Pathogenic Escherichia coli strains producing extended-spectrum β-lactamases in the Yeongsan River basin of South Korea

Isolation and characterization of cefotaxime resistant Escherichia coli from household floors in rural Bangladesh

Antimicrobial resistance (AMR) is a rising health concern worldwide. As an indicator organism, E. coli, specifically extended-spectrum β-lactamase (ESBL) producing E. coli, can be used to detect AMR in the environment and estimate the risk of transmitting resistance among humans, animals and the environment. This study focused on detecting cefotaxime resistant E. coli in floor swab samples from 49 households in rural villages in Bangladesh. Following isolation of cefotaxime resistant E. coli, DNA extracted from isolates was subjected to molecular characterization for virulence and resistance genes, determination of resistance to multiple classes of antibiotics to define multidrug resistant (MDR) and extensively drug resistant (XDR) strains, and the biofilm forming capacity of the isolates. Among 49 households, floor swabs from 35 (71 %) households tested positive for cefotaxime resistant E. coli. Notably, all of the 91 representative isolates were ESBL producers, with the majority (84.6 %) containing the bla CTX-M gene, followed by the bla TEM and bla SHV genes detected in 22.0 % and 6.6 % of the isolates, respectively. All isolates were MDR, and one isolate was XDR. In terms of pathogenic strains, 8.8 % of the isolates were diarrheagenic and 5.5 % were extraintestinal pathogenic E. coli (ExPEC). At 25 °C, 45 % of the isolates formed strong biofilm, whereas 43 % and 12 % formed moderate and weak biofilm, respectively. On the other hand, at 37 °C, 1.1 %, 4.4 % and 93.4 % of the isolates were strong, moderate and weak biofilm formers, respectively, and 1.1 % showed no biofilm formation. The study emphasizes the importance of screening and characterizing cefotaxime resistant E. coli from household floors in a developing country setting to understand AMR exposure associated with floors.

CTX-M-producing Escherichia coli ST602 carrying a wide resistome in South American wild birds: Another pandemic clone of One Health concern

Wild birds have emerged as novel reservoirs and potential spreaders of antibiotic-resistant priority pathogens, being proposed as sentinels of anthropogenic activities related to the use of antimicrobial compounds. The aim of this study was to investigate the occurrence and genomic features of extended-spectrum β-lactamase (ESBL)-producing bacteria in wild birds in South America. In this regard, we have identified two ESBL (CTX-M-55 and CTX-M-65)-positive Escherichia coli (UNB7 and GP188 strains) colonizing Creamy-bellied Thrush (Turdus amaurochalinus) and Variable Hawk (Geranoaetus polyosoma) inhabiting synanthropic and wildlife environments from Brazil and Chile, respectively. Whole-genome sequence (WGS) analysis revealed that E. coli UNB7 and GP188 belonged to the globally disseminated clone ST602, carrying a wide resistome against antibiotics (β-lactams), heavy metals (arsenic, copper, mercury), disinfectants (quaternary ammonium compounds), and pesticides (glyphosate). Additionally, E. coli UNB7 and GP188 strains harbored virulence genes encoding hemolysin E, type II and III secretion systems, increased serum survival, adhesins and siderophores. SNP-based phylogenomic analysis, using an international genome database, revealed genomic relatedness (19-363 SNP differences) of GP188 with livestock and poultry strains, and genomic relatedness (61-318 differences) of UNB7 with environmental, human and livestock strains (Table S1), whereas phylogeographical analysis confirmed successful expansion of ST602 as a global clone of One Health concern. In summary, our results support that ESBL-producing E. coli ST602 harboring a wide resistome and virulome have begun colonizing wild birds in South America, highlighting a potential new reservoir of critical priority pathogens.

