Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens

pirABvp -Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids

Acute hepatopancreatic necrosis disease (AHPND) is a severe shrimp disease originally shown to be caused by virulent strains of Vibrio parahaemolyticus (VP_AHPND). Rare cases of AHPND caused by Vibrio species other than V. parahaemolyticus were reported. We compared an AHPND-causing V. campbellii (VC_AHPND) and a VP_AHPND isolate from the same AHPND-affected pond. Both strains are positive for the virulence genes pirAB^vp. Immersion challenge test with Litopenaeus vannamei indicated the two strains possessed similar pathogenicity. Complete genome comparison showed that the pirAB^vp-bearing plasmids in the two strains were highly homologous, and they both shared high homologies with plasmid pVA1, the reported pirAB^vp-bearing plasmid. Conjugation and DNA-uptake genes were found on the pVA1-type plasmids and the host chromosomes, respectively, which may facilitate the dissemination of pirAB^vp. Novel variations likely driven by ISVal1 in the genetic contexts of the pirAB^vp genes were found in the two strains. Moreover, the VC_AHPND isolate additionally contains multiple antibiotic resistance genes, which may bring difficulties to control its future outbreak. The dissemination of the pirAB^vp in non-parahaemolyticus Vibrio also rises the concern of missing detection in industrial settings since the isolation method currently used mainly targeting V. parahaemolyticus. This study provides timely information for better understanding of the causes of AHPND and molecular epidemiology of pirAB^vp and also appeals for precautions to encounter the dissemination of the hazardous genes.

Molecular characterization of antibiotic resistance in cultivable multidrug-resistant bacteria from livestock manure

Diverse antibiotic-resistance genes (ARGs) are frequently reported to have high prevalence in veterinary manure samples due to extensive use of antibiotics in farm animals. However, the characteristics of the distribution and transmission of ARGs among bacteria, especially among different species of multiple antibiotic-resistant bacteria (MARB), have not been well explored. By applying high-throughput sequencing methods, our study uncovered a vast MARB reservoir in livestock manure. The genera Escherichia, Myroides, Acinetobacter, Proteus, Ignatzschineria, Alcaligenes, Providencia and Enterococcus were the predominant cultivable MARB, with compositions of 40.6%-85.7%. From chicken manure isolates, 33 MARB were selected for investigation of the molecular characteristics of antibiotic resistance. A total of 61 ARGs and 18 mobile genetic elements (MGEs) were investigated. We found that 47 ARGs were widely distributed among the 33 MARB isolates. Each isolate carried 27-36 genes responsible for resistance to eight classes of antibiotics frequently used in clinic or veterinary settings. ARGs to the six classes of antibiotics other than streptogramins and vancomycin were present in all 33 MARB isolates with a prevalence of 80%-100%. A total of 12 MGEs were widely distributed among the 33 MARB, with intI1, IS26, ISaba1, and ISEcp1 simultaneously present in 100% of isolates. In addition, 9 gene cassettes within integrons and ISCR1 were detected among MARB isolates encoding resistance to different antibiotic classes. This is the first report revealing the general co-presence of multiple ARGs, various MGEs and ARG cassettes in different species of individual MARB isolates in chicken manure. The results highlight a much higher risk of ARGs spreading through livestock manure to humans than we expected.

Antimicrobial Resistance Profiles of Bacteria Isolated from the Nasal Cavity of Camels in Samburu, Nakuru, and Isiolo Counties of Kenya

This study was designed to determine antimicrobial resistance profiles of bacteria isolated from the nasal cavity of healthy camels. A total of 255 nasal samples (swabs) were collected in Isiolo, Samburu, and Nakuru counties, Kenya, from which 404 bacterial isolates belonging to various genera and species were recovered. The bacterial isolates included Bacillus (39.60%), coagulase-negative Staphylococcus (29.95%), Streptococcus species other than Streptococcus agalactiae (25.74%), coagulase-positive Staphylococcus (3.96%), and Streptococcus agalactiae (0.74%). Isolates were most susceptible to Gentamicin (95.8%), followed by Tetracycline (90.5%), Kanamycin and Chloramphenicol (each at 85.3%), Sulphamethoxazole (84.2%), Co-trimoxazole (82.1%), Ampicillin (78.9%), and finally Streptomycin (76.8%). This translated to low resistance levels. Multidrug resistance was also reported in 30.5% of the isolates tested. Even though the antibiotic resistance demonstrated in this study is low, the observation is significant, since the few resistant normal flora could be harboring resistance genes which can be transferred to pathogenic bacteria within the animal, to other animals' bacteria and, most seriously, to human pathogens.

