scholarly journals Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Susan M. Joseph ◽  
Thomas Battaglia ◽  
Julia M. Maritz ◽  
Jane M. Carlton ◽  
Martin J. Blaser
Keyword(s):  
New York ◽  
New York City ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
York City ◽  
Bacterial Resistance ◽  
Hot Spot ◽  
Antibiotic Resistance Genes ◽  
Anthropogenic Activity ◽  
Time Points

ABSTRACT Bacterial resistance to antibiotics is a pressing health issue around the world, not only in health care settings but also in the community and environment, particularly in crowded urban populations. The aim of our work was to characterize the microbial populations in sewage and the spread of antibiotic resistance within New York City (NYC). Here, we investigated the structure of the microbiome and the prevalence of antibiotic resistance genes in raw sewage samples collected from the fourteen NYC Department of Environmental Protection wastewater treatment plants, distributed across the five NYC boroughs. Sewage, a direct output of anthropogenic activity and a reservoir of microbes, provides an ecological niche to examine the spread of antibiotic resistance. Taxonomic diversity analysis revealed a largely similar and stable bacterial population structure across all the samples, which was found to be similar over three time points in an annual cycle, as well as in the five NYC boroughs. All samples were positive for the presence of the seven antibiotic resistance genes tested, based on real-time quantitative PCR assays, with higher levels observed for tetracycline resistance genes at all time points. For five of the seven genes, abundances were significantly higher in May than in February and August. This study provides characteristics of the NYC sewage resistome in the context of the overall bacterial populations. IMPORTANCE Urban sewage or wastewater is a diverse source of bacterial growth, as well as a hot spot for the development of environmental antibiotic resistance, which can in turn influence the health of the residents of the city. As part of a larger study to characterize the urban New York City microbial metagenome, we collected raw sewage samples representing three seasonal time points spanning the five boroughs of NYC and went on to characterize the microbiome and the presence of a range of antibiotic resistance genes. Through this study, we have established a baseline microbial population and antibiotic resistance abundance in NYC sewage which can prove to be very useful in studying the load of antibiotic usage, as well as for developing effective measures in antibiotic stewardship.

scholarly journals COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics

2021 ◽  
Vol 22 (13) ◽  
pp. 6891
Author(s):  
João S. Rebelo ◽  
Célia P. F. Domingues ◽  
Francisco Dionisio ◽  
Manuel C. Gomes ◽  
Ana Botelho ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Human Microbiome ◽  
Antibiotic Resistance Genes ◽  
Public Health Problem ◽  
Small World ◽  
Physical Contact ◽  
Hygiene Measures

Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal–Wallis and Dunn’s pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η2 = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics.

scholarly journals The Influencing Factors of Bacterial Resistance Related to Livestock Farm: Sources and Mechanisms

2021 ◽  
Vol 2 ◽  
Author(s):  
Kaixuan Guo ◽  
Yue Zhao ◽  
Luqing Cui ◽  
Zhengzheng Cao ◽  
Fan Zhang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Influencing Factors ◽  
Resistance Genes ◽  
Bacterial Resistance ◽  
Genetic Material ◽  
Resistance Mechanism ◽  
Antibiotic Resistance Genes ◽  
Direct Selection ◽  
Adaptive Mutation ◽  
Specific Response

Bacterial resistance is a complex scientific issue. To manage this issue, we need to deeply understand the influencing factors and mechanisms. Based on the background of livestock husbandry, this paper reviews the factors that affect the acquisition of bacterial resistance. Meanwhile, the resistance mechanism is also discussed. “Survival of the fittest” is the result of genetic plasticity of bacterial pathogens, which brings about specific response, such as producing adaptive mutation, gaining genetic material or changing gene expression. To a large extent, bacterial populations acquire resistance genes directly caused by the selective pressure of antibiotics. However, mobile resistance genes may be co-selected by other existing substances (such as heavy metals and biocides) without direct selection pressure from antibiotics. This is because the same mobile genetic elements as antibiotic resistance genes can be co-located by the resistance determinants of some of these compounds. Furthermore, environmental factors are a source of resistance gene acquisition. Here, we describe some of the key measures that should be taken to mitigate the risk of antibiotic resistance. We call on the relevant governments or organizations around the world to formulate and improve the monitoring policies of antibiotic resistance, strengthen the supervision, strengthen the international cooperation and exchange, and curb the emergence and spread of drug-resistant strains.

scholarly journals Antibiotic Resistance Genes in Different Animal Manure and their Derived Organic Fertilizer

2020 ◽  
Author(s):  
Yan Xu ◽  
Houyu Li ◽  
Rongguang Shi ◽  
Jiapei Lv ◽  
Bihan Li ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Organic Fertilizer ◽  
Poultry Manure ◽  
Antibiotic Resistance Genes ◽  
Animal Manure ◽  
Procrustes Analysis ◽  
Organic Fertilizers