Multidrug-resistant Escherichia coli isolated from patients and surrounding hospital environments in Bangladesh: A molecular approach for the determination of pathogenicity and resistance

Extended spectrum β-lactamase producing Escherichia coli (ESBL E. coli) is a primary concern for hospital and community healthcare settings, often linked to an increased incidence of nosocomial infections. This study investigated the characteristics of ESBL E. coli isolated from hospital environments and clinical samples. In total, 117 ESBL E. coli isolates were obtained. The isolates were subjected to molecular analysis for the presence of resistance and virulence genes, antibiotic susceptibility testing, quantitative adherence assay, ERIC-PCR for phylogenetic analysis and whole genome sequencing of four highly drug resistant isolates. Out of the 117 isolates, 68.4% were positive for blaCTX-M, 39.3% for blaTEM, 30.8% for blaNDM-1, 13.7% for blaOXA and 1.7% for blaSHV gene. Upon screening for diarrheagenic genes, no isolates were found to harbour any of the tested genes. In the case of extraintestinal pathogenic E. coli (ExPEC) virulence factors, 7.6%, 11%, 5.9%, 4.3% and 21.2% of isolates harbored the focG, kpsMII, sfaS, afa and iutA genes, respectively. At a temperature of 25°C, 14.5% of isolates exhibited strong biofilm formation with 21.4% and 28.2% exhibiting moderate and weak biofilm formation respectively, whereas 35.9% were non-biofilm formers. On the other hand at 37°C, 2.6% of isolates showed strong biofilm formation with 3.4% and 31.6% showing moderate and weak biofilm formation respectively, whereas, 62.4% were non-biofilm formers. Regarding antibiotic susceptibility testing, all isolates were found to be multidrug-resistant (MDR), with 30 isolates being highly drug resistant. ERIC-PCR resulted in 12 clusters, with cluster E-10 containing the maximum number of isolates. Hierarchical clustering and correlation analysis revealed associations between environmental and clinical isolates, indicating likely transmission and dissemination from the hospital environment to the patients. The whole genome sequencing of four highly drug resistant ExPEC isolates showed the presence of various antimicrobial resistance genes, virulence factors and mobile genetic elements, with isolates harbouring the plasmid incompatibility group IncF (FII, FIB, FIA). The sequenced isolates were identified as human pathogens with a 93.3% average score. This study suggests that ESBL producing E. coli are prevalent in the healthcare settings of Bangladesh, acting as a potential reservoir for AMR bacteria. This information may have a profound effect on treatment, and improvements in public healthcare policies are a necessity to combat the increased incidences of hospital-acquired infections in the country.

Effect of the pH on the Antibacterial Potential and Cytotoxicity of Different Plasma-Activated Liquids

In this study, different plasma-activated liquids were evaluated for their antimicrobial effects against Escherichia coli, as well as for their cytotoxicity on mammalian cells. The PALs were prepared from distilled (DIS), deionized (DI), filtered (FIL), and tap (TAP) water. Additionally, 0.9% NaCl saline solution (SAL) was plasma-activated. These PALs were prepared using 5 L/min air gliding arc plasma jet for up to 60.0 min of exposure. Subsequently, the physicochemical properties, such as, the oxidation-reduction potential (ORP), the pH, the conductivity, and the total dissolved solids (TDS) were characterized by a water multiparameter. The PALs obtained showed a drastic decrease in the pH with increasing plasma exposure time, in contrast, the conductivity and TDS increased. In a general trend, the UV-vis analyses identified a higher production of the following reactive species of nitrogen and oxygen (RONS), HNO₂, H₂O₂, NO₃^-, and NO₂^-. Except for the plasma-activated filtered water (PAW-FIL), where there was a change in the position of NO₂^- and NO₃^- at some pHs, The higher production of HNO₂ and H₂O₂-reactive species was observed at a low pH. Finally, the standardized suspensions of Escherichia coli were exposed to PAL for up to 60.0 min. The plasma-activated deionized water (PAW-DI pH 2.5), plasma-activated distilled water (PAW-DIS pH 2.5 and 3), and plasma-activated tap water (PAW-TAP 3.5) showed the best antimicrobial effects at exposure times of 3.0, 10.0, and 30.0 min, respectively. The MTT analysis demonstrated low toxicity of all of the PAL samples. Our results indicate that the plasma activation of different liquids using the gliding arc system can generate specific physicochemical conditions that produce excellent antibacterial effects for E. coli with a safe application, thus bringing future contributions to creating new antimicrobial protocols.