Resistance to Antibiotics, Biocides, Preservatives and Metals in Bacteria Isolated from Seafoods: Co-Selection of Strains Resistant or Tolerant to Different Classes of Compounds

Multi-drug resistant bacteria (particularly those producing extended-spectrum β-lactamases) have become a major health concern. The continued exposure to antibiotics, biocides, chemical preservatives, and metals in different settings such as the food chain or in the environment may result in development of multiple resistance or co-resistance. The aim of the present study was to determine multiple resistances (biocides, antibiotics, chemical preservatives, phenolic compounds, and metals) in bacterial isolates from seafoods. A 75.86% of the 87 isolates studied were resistant to at least one antibiotic or one biocide, and 6.90% were multiply resistant to at least three biocides and at least three antibiotics. Significant (P < 0.05) moderate or strong positive correlations were detected between tolerances to biocides, between antibiotics, and between antibiotics with biocides and other antimicrobials. A sub-set of 30 isolates selected according to antimicrobial resistance profile and food type were identified by 16S rDNA sequencing and tested for copper and zinc tolerance. Then, the genetic determinants for biocide and metal tolerance and antibiotic resistance were investigated. The selected isolates were identified as Pseudomonas (63.33%), Acinetobacter (13.33%), Aeromonas (13.33%), Shewanella, Proteus and Listeria (one isolate each). Antibiotic resistance determinants detected included sul1 (43.33% of tested isolates), sul2 (6.66%), blaTEM (16.66%), blaCTX-M (16.66%), blaPSE (10.00%), blaIMP (3.33%), blaNDM-1 (3.33%), floR (16.66%), aadA1 (20.0%), and aac(6')-Ib (16.66%). The only biocide resistance determinant detected among the selected isolates was qacEΔ1 (10.00%). A 23.30 of the selected isolates were able to grow on media containing 32 mM copper sulfate, and 46.60% on 8 mM zinc chloride. The metal resistance genes pcoA/copA, pcoR, and chrB were detected in 36.66, 6.66, and 13.33% of selected isolates, respectively. Twelve isolates tested positive for both metal and antibiotic resistance genes, including one isolate positive for the carbapenemase gene blaNDM-1 and for pcoA/copA. These results suggest that exposure to metals could co-select for antibiotic resistance and also highlight the potential of bacteria on seafoods to be involved in the transmission of antimicrobial resistance genes.

The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration.

FDA regulations on agricultural antibiotic use have focused on antibiotics that are important for human medicine. Carbadox is an antibiotic not used in humans but frequently used on U.S. pig farms. It is important to study possible side effects of carbadox use because it has been shown to promote bacterial evolution, which could indirectly impact antibiotic resistance in bacteria of clinical importance. Interestingly, the present study shows greater prophage gene expression in feces from carbadox-fed animals than in feces from nonmedicated animals 2 days after the initiation of in-feed carbadox treatment. Importantly, the phage genetic material isolated in this study contained genes that could provide resistance to antibiotics that are important in human medicine, indicating that human-relevant antibiotic resistance genes are mobile between bacteria via phages. This study highlights the collateral effects of antibiotics and demonstrates the need to consider diverse antibiotic effects whenever antibiotics are being used or new regulations are considered.

Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers

Antimicrobial resistance genes (ARGs) present in the environment pose a risk to human health due to potential for transfer to human pathogens. Surveillance is an integral part of mitigating environmental dissemination. Quantification of the mobile genetic element class 1 integron-integrase gene (intI1) has been proposed as a surrogate to measuring multiple ARGs. Measurement of such indicator genes can be further simplified by adopting emerging nucleic acids methods such as loop mediated isothermal amplification (LAMP). In this study, LAMP assays were designed and tested for estimating relative abundance of the intI1 gene, which included design of a universal bacteria 16S rRNA gene assay. Following validation of sensitivity and specificity with known bacterial strains, the assays were tested using DNA extracted from river and lake samples. Results showed a significant Pearson correlation (R² = 0.8) between the intI1 gene LAMP assay and ARG relative abundance (measured via qPCR). To demonstrate the ruggedness of the LAMP assays, experiments were also run in the hands of relatively "untrained" personnel by volunteer undergraduate students at a local community college using a hand-held real-time DNA analysis device - Gene-Z. Overall, results support use of the intI1 gene as an indicator of ARGs and the LAMP assays exhibit the opportunity for volunteers to monitor environmental samples for anthropogenic pollution outside of a specialized laboratory.

On-site removal of antibiotics and antibiotic resistance genes from leachate by aged refuse bioreactor: Effects of microbial community and operational parameters

The abuse of antibiotics has raised the prevalence of antibiotic resistance, which will pose potential risk to human health. Leachate, generated during the landfill treatment of municipal solid waste, is the important hotspot of the antibiotics and antibiotic resistance genes (ARGs), and no effective on-site treatment has been put forward for preventing ARGs dissemination. Herein, the aged refuse bioreactor was employed to remove antibiotics and ARGs from leachate, and the great removal performance was observed. For the detected antibiotics, the total removal efficiency was about 76.75%, and sulfanilamide and macrolide were removed with high efficiencies (>80%). Among the target ARGs, tetracycline and macrolide resistance genes (tetM, tetQ and ermB) were eliminated with 1.2-2.0 orders of magnitude. The occurrences of ARGs did not correlated with water quality parameters such as COD, total nitrogen, ammonia, nitrate and nitrite, but closely linked to the variations of the bacterial community structure. Redundancy analysis (RDA) indicated the significant correlations between four genera and the distribution of ARGs, which implied that these key genera (including potential pathogens) drove the ARGs removal. Furthermore, the hydraulic loading test confirmed that the aged refuse bioreactor was capable of achieving high removal efficiencies even under shock loading for the higher loading was negative for the proliferations of potential ARGs hosts. This study suggested that aged refuse bioreactor could be a promising way for antibiotics and ARGs on-site removal from leachate.

