and Wetlands, an urban-impacted wetland system in Los Angeles, California. The goals were (1) to assess the overall prevalence of ARB, and (2) compare differences in ARB abundance and the types of antibiotic resistance (AR) among the following sample types: lagoon water from Del Rey Lagoon, urban runoff from Ballona Creek, and water from the Ballona Wetlands (tidal water flooding in from the adjacent estuary, and ebbing out from the salt marsh). Antibiotic resistance distributions were analyzed using the Kolmogorov-Smirnov test to develop the cumulative frequency of bacteria having resistance of up to eight antibiotics. Distributions from the environmental water samples were compared to unchlorinated secondary effluent from the Hyperion Water Reclamation Plant that was used as comparator samples likely to have an abundance of ARB. As expected, densities of total and ARB were highest in secondary effluent, followed by urban runoff. Samples of water flooding into the wetlands showed similar results to urban runoff; however, a reduction in densities of total and ARB occurred in water ebbing out of the wetlands. During preliminary work to identify ARB species, several bacterial species of relevance to human illness (e.g., Staphylococcus aureus, Enterococcus hirae, Pseudomonas aeruginosa, Aeromonas veronii, Enterobacter cancerogenus, Serratia marcescens, Pseudomonas stutzeri, and Staphylococcus intermedius) were isolated from sampled waters. If wetlands are a sink for ARB, construction and restoration of wetlands can help in the mediation of this human and environmental health concern.