ESBL Producing Escherichia coli in Faecal Sludge Treatment Plants: An Invisible Threat to Public Health in Rohingya Camps, Cox's Bazar, Bangladesh

Introduction: Human faecal sludge contains diverse harmful microorganisms, making it hazardous to the environment and public health if it is discharged untreated. Faecal sludge is one of the major sources of E. coli that can produce extended-spectrum β-lactamases (ESBLs).

Objective: This study aimed to investigate the prevalence and molecular characterization of ESBL-producing E. coli in faecal sludge samples collected from faecal sludge treatment plants (FSTPs) in Rohingya camps, Bangladesh.

Methods: ESBL producing E. coli were screened by cultural as well as molecular methods and further characterized for their major ESBL genes, plasmid profiles, pathotypes, antibiotic resistance patterns, conjugation ability, and genetic similarity.

Results: Of 296 isolates, 180 were phenotypically positive for ESBL. All the isolates, except one, contained at least one ESBL gene that was tested (bla_CTX−M−1, bla_CTX−M−2, bla_CTX−M−8, bla_CTX−M−9, bla_CTX−M−15, bla_CTX−M−25, bla_TEM, and bla_SHV). From plasmid profiling, it was observed that plasmids of 1–211 MDa were found in 84% (151/180) of the isolates. Besides, 13% (24/180) of the isolates possessed diarrhoeagenic virulence genes. From the remaining isolates, around 51% (79/156) harbored at least one virulence gene that is associated with the extraintestinal pathogenicity of E. coli. Moreover, 4% (3/156) of the isolates were detected to be potential extraintestinal pathogenic E. coli (ExPEC) strains. Additionally, all the diarrhoeagenic and ExPEC strains showed resistance to three or more antibiotic groups which indicate their multidrug-resistant potential. ERIC-PCR differentiated these pathogenic isolates into seven clusters. In addition to this, 16 out of 35 tested isolates transferred plasmids of 32–112 MDa to E. coli J53 recipient strain.

Conclusion: The present study implies that the faecal sludge samples examined here could be a potential origin for spreading MDR pathogenic ESBL-producing E. coli. The exposure of Rohingya individuals, living in overcrowded camps, to these organisms poses a severe threat to their health.

Multidrug-Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Vegetable Farm Soil in South Korea

The populations of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) have increasingly disseminated in humans, animals, and the environment. This study aimed to determine the prevalence, antimicrobial susceptibilities, and molecular characteristics of ESBL-EC isolates obtained from vegetable farm soil. In total, 200 soil samples were collected from vegetable farms in Incheon, South Korea, between 2018 and 2019 and cultured on MacConkey screening plates supplemented with 2 μg/mL cefotaxime. Cefotaxime-resistant ESBL-EC isolates were recovered from 4.0% (8/200) of the soil samples. All eight isolates were nonsusceptible to ampicillin, piperacillin, cefazolin, cefotaxime, and cefepime and harbored bla_CTX-M-type ESBL genes, including bla_CTX-M-15 (50.0%), bla_CTX-M-55 (25.0%), and bla_CTX-M-14 (25.0%). Phylogenetic analysis showed that the B1 lineage was predominant (75.0%), followed by A (12.5%) and B2 (12.5%) lineages. Multilocus sequence typing revealed eight different E. coli sequence types (STs), including ST10, ST73, ST155, ST847, ST2521, ST3285, ST5173, and ST9479. Notably, ST10 and ST73 belong to the global extraintestinal pathogenic E. coli lineages. Our findings demonstrated that the farm soil environment may serve as a reservoir of human-associated multidrug-resistant ESBL-producing pathogens.