Perspectiva histórica del origen evolutivo de la resistencia a antibióticos

La resistencia a antimicrobianos representa un aspecto natural de evolución bacteriana, que puede resultar de mutaciones o por adquisición de genes foráneos. Hay diferentes posturas sobre el origen de ésta resistencia que explican la habilidad de estos microorganismos de adquirir nuevas características. Las teorías de la evolución de Lamarck y Darwin, han dado pie a experimentos diseñados para explorar el origen de la variación bacteriana y surgimiento de nuevas características. Estos estudios muestran que la resistencia está relacionada con mutaciones en genes cromosomales y/o la transferencia de elementos genéticos extracromosomales, que se expresan según la presión antibiótica ejercida. Está revisión recopila los principales experimentos y las conclusiones derivadas para explicar el fenómeno de resistencia a antibióticos.

Emerging functions as host cell factors - an encyclopedia of annexin-pathogen interactions

Emerging infectious diseases and drug-resistant infectious agents call for the development of innovative antimicrobial strategies. With pathogenicity now considered to arise from the complex and bi-directional interplay between a microbe and the host, host cell factor targeting has emerged as a promising approach that might overcome the limitations of classical antimicrobial drug development and could open up novel and efficient therapeutic strategies. Interaction with and modulation of host cell membranes is a recurrent theme in the host-microbe relationship. In this review, we provide an overview of what is currently known about the role of the Ca2+ dependent, membrane-binding annexin protein family in pathogen-host interactions, and discuss their emerging functions as host cell derived auxiliary proteins in microbe-host interactions and host cell targets.

Selection of broad-spectrum cephalosporin-resistant Escherichia coli in the feces of healthy dogs after administration of first-generation cephalosporins

Although antimicrobial products are essential for treating diseases caused by bacteria, antimicrobial treatment selects for antimicrobial-resistant (AMR) bacteria. The aim of this study was to determine the effects of administration of first-generation cephalosporins on development of resistant Escherichia coli in dog feces. The proportions of cephalexin (LEX)-resistant E. coli in fecal samples of three healthy dogs treated i.v. with cefazolin before castration and then orally with LEX for 3 days post-operation (PO) were examined using DHL agar with or without LEX (50 µg/mL). LEX-resistant E. coli were found within 3 days PO, accounted for 100% of all identified E. coli 3-5 days PO in all dogs, and were predominantly found until 12 days PO. LEX-resistant E. coli isolates on DHL agar containing LEX were subjected to antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE) genotyping, β-lactamase typing and plasmid profiling. All isolates tested exhibited cefotaxime (CTX) resistance (CTX minimal inhibitory concentration ≥4 µg/mL). Seven PFGE profiles were classified into five groups and three β-lactamase combinations (bla_CMY-4 -bla_TEM-1 , bla_TEM-1 -bla_CTX-M-15 and bla_TEM-1 -bla_CTX-M-15 -bla_CMY-4 ). All isolates exhibited identical PFGE profiles in all dogs on four days PO and subsequently showed divergent PFGE profiles. Our results indicate there are two selection periods for AMR bacteria resulting from the use of antimicrobials. Thus, continuing hygiene practices are necessary to prevent AMR bacteria transfer via dog feces after antimicrobial administration.

Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10^-3 to 1.08 × 10^-1 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion for ARGs removal. ARGs in all the samples were composed of 175 ARG subtypes; however, only 7 ARG subtypes were shared by all the samples. Principal component analysis and canonical correspondence analysis clustered the samples into three groups (samples from manure-based mesophilic reactors, manure-based thermophilic reactors, and sludge-based mesophilic reactors), and substrate, temperature, and hydraulic retention time (HRT) as well as volatile fatty acids (VFAs) were identified as crucial environmental variables affecting the ARGs compositions. Procrustes analysis revealed microbial community composition was the determinant of ARGs composition in biogas reactors, and there was also a significant correlation between ARGs composition and MRGs composition. Network analysis further revealed the co-occurrence of ARGs with specific microorganisms and MRGs.

Metal Resistance and Its Association With Antibiotic Resistance

Antibiotic resistance is recognised as a major global threat to public health by the World Health Organization. Currently, several hundred thousand deaths yearly can be attributed to infections with antibiotic-resistant bacteria. The major driver for the development of antibiotic resistance is considered to be the use, misuse and overuse of antibiotics in humans and animals. Nonantibiotic compounds, such as antibacterial biocides and metals, may also contribute to the promotion of antibiotic resistance through co-selection. This may occur when resistance genes to both antibiotics and metals/biocides are co-located together in the same cell (co-resistance), or a single resistance mechanism (e.g. an efflux pump) confers resistance to both antibiotics and biocides/metals (cross-resistance), leading to co-selection of bacterial strains, or mobile genetic elements that they carry. Here, we review antimicrobial metal resistance in the context of the antibiotic resistance problem, discuss co-selection, and highlight critical knowledge gaps in our understanding.

Lateral Antimicrobial Resistance Genetic Transfer is active in the open environment

Historically, the environment has been viewed as a passive deposit of antimicrobial resistance mechanisms, where bacteria show biological cost for maintenance of these genes. Thus, in the absence of antimicrobial pressure, it is expected that they disappear from environmental bacterial communities. To test this scenario, we studied native IntI1 functionality of 11 class 1 integron-positive environmental strains of distant genera collected in cold and subtropical forests of Argentina. We found natural competence and successful site-specific insertion with no significant fitness cost of both aadB and bla_VIM-2 antimicrobial resistance gene cassettes, in a model system without antibiotic pressure. A bidirectional flow of antimicrobial resistance gene cassettes between natural and nosocomial habitats is proposed, which implies an active role of the open environment as a reservoir, recipient and source of antimicrobial resistance mechanisms, outlining an environmental threat where novel concepts of rational use of antibiotics are extremely urgent and mandatory.