Abstract Background: The prevalence of antibiotic resistance genes (ARGs) in animal manure poses threats to the environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland, which would cause the potential outbreak of bacterial resistance in agricultural environment. This study investigated the composition of ARGs in different animal manure and their derived organic fertilizers. Results: Results showed that the abundance of several ARGs, such as sul 2, Tet B-01, Tet G-01 and Tet M-01 in organic fertilizer samples was 12%~96% lower than in animal manure. However, there was an increasing of Tet K and erm C abundance from animal manure to the organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, antibiotics was observed by Redundancy analysis (RDA). Procrustes analysis revealed the significant correlation between bacterial community structures and the ARGs abundance (r=0.799, p<0.01). Non-metric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additional, pathogenic bacteria (especially Actinomadura ) would proliferate rather than decrease from manure to organic fertilizer. Conclusion: Overall, this research suggests that the composting treatment of manure could effectively reduce these ARGs and pathogens,even cause partial ARGs and pathogens proliferation. It also shows that the microorganism might significantly influence ARGs profiles in composting.

scholarly journals Increasing Antibiotic Resistance in Shigella spp. from Infected New York City Residents, New York, USA

2017 ◽  
Vol 23 (2) ◽  
pp. 332-335 ◽  
Author(s):  
Kenya Murray ◽  
Vasudha Reddy ◽  
John S. Kornblum ◽  
HaeNa Waechter ◽  
Ludwin F. Chicaiza ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Antibiotic Resistance ◽  
York City ◽  
Shigella Spp

scholarly journals Impact of trimethoprim on the river microbiome and antimicrobial resistance

2020 ◽  
Author(s):  
J. Delaney ◽  
S. Raguideau ◽  
J. Holden ◽  
L. Zhang ◽  
H.J. Tipper ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Waste Water Treatment ◽  
Marker Gene ◽  
Antibiotic Resistance Genes ◽  
Anthropogenic Activity ◽  
Class 1 Integron ◽  
Drug Concentrations ◽  
Depth Analysis

Recent evidence suggests that anthropogenic activity can increase the levels of antimicrobial resistance (AMR) in the environment. Rivers and waterways are significant examples of environmental settings that have become repositories of antibiotics and antibiotic resistance genes (ARGs). Our recent study quantified drug concentrations in freshwater samples taken at a range of sites located on the Thames catchment; the highest levels of antibiotics and other drugs were recorded downstream of waste water treatment plants (WWTPs). One specific antibiotic: Trimethoprim (TMP) was shown at elevated concentrations reaching 2000ng/L at particular sites. We have also shown a correlative relationship between the residue of TMP and the prevalence of sulfonamide antibiotic resistance genes such as sul1. Despite this, there is still no evidence of a causative relationship between TMP concentrations and the prevalence of the ARGs at river sites. The aim of the current study was to conduct in-depth analysis using a combination of large metagenomic, geospatial and chemical datasets, in order to conduct a comparison between those sites with the highest TMP and lowest TMP levels across the Thames catchment. We aimed to establish the proximity of these sites to WWTPs, their population equivalence (PE) and land coverage. A secondary aim was to investigate seasonal variation in TMP and ARGs. Exploring these factors will help to decipher the clinical relevance of ARG accumulation at river sites. A significant correlation was shown between TMP levels at river sites and their distance downstream from a WWTP. Three sites located on the Rivers Cut and Ray showed significantly higher TMP concentrations in winter compared to summer. The population equivalence (PE) for sites with the highest TMP levels was significantly higher than those with the lowest levels. The land coverage of sites with the highest TMP levels was significantly more urban/suburban than sites with the lowest TMP concentrations, which were found to be significantly more arable. Five ARGs relevant to TMP and sulfonamides were identified across the Thames catchment. The most prevalent ARG was sul1, which was significantly more prevalent in winter compared to summer. By contrast sul2 was found to be significantly more prevalent in summer compared to winter at a site on the River Coln. The prevalence of the class 1 integron marker gene (inti1) did not differ significantly by season or between sites with the highest/lowest TMP levels.

scholarly journals Using Real-Time PCR to Investigate Some of Antibiotic Resistance Genes from Streptococcus agalactiae Isolates from ewe Mastitis cases in Nineveh province

2020 ◽  
Vol 17 (3(Suppl.)) ◽  
pp. 0931
Author(s):  
Ayman Mohamed Jaber Albanna ◽  
Aseel A. H. Al-Layla
Keyword(s):  
Antibiotic Resistance ◽  
Real Time ◽  
Resistance Genes ◽  
Streptococcus Agalactiae ◽  
Real Time Pcr ◽  
Bacterial Resistance ◽  
Single Gene ◽  
Antibiotic Resistance Genes ◽  
Antibiotics Resistance ◽  
Dilution Method