Simultaneous elimination of amoxicillin and antibiotic resistance genes in activated sludge process: Contributions of easy-to-biodegrade food

Antibiotics are continuously released into aquatic environments and ecosystems where they accumulate, which increases risks from the transmission of antibiotic resistance genes (ARGs). However, it is difficult to completely remove antibiotics by conventional biological methods, and during such treatment, ARGs may spread via the activated sludge process. Easy-to-biodegrade food have been reported to improve the removal of toxic pollutants, and therefore, this study investigated whether such co-substrates may also decrease the abundance of ARGs and their transferal. This study investigated amoxicillin (AMO) degradation using 0-100 mg/L acetate sodium as co-substrate in a sequencing biological reactor. Proteobacteria, Bacteroidetes, and Actinobacteria were identified as dominant phyla for AMO removal and mineralization. Furthermore, acetate addition increased the abundances of adeF and mdsC as efflux resistance genes, which improved microbial resistance, the coping ability of AMO toxicity, and the repair of the damage from AMO. As a result, acetate addition contributed to almost 100% AMO removal and stabilized the chemical oxygen demand (~20 mg/L) in effluents when the influent AMO fluctuated from 20 to 100 mg/L. Moreover, the total abundance of ARGs decreased by approximately ~30%, and the proportion of the most dominant antibiotic resistance bacteria Proteobacteria decreased by ~9%. The total abundance of plasmids that encode ARGs decreased by as much as ~30%, implying that the ARG spreading risks were alleviated. In summary, easy-to-biodegrade food contributed to the simultaneous elimination of antibiotics and ARGs in an activated sludge process.

Investigating the impact of hospital antibiotic usage on aquatic environment and aquaculture systems: A molecular study of quinolone resistance in Escherichia coli

Quinolones are one of the most important classes of antibacterials available for the treatment of infectious diseases in humans. However, there is a growing concern about bacterial resistance to antimicrobials including quinolones. The spread of antibiotic-resistant bacteria in the aquatic environment has been recognized as a growing threat to public health and hospitals appear to be a major contributor to this. The objective of this study was to investigate the prevalence of quinolone resistance in Escherichia coli from selected water bodies receiving direct hospital effluents in Kerala, India. Standard disc diffusion and E-test were used for antibiotic susceptibility testing. As antibiotic resistance can develop in bacterial isolates by different means, EtBr Agar Cartwheel method was used to detect the efflux pump activity and presence of resistant genes was detected by PCR. The mechanism of transfer of plasmid mediated resistance was confirmed by conjugation experiments. A total of 209 multidrug-resistant Escherichia coli were isolated from different hospital effluent discharge sites and aquaculture farms located in their vicinity. Among them, qnrB was found to be most prevalent followed by qnrS, OqxAB, qnrA and aac (6')-Ib-cr. The results suggested that the antibiotics present at sub-inhibitory concentrations in direct hospital effluents increases the selection pressure impacting the cell function of even normal microorganisms in the aquatic environment to change the genetic expression of virulence factors or acquire resistance genes by different transfer mechanisms, posing a serious threat to public health.

Extended-spectrum β-lactamase-producing Escherichia coli isolated from raw vegetables in South Korea

The increasing prevalence of oxyimino-cephalosporin-resistant Enterobacteriaceae has become a global concern because of their clinical impact on both human and veterinary medicine. The present study determined the prevalence, antimicrobial susceptibility, and molecular genetic features of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBL-EC) isolates from raw vegetables. A total of 1324 samples were collected from two agricultural wholesale markets in Incheon, South Korea in 2018. The ESBL-EC strains were isolated from 0.83% (11/1324) samples, and all of them were resistant to ampicillin, piperacillin, cefazoline, cefotaxime, and nalidixic acid and yielded CTX-M-type ESBL, including CTX-M-14, CTX-M-15, CTX-M-55, CTX-M-27, and CTX-M-65. The isolates belonged to phylogenetic subgroups D (n = 5), A (n = 4), and B1 (n = 2). Multilocus sequence typing revealed nine known E. coli sequence types (STs), including ST10, ST38, ST69, ST101, ST224, ST349, ST354, ST2509, ST2847, and two new STs. Notably, ST69, ST10, ST38, and ST354 belong to the major human-associated extraintestinal pathogenic E. coli lineages. Our results demonstrate that ESBL-producing multidrug-resistant pathogens may be transmitted to humans through the vegetable intake, highlighting the importance of resistance monitoring and intervention in the One Health perspective.