Pathogenic potentials of Aeromonas species isolated from aquaculture and abattoir environments

The present study elucidated the presence of antibiotics resistance, virulence genes and biofilm potentials among Aeromonas species isolated from abattoir and aquaculture environments in Benin City, Nigeria. A total of 144 wastewater samples were obtained from two independent aquaculture and abattoir environments between May and October 2016. Aeromonas species were isolated on Glutamate Starch Phenol Red (GSP) agar and confirmed using API 20NE kits. Antimicrobial susceptibility profile of the isolates was carried out using standard disc diffusion assay while biofilm potentials were detected by the microtitre plate method and PCR technique was used to detect antibiotics resistance and virulence gene markers. Overall, 32 and 26 Aeromonas species were isolated from the abattoir and aquaculture environments respectively. Isolates from both environments were completely resistant (100%) to penicillin G, ertapenem and tetracycline; whereas aquaculture isolates exhibited absolute sensitivity (100%) towards cefepime. All the virulence gene markers (aerA, hlyA, alt, ast, laf, ascF-G, fla, lip, stx1, and stx2) investigated in this study (except laf) were detected in isolates from both environments. The laf genes were only detected in isolates from abattoir environments. Antibiotics resistant genes including pse, bla_TEM and class 1 integron were detected in isolates from both environments. Majority of the isolates (53/58 91.4%) from both environments; demonstrated capacity for biofilm potential. The detection of antibiotic resistance and virulence gene markers as well as biofilm forming ability in Aeromonas species isolated from aquaculture and abattoir environments raise serious public health concern worthy of further investigation.

Genetic Analysis of the IncX4 Plasmids: Implications for a Unique Pattern in the mcr-1 Acquisition

IncX4 plasmids are associated with the dissemination of the mcr-1 genes in Enterobacteriaceae. We screened IncX4 plasmids among 2,470 isolates of Enterobacteriaceae and determined the mcr-1 positive isolates. Forty-three isolates were observed to carry IncX4 type plasmid, among which 13 were identified to carry mcr-1 gene. Three representative mcr-1-positive IncX4 plasmids were selected for high-throughput sequencing. Comparative genomics showed that the mcr-1-carrying IncX4 plasmids exhibit remarkable similarity in the backbone, and the major distinction lies in the region containing mcr-1. The major variable regions of all the IncX4 plasmids were fully characterized by PCR-RFLP. The results revealed that the mcr-1 was located on the Variable Region I of IncX4 plasmids in 11 E. coli isolates. Among them, nine E. coli strains possess an epidemic pCSZ4-like IncX4 plasmid containing mcr-1. ISApl1 was presumably involved in the transposition of the mcr-1 cassette and then was lost. Similar genetic contexts were found in different plasmids, even the E. coli chromosome, implying the acquisition of mcr-1 by a unique common mechanism.

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments

Aeromonas spp. and fecal coliforms, two abundant and cultivable bacterial populations that can be found in water ecosystems, might substantially contribute to the spread of antibiotic resistance. We investigated the presence and spread of transposons (elements that can move from one location to another in the genome), integrons (structures able to capture and incorporate gene cassettes) and resistance plasmids in strains isolated from polluted and unpolluted water. We recovered 231 Aeromonas and 250 fecal coliforms from water samplings with different degrees of pollution (hospital sewage, activated sludge of a wastewater treatment plant, river water before and after treatment and water from an alpine lake). Sixteen Aeromonas spp. and 22 fecal coliforms carried intI, coding for the site-specific integrase of class 1 integrons, while 22 Aeromonas spp. and 14 fecal coliforms carried tnpA, the transposase gene of the Tn3-family of replicative transposons. The majority of intI and tnpA-positive strains were phenotypically resistant to at least four antibiotics. Integrons and transposons were mainly located on mobilizable plasmids. Our results did not detect common mobile structures in the two populations and therefore relativize the role played by Aeromonas spp. as vectors of antimicrobial resistance determinants between water and commensal gut bacteria.

Wireless electrostimulation: a new approach in combating infection?

Electrostimulation (ES), hitherto successfully employed in wound treatment, has shown potential in antimicrobial applications, suggesting its use as synergistic to or replacement of antibiotics. The differential susceptibility of pathogens and host tissue and organs to various ES modalities might allow selective use against specific infections. The use of ES is cheaper in terms of development/testing, routine application and environmental footprint. If extensive substitution of chemical compounds is achieved, the development of resistance might be reversed through negative selection. A promising setup of ES seems to be the noncontact current transfer, due to low amperage similar to innate bioelectricity, painlessness, simple logistics and low risk for treatment-caused infection.

Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.