In this study, from a total of 856 mastitis cases in lactating ewes, only 34 Streptococcus agalactiae isolates showed various types of resistance to three types of antibiotics (Penicillin, Erythromycin and Tetracycline). St. agalactiae isolates were identified according to the standard methods, including a new suggested technique called specific Chromogenic agar. It was found that antibiotic bacterial resistance was clearly identified by using MIC-microplate assay (dilution method). Also, by real-time PCR technique, it was determined that there were three antibiotics genes resistance ( pbp2b, tetO and mefA ). The high percentage of isolate carried of a single gene which was the Tetracycline (20.59%) followed by percentage Penicillin was (17.65%) and the lowest was in Erythromycin (11.77%). However, there were many isolates that carried two genes of antibiotics resistance represented by Penicillin and Erythromycin with collective present of 38.22%, and for the Penicillin and Tetracycline, the percentage was found to be 11.77%. In contrast, no common gene with two antibiotics (Erythromycin and  Tetracycline) was detected. On the other hand, it was found that no bacterial sharing with three kinds of antibiotic resistance genes ( pbp2b, tetO and mefA ). This study has revealed that the St. agalactiae isolates did induce recurrent mastitis in lactating Iraqi's ewes. 

scholarly journals Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

2021 ◽  
Vol 18 (5) ◽  
pp. 2348
Author(s):  
Ana María Sánchez-Baena ◽  
Luz Dary Caicedo-Bejarano ◽  
Mónica Chávez-Vivas
Keyword(s):  
Systematic Review ◽  
Antibiotic Resistance ◽  
Bacterial Community ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Water Systems ◽  
Anthropogenic Activity ◽  
Aquatic Environments ◽  
Resistance To Antibiotics ◽  
Artificial Water

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., “reporting the water bacterial community composition”, “resistance to antibiotics”, and “antibiotic resistance genes (ARG)”, were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

scholarly journals Population Dynamics of Patients with Bacterial Resistance in Hospital Environment

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Leilei Qu ◽  
Qiuhui Pan ◽  
Xubin Gao ◽  
Mingfeng He
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Resistance ◽  
Equilibrium Points ◽  
Antibiotic Resistance Genes ◽  
Hospital Environment ◽  
Positive Equilibrium ◽  
Transmission Mechanisms ◽  
Dynamics Of Population ◽  
New Type

During the past decades, the increase of antibiotic resistance has become a major concern worldwide. The researchers found that superbugs with new type of resistance genes (NDM-1) have two aspects of transmission characteristics; the first is that the antibiotic resistance genes can horizontally transfer among bacteria, and the other is that the superbugs can spread between humans through direct contact. Based on these two transmission mechanisms, we study the dynamics of population in hospital environment where superbugs exist. In this paper, we build three mathematic models to illustrate the dynamics of patients with bacterial resistance in hospital environment. The models are analyzed using stability theory of differential equations. Positive equilibrium points of the system are investigated and their stability analysis is carried out. Moreover, the numerical simulation of the proposed model is also performed which supports the theoretical findings.

scholarly journals The urgency of utilizing COVID-19 biospecimens for research in the heart of the global pandemic

2020 ◽  
Author(s):  
Iman Osman ◽  
Paolo Cotzia ◽  
Una Moran ◽  
Douglas Donnelly ◽  
Carolina Arguelles-Grande ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Hot Spot ◽  
The Novel ◽  
City Region ◽  
New York University ◽  
Global Crisis ◽  
Successful Model ◽  
Novel Virus

Abstract The outbreak of the novel coronavirus disease 2019 (COVID-19) and consequent social distancing practices have disrupted essential clinical research functions worldwide. Ironically, this coincides with an immediate need for research to comprehend the biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the pathology of COVID-19. As the global crisis has already led to over 15,000 deaths out of 175,000 confirmed cases in New York City and Nassau County, NY alone, it is increasingly urgent to collect patient biospecimens linked to active clinical follow up. However, building a COVID-19 biorepository amidst the active pandemic is a complex and delicate task. To help facilitate rapid, robust, and regulated research on this novel virus, we report on the successful model implemented by New York University Langone Health (NYULH) within days of outbreak in the most challenging hot spot of infection globally. Using an amended institutional biobanking protocol, these efforts led to accrual of 11,120 patients presenting for SARS-CoV-2 testing, 4,267 (38.4%) of whom tested positive for COVID-19. The recently reported genomic characterization of SARS-CoV-2 in the New York City Region, which is a crucial development in tracing sources of infection and asymptomatic spread of the novel virus, is the first outcome of this effort. While this growing resource actively supports studies of the New York outbreak in real time, a worldwide effort is necessary to build a collective arsenal of research tools to deal with the global crisis now, and to exploit the virus’s biology for translational innovation that outlasts humanity’s current dilemma.

Sign in / Sign up

Export Citation Format

Share Document