High Prevalence of Human-Associated Escherichia coli in Wetlands Located in Eastern France

Escherichia coli that are present in the rivers are mostly brought by human and animal feces. Contamination occurs mostly through wastewater treatment plant (WWTP) outflows and field amendment with sewage sludge or manure. However, the survival of these isolates in river-associated wetlands remains unknown. Here, we assessed E. coli population structure in low-anthropized wetlands located along three floodplains to identify the major source of contamination of wetlands, whose functioning is different from the rivers. We retrieved 179 E. coli in water samples collected monthly from 19 sites located in eastern France over 1 year. Phylogroups B1 and B2 were dominant in the E. coli population, while phylogroup A was dominant in isolates resistant to third-generation cephalosporins, which harbored the extended-spectrum β-lactamase (ESBL) encoding genes bla_CTX–M–15 and bla_CTX–M–27 in half of the cases. The high proportion of isolates from human source can be attributed to WWTP outflows and the spread of sewage sludge. We analyzed the distribution of the isolates belonging to the most human-associated phylogroups (B2 and D) on a phylogenetic tree of the whole species and compared it with that of isolates retrieved from patients and from WWTP outflows. The distribution of the three E. coli populations was similar, suggesting the absence of a specific population in the environment. Our results suggest that a high proportion of E. coli isolates that reach and survive in low-anthropized environments such as wetlands are from human source. To the best of our knowledge, this is the first study assessing E. coli contamination and resistance genes in natural freshwater wetlands.

Whole Genome Sequencing and Characterization of Multidrug-Resistant (MDR) Bacterial Strains Isolated From a Norwegian University Campus Pond

The presence of extended-spectrum β-lactamase (ESBL)-producing bacteria in environmental sources has been reported worldwide and constitutes a serious risk of community-acquired infections with limited treatment options. The current study aimed to explore the presence of these worrisome bacteria in a pond located at the Norwegian University of Life Sciences in Ås, Norway. A total of 98 bacterial isolates survived growth on selective chromogenic media and were identified by 16S rRNA Sanger sequencing. All strains were evaluated for the presence of the most commonly found β-lactamases and ESBLs in clinical settings (bla_CTX–M groups 1, 2, and 9, bla_CMY, bla_SHV, and bla_TEM) and carbapenemases (bla_IMP, bla_KPC, bla_NDM, bla_OXA, bla_SFC1, bla_VIM) through multiplex PCR. A total of eight strains were determined to contain one or more genes of interest. Phenotypic resistance to 18 antimicrobial agents was assessed and isolates were subjected to whole genome sequencing through a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq. Results revealed the presence of β-lactamase and ESBL-producing Escherichia coli, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and a Paraburkholderia spp. Identified β-lactamases and ESBLs include bla_CTX–M, bla_TEM, bla_CMY, bla_SHV and a possible bla_KPC-like gene, with both documented and novel sequences established. In addition, two inducible β-lactamases were found, a class A β-lactamase (L1) and a cephalosporinase (L2). All strains were determined to be multidrug resistant and numerous resistance genes to non-β-lactams were observed. In conclusion, this study demonstrates that environmental sources are a potential reservoir of clinically relevant ESBL-producing bacteria that may pose a health risk to humans upon exposure.