Veterinary pharmaceuticals in aqueous systems and associated effects: an update

Environmental studies have shown that pharmaceuticals can contaminate aqueous matrices, such as groundwater, surface water, sediment as well as aquatic flora and fauna. Effluents from sewage and wastewater treatment plants, pharmaceutical industries and hospitals have been implicated in such contamination. Recent studies have however revealed significant concentrations of pharmaceuticals in wastewater from animal facilities in proximal aquatic habitats. Furthermore, epidemiological studies have shown a consistent positive correlation between exposure to some drugs of veterinary importance and increased adverse effects in aquatic biota largely due to induction of endocrine disruption, antibiotic resistance, neurotoxicity, genotoxicity and oxidative stress. The aquatic habitats and associated biota are important in the maintenance of global ecosystem and food chain. For this reason, anything that compromises the integrity and functions of the aquatic environment may lead to major upset in the world's ecosystems. Therefore, knowledge about this route of exposure cannot be neglected and monitoring of their occurrence in the environment is required. This review focuses on scientific evidence that link the presence of pharmaceuticals in aqueous matrices to animal production facilities and presents means to reduce the occurrence of veterinary pharmaceutical residues in the aquatic habitats.

The prevalence and characterization of antibiotic-resistant and virulent Escherichia coli strains in the municipal wastewater system and their environmental fate

Antibiotics are widely used in human and veterinary medicine and in animal production, which increases their concentrations in aquatic ecosystems and contributes to selective pressure on environmental microorganisms. The objective of this study was to identify antibiotic resistance determinants in Escherichia coli strains isolated from untreated and treated wastewater (UWW and TWW) and from river water sampled downstream and upstream (URW and DRW) from the effluent discharge point. The analyzed antibiotic groups were beta-lactams, tetracyclines and fluoroquinolones which are widely used in human and veterinary medicine. The virulence of the isolated E. coli strains was also analyzed, and their clonal relatedness was determined by ERIC (enterobacterial repetitive intergenic consensus sequence) PCR. The highest counts of bacteria resistant to beta-lactams, tetracyclines and fluoroquinolones were noted in UWW at 6.4×10⁴, 4.2×10⁴ and 3.1×10³CFU/mL, respectively. A total of 317 E. coli isolates resistant to at least one group of antibiotics were selected among bacterial isolates from river water and wastewater samples. Nearly 38% of those isolates were resistant to all of the tested antibiotics. The highest percent (43%) of multidrug-resistant isolates was noted in UWW samples. Isolates resistant to beta-lactams most frequently harbored bla_TEM and bla_OXA genes. The group of genes encoding resistance to tetracyclines was most frequently represented by tetA, tetB and tetK, whereas the qnrS gene was noted in isolates resistant to fluoroquinolones. Virulence genes bfpA (65%), ST (56%) and eae (39%) were most widely distributed in all isolates, regardless of their origin. The results of this experiment reveal the dangers associated with environmental contamination by drug-resistant and virulent E. coli strains distributed with treated wastewater. Multidrug resistance was determined more frequently in strains isolated from DRW than in isolates from URW samples. Our findings provide valuable inputs for evaluating public health hazards associated with bacterial contamination.

The influence of antibiotic prophylaxis on bacterial resistance in urinary tract infections in children with spina bifida

Background

Bacterial resistance to antibiotics is an increasingly threatening consequence of antimicrobial exposure for many decades now. In urinary tract infections (UTIs), antibiotic prophylaxis (AP) increases bacterial resistance. We studied the resistance patterns of positive urinary cultures in spina bifida children on clean intermittent catheterization, both continuing and stopping AP.

Methods

In a cohort of 176 spina bifida patients, 88 continued and 88 stopped using AP. During 18 months, a fortnightly catheterized urine sample for bacterial pathogens was cultured. UTIs and significant bacteriuria (SBU) were defined as a positive culture with a single species of bacteria, respectively with and without clinical symptoms and leukocyturia. We compared the percentage of resistance to commonly used antibiotics in the isolated bacteria in both groups.

Results

In a total of 4917 cultures, 713 (14.5%) had a positive monoculture, 54.3% of which were Escherichia coli. In the group stopping AP, the resistance percentage to antibiotics in UTI / SBU bacteria was lower than in the group remaining on AP, even when excluding the administered prophylaxis.

Conclusion

Stopping antibiotic prophylaxis for urinary tract infections is associated with reduced bacterial resistance to antibiotics in children with spina bifida.

Trial registration

ISRCTN ISRCTN56278131. Registered 20 December 2005.

Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism

The intracellular facultative bacteria Piscirickettsia salmonis is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS) of RNA (RNA-seq) to study the whole transcriptome of an isolate of P. salmonis (FAVET-INBIOGEN) using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake) that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament), which may play roles in other basic processes rather than been restricted to virulence.

Prevalence and dissemination of antibiotic resistance genes and coselection of heavy metals in Chinese dairy farms

This study aims to explore prevalence and dissemination of antibiotic resistance genes (ARGs) in dairy farms. A variety of ARGs conferring resistance to most classes of antibiotics were detected in feces and soil samples obtained from dairy farms, using a high-throughput metagenomic sequencing approach. The ARGs observed in the feces and the soil samples were significantly correlated (p<0.01). The abundance of mobile genetics elements, such as transposase, was also examined to evaluate the potential risk of horizontal ARGs transfer. The positive correlation (p<0.001) between the total abundance of transposase genes and ARGs in the soil samples suggested strong dissemination capacity of ARGs in soil. In addition, the ARGs and metal resistance genes (MRGs) were significantly correlated with heavy metals in the feces (p<0.01), suggesting that the heavy metals promoted the emergence of metal resistance, and participated in the coselection processes for ARGs. The prevalence of ARGs with high levels of genetic mobile elements in the dairy farms suggests that cattle excrement is a major reservoir of ARGs with a high risk of dissemination, which increases the potential risk of environmental pollution and threatens public health.

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

The high frequency of antibiotic resistance is a global public health concern. More seriously, widespread metal pressure in the environment may facilitate the proliferation of antibiotic resistance via coselection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). Given the lack of comprehensive understanding of the ARG and MRG coselection, in this study both abundance relationship and genetic linkage between ARGs and MRGs were rigorously investigated by performing a genomic analysis of a large complete genome collection. Many more ARGs were enriched in human-associated bacteria compared with those subjected to less anthropogenic interference. The signatures of ARG and MRG co-occurrence were much more frequent and the distance linkages between ARGs and MRGs were much more intimate in human pathogens than those less human-associated bacteria. Moreover, the co-occurrence structures in the habitat divisions were significantly different, which could be attributed to their distinct gene transfer potentials. More exogenous ARGs and MRGs on the genomes of human pathogens indicated the importance of recent resistance acquisition in resistome development of human commensal flora. Overall, the study emphasizes the potential risk associated with ARG and MRG coselection of both environmental and medical relevance.

Antibiotic Resistance and the Biology of History

Beginning in the 1940s, mass production of antibiotics involved the industrial-scale growth of microorganisms to harvest their metabolic products. Unfortunately, the use of antibiotics selects for resistance at answering scale. The turn to the study of antibiotic resistance in microbiology and medicine is examined, focusing on the realization that individual therapies targeted at single pathogens in individual bodies are environmental events affecting bacterial evolution far beyond bodies. In turning to biological manifestations of antibiotic use, sciences fathom material outcomes of their own previous concepts. Archival work with stored soil and clinical samples produces a record described here as 'the biology of history': the physical registration of human history in bacterial life. This account thus foregrounds the importance of understanding both the materiality of history and the historicity of matter in theories and concepts of life today.

Effects of electron acceptors on removal of antibiotic resistant Escherichia coli, resistance genes and class 1 integrons under anaerobic conditions

Anaerobic biotechnologies can effectively remove antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), but there is a need to better understand the mechanisms. Here we employ bioelectrochemical systems (BES) as a platform to investigate the fate of a native tetracycline and sulfonamide-resistant Escherichia coli strain and its ARGs. The E. coli strain carrying intI1, sulI and tet(E) was isolated from domestic wastewater and dosed into a tubular BES. The BES was first operated as a microbial fuel cell (MFC), with aeration in the cathode, which resulted in enhanced removal of E. coli and ARGs by ~2 log (i.e., order of magnitude) when switched from high current to open circuit operation mode. The BES was then operated as a microbial electrolysis cell (MEC) to exclude the effects of oxygen diffusion, and the removal of E. coli and ARGs during the open circuit configuration was again 1-2 log higher than that at high current mode. Significant correlations of E. coli vs. current (R(2)=0.73) and ARGs vs. E. coli (R(2) ranged from 0.54 to 0.87), and the fact that the BES substrate contained no electron acceptors, implied that the persistence of the E. coli and its ARGs was determined by the availability of indigenous electron acceptors in the BES, i.e., the anode electrode or the electron shuttles generated by the exoelectrogens. Subsequent experiments with pure-culture tetracycline and sulfonamide-resistant E. coli being incubated in a two-chamber MEC and serum bottles demonstrated that the E. coli could survive by respiring anode electrode and/or electron shuttles released by exoelectrogens, and ARGs persisted with their host E. coli.

Exploring the Role of Coliform Bacteria in Class 1 Integron Carriage and Biofilm Formation During Drinking Water Treatment

This study investigates the role of coliforms in the carriage of class 1 integron and biocide resistance genes in a drinking water treatment plant and explores the relationship between the carriage of such genes and the biofouling abilities of the strain. The high incidence of class 1 integron and biocide resistance genes (33.3 % of the isolates) highlights the inherent risk of genetic contamination posed by coliform populations during drinking water treatment. The association between the presence of intI1 gene and qac gene cassettes, especially qacH, was greater in biofilm cells. In coliforms recovered from biofilms, a higher frequency of class 1 integron elements and higher diversity of genetic patterns occurred, compared to planktonic cells. The coliform isolates under the study proved to mostly carry non-classical class 1 integrons lacking the typical qacEΔ1/sul1 genes or a complete tni module, but bearing the qacH gene. No link was found between the carriage of integron genes and the biofouling degree of the strain, neither in aerobic or in anaerobic conditions. Coliform bacteria isolated from established biofilms rather adhere in oxygen depleted environments, while the colonization ability of planktonic cells is not significantly affected by oxygen availability.

Abundance of Class 1 Integron-Integrase and Sulfonamide Resistance Genes in River Water and Sediment Is Affected by Anthropogenic Pressure and Environmental Factors

In this study, we determined the presence of class 1 integron-integrase gene in culturable heterotrophic bacteria isolated from river water and sediment sampled upstream and downstream of a wastewater treatment plant effluent discharge. Moreover, we quantified intI1 and sulfonamide resistance genes (sul1 and sul2) in the water and sediment using qPCR. There was no correlation between the results from water and sediment samples, which suggests integron-containing bacteria are differentially retained in these two environmental compartments. The discharge of treated wastewater significantly increased the frequency of intI1 among culturable bacteria and the gene copy number in river water, and increased the number of sul1 genes in the sediment. We also observed seasonal differences in the frequency of the class 1 integron-integrase gene among culturable heterotrophs as well as intI1 copy number in water, but not in sediment. The results suggest that the abundance of class 1 integrons in aquatic habitat depends on anthropogenic pressure and environmental factors.

Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes

Microbial communities contain diverse bacteria that play important roles in every environment. Advances in sequencing and computational methodologies over the past decades have illuminated the phylogenetic and functional diversity of microbial communities from diverse habitats. Among the activities encoded in microbiomes are the abilities to synthesize and resist small molecules, yielding antimicrobial activity. These functions are of particular interest when viewed in light of the public health emergency posed by the increase in clinical antimicrobial resistance and the dwindling antimicrobial discovery and approval pipeline, and given the intimate ecological and evolutionary relationship between antimicrobial biosynthesis and resistance. Here, we review genomic and functional methods that have been developed for accessing the antimicrobial biosynthesis and resistance capacity of microbiomes and highlight outstanding examples of their applications.

Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics

Horizontal gene transfer (HGT) is a major mechanism responsible for the spread of antibiotic resistance. Conversely, it is often assumed that antibiotics promote HGT. Careful dissection of the literature, however, suggests a lack of conclusive evidence supporting this notion in general. This is largely due to the lack of well-defined quantitative experiments to address this question in an unambiguous manner. In this review, we discuss the extent to which HGT is responsible for the spread of antibiotic resistance and examine what is known about the effect of antibiotics on the HGT dynamics. We focus on conjugation, which is the dominant mode of HGT responsible for spreading antibiotic resistance on the global scale. Our analysis reveals a need to design experiments to quantify HGT in such a way to facilitate rigorous data interpretation. Such measurements are critical for developing novel strategies to combat resistance spread through HGT.

Dynamics of a Class 1 Integron Located on Plasmid or Chromosome in Two Aeromonas spp. Strains

Integrons are non-mobile bacterial genetic elements that carry different cassettes conferring antibiotic resistance. Cassettes can excise or integrate by action of an integron-encoded integrase, enabling bacteria to face environmental challenges. In this work, the functionality and dynamics of two integrons carrying the same cassette arrangement (dfrA12–orfF–aadA2), but located on plasmid or chromosome in two different strains were studied. In order to demonstrate the functionality of the Class 1 integrase, circular cassette integration intermediaries were PCR amplified by PCR using extrachromosomal DNA extracted from bacteria grown in the presence or absence of cassette-encoded antibiotics. Circular aadA2 and dfrA12–orfF–aadA2 cassettes were detected in cultures grown either in the presence or absence of antibiotics in both strains. No dfrA12–orfF circular intermediates could be detected under any culture conditions. These results show that both integrons are functional. However, these elements show different dynamics and functionality since the presence of streptomycin led to detectable gene rearrangements in the variable region only in the strain with the plasmid-born integron. In addition, complete integration products were demonstrated using a receptor molecule carrying an empty integron. In this case, integration products were observed in both strains even in the absence of antibiotics, but they were more evident in the strain with the plasmid-located integron when streptomycin was present in the culture medium. This suggests that integrons in the two strains respond differently to streptomycin even though DNA sequences upstream the intI1 gene, including the lexA boxes of both integrons are identical.

Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered among Fruits and Vegetables

The spread of antibiotic resistant bacteria throughout the food chain constitutes a public health concern. To understand the contribution of fresh produce in shaping antibiotic resistance bacteria and integron prevalence in the food chain, 333 antibiotic resistance Gram negative isolates were collected from organic and conventionally produced fruits (pears, apples, and strawberries) and vegetables (lettuces, tomatoes, and carrots). Although low levels of resistance have been detected, the bacterial genera identified in the assessed fresh produce are often described not only as environmental, but mostly as commensals and opportunistic pathogens. The genomic characterization of integron-harboring isolates revealed a high number of mobile genetic elements and clinically relevant antibiotic resistance genes, of which we highlight the presence of as mcr-1, qnrA1, bla_GES−11, mphA, and oqxAB. The study of class 1 (n = 8), class 2 (n = 3) and class 3 (n = 1) integrons, harbored by species such as Morganella morganii, Escherichia coli, Klebsiella pneumoniae, led to the identification of different integron promoters (PcW, PcH1, PcS, and PcW_TNG−10) and cassette arrays (containing drfA, aadA, cmlA, estX, sat, and bla_GES). In fact, the diverse integron backbones were associated with transposable elements (e.g., Tn402, Tn7, ISCR1, Tn2^*, IS26, IS1326, and IS3) that conferred greater mobility. This is also the first appearance of In1258, In1259, and In3-13, which should be monitored to prevent their establishment as successfully dispersed mobile resistance integrons. These results underscore the growing concern about the dissemination of acquired resistance genes by mobile elements in the food chain.

Human migration activities drive the fluctuation of ARGs: Case study of landfills in Nanjing, eastern China

Landfills are perfect sites to study the effect of human migration on fluctuation of antibiotic resistance genes (ARGs) as they are the final destination of municipal waste. For example, large-scale human migration during the holidays is often accompanied by changes in waste dumping having potential effects on ARG abundance. Three landfills were selected to examine fluctuation in the abundance of fifteen ARGs and Intl1 genes for 14 months in Nanjing, eastern China. Mass human migration, the amount of dumped waste and temperature exerted the most significant effects on bimonthly fluctuations of ARG levels in landfill sites. As a middle-sized cosmopolitan city in China, millions of college students and workers migrate during holidays, contributing to the dramatic increases in waste production and fluctuation in ARG abundances. In line with this, mass migration explained most of the variation in waste dumping. The waste dumping also affected the bioaccessibility of mixed-compound pollutants that further positively impacted the level of ARGs. The influence of various bioaccessible compounds on ARG abundance followed the order: antibiotics>nutrients>metals>organic pollutants. Concentrations of bioaccessible compounds were more strongly correlated with ARG levels compared to total compound concentrations. Improved waste classification and management strategies could thus help to decrease the amount of bioaccessible pollutants leading to more effective control for urban ARG dissemination.

Insights on the Horizontal Gene Transfer of Carbapenemase Determinants in the Opportunistic Pathogen Acinetobacter baumannii

Horizontal gene transfer (HGT) is a driving force to the evolution of bacteria. The fast emergence of antimicrobial resistance reflects the ability of genetic adaptation of pathogens. Acinetobacter baumannii has emerged in the last few decades as an important opportunistic nosocomial pathogen, in part due to its high capacity of acquiring resistance to diverse antibiotic families, including to the so-called last line drugs such as carbapenems. The rampant selective pressure and genetic exchange of resistance genes hinder the effective treatment of resistant infections. A. baumannii uses all the resistance mechanisms to survive against carbapenems but production of carbapenemases are the major mechanism, which may act in synergy with others. A. baumannii appears to use all the mechanisms of gene dissemination. Beyond conjugation, the mostly reported recent studies point to natural transformation, transduction and outer membrane vesicles-mediated transfer as mechanisms that may play a role in carbapenemase determinants spread. Understanding the genetic mobilization of carbapenemase genes is paramount in preventing their dissemination. Here we review the carbapenemases found in A. baumannii and present an overview of the current knowledge of contributions of the various HGT mechanisms to the molecular epidemiology of carbapenem resistance in this relevant opportunistic pathogen.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.

The Prehistory of Antibiotic Resistance

Antibiotic resistance is a global problem that is reaching crisis levels. The global collection of resistance genes in clinical and environmental samples is the antibiotic "resistome," and is subject to the selective pressure of human activity. The origin of many modern resistance genes in pathogens is likely environmental bacteria, including antibiotic producing organisms that have existed for millennia. Recent work has uncovered resistance in ancient permafrost, isolated caves, and in human specimens preserved for hundreds of years. Together with bioinformatic analyses on modern-day sequences, these studies predict an ancient origin of resistance that long precedes the use of antibiotics in the clinic. Understanding the history of antibiotic resistance is important in predicting its future evolution.

QnrS1- and Aac(6')-Ib-cr-Producing Escherichia coli among Isolates from Animals of Different Sources: Susceptibility and Genomic Characterization

Salmonella enterica and Escherichia coli can inhabit humans and animals from multiple origins. These bacteria are often associated with gastroenteritis in animals, being a frequent cause of resistant zoonotic infections. In fact, bacteria from animals can be transmitted to humans through the food chain and direct contact. In this study, we aimed to assess the antibiotic susceptibility of a collection of S. enterica and E. coli recovered from animals of different sources, performing a genomic comparison of the plasmid-mediated quinolone resistance (PMQR)-producing isolates detected. Antibiotic susceptibility testing revealed a high number of non-wild-type isolates for fluoroquinolones among S. enterica recovered from poultry isolates. In turn, the frequency of non-wild-type E. coli to nalidixic acid and ciprofloxacin was higher in food-producing animals than in companion or zoo animals. Globally, we detected two qnrS1 and two aac(6′)-Ib-cr in E. coli isolates recovered from animals of different origins. The genomic characterization of QnrS1-producing E. coli showed high genomic similarity (O86:H12 and ST2297), although they have been recovered from a healthy turtle dove from a Zoo Park, and from a dog showing symptoms of infection. The qnrS1 gene was encoded in a IncN plasmid, also carrying bla_TEM−1−containing Tn3. Isolates harboring aac(6′)-Ib-cr were detected in two captive bottlenose dolphins, within a time span of two years. The additional antibiotic resistance genes of the two aac(6′)-Ib-cr-positive isolates (bla_OXA−1, bla_TEM−1,bla_CTX−M−15, catB3, aac(3)-IIa, and tetA) were enclosed in IncFIA plasmids that differed in a single transposase and 60 single nucleotide variants. The isolates could be assigned to the same genetic sublineage—ST131 fimH30-Rx (O25:H4), confirming clonal spread. PMQR-producing isolates were associated with symptomatic and asymptomatic hosts, which highlight the aptitude of E. coli to act as silent vehicles, allowing the accumulation of antibiotic resistance genes, mobile genetic elements and other relevant pathogenicity determinants. Continuous monitoring of health and sick animals toward the presence of PMQR should be strongly encouraged in order to restrain the clonal spread of these antibiotic resistant strains.