Growth and antibiotic resistance acquisition of Escherichia coli in a river that receives treated sewage effluent

Wastewater treatment plants could discharge Escherichia coli and antibiotic resistant bacteria to the environment adjacent to, or downstream of their discharge point. However, their discharge also contains nutrients which could promote growth of E. coli in water environments. This study was done to clarify the potential of growth and antibiotic resistance acquisition of E. coli in a river environment. Levels of E. coli were monitored in a river that receives treated sewage effluent for over four years. River water, periphyton and sediment samples were collected at sites upstream and downstream of treated sewage inflow. Concentrations of E. coli increased in river water and periphyton at the sites downstream of the treated sewage inflow, although levels of E. coli were very low or below detection limit in the treated sewage samples. Concentrations of Chlorophyll a increased at the downstream sites, likely due to nutrient input from the treated sewage. Based on pulsed field gel electrophoresis, identical genotype occurred at multiple sites both upstream and downstream of the treated sewage inflow. However, strains resistant to antibiotics such as ampicillin, cefazolin, ciprofloxacin, and chloramphenicol were more frequently obtained from the downstream sites than the upstream sites. Multidrug resistant E. coli strains were detected in periphyton and sediment samples collected at the downstream sites. Non-resistant strains with PDGE genotype identical to the multi-drug strains were also detected, indicating that E. coli might have become resistant to antibiotics by acquiring resistance genes via horizontal gene transfer. Laboratory incubation experiment showed the growth of E. coli in periphyton or sediment-fed river water samples. These results suggest that the wastewater treatment inflow did not directly provide E. coli to the river water, but could promote the growth of periphyton, which could lead to the elevated levels of E. coli and the emergence of antibiotic resistant E. coli.

Evaluation of virulence factors profiles and antimicrobials resistance of Escherichia coli isolated from bulk tank milk and raw milk filters

Data on the presence of pathogenic Escherichia coli in bulk tank milk (BTM) and raw milk filters (RMF) are not available in Italy and there are few studies worldwide. Therefore, a study under field condition was conducted to assess the presence of E.coli pathogenic and commensal (CoEC) strains in BTM and RMF samples and their associated AMR pattern. One hundred forty-nine E.coli isolates were characterized. Among all the isolates, 53 (35.6%) were classified as pathogenic while the other ones were classified as CoEC. Among the pathogenic ones, 23 (54.7%) were classified as enterotoxigenic E.coli (ETEC), 6 (11.3%) as enteroinvasive E.coli (EIEC), 2 (3.8%) as enteroaggregative E.coli (EAEC), 12 (22.6%) harboured virulence factors (VF) common to ETEC+EIEC, and 2 (3.8%) common to ETEC+EAEC. To our knowledge, it is the first time that ETEC isolates harboring VF associated with EAEC or EIEC are observed in raw milk. These data support the presence of transmission of VFs genes among isolates. None of the isolates showed resistance to three or more antimicrobials. The CoEC role as a vector of AMR was confirmed by the presence of 18% ampicillin- and cephalexin-resistant isolates. The presence of AMR in CoEC supports the role of these bacteria as source of resistance genes. Monitoring raw milk by either BTM or RMF analysis, and the relatively cheap procedure applied to identify E.coli pathotypes can be useful to identify hazards related to the spread of enteric diseases and antimicrobial resistance.

Occurrence of extended-spectrum β-lactamase-producing bacteria in urban Clinton River habitat

OBJECTIVE

The aim of this study was to determine whether Clinton River water is contaminated with antibiotics and is a reservoir of antimicrobial-resistant bacteria.

METHODS

Water samples were taken from two sites of Clinton River. Antimicrobial-resistant bacteria were enumerated on agar plates supplemented with six commonly used antibiotics. Extended-spectrum β-lactamase (ESBL)-producing bacteria were identified using a BD Phoenix™ System and by 16S rRNA gene sequencing. Antimicrobial resistance gene transfer was performed by conjugation studies and the location of genes was determined by Southern hybridisation. Virulence properties of ESBL-producing isolates were determined by assessing their biofilm-forming ability, cellular toxicity, and induction of an inflammatory response in intestinal epithelial (Caco-2) cells.

RESULTS

16S rRNA analysis of water samples showed the presence of potentially pathogenic bacteria (e.g. Shigella flexneri, Klebsiella pneumoniae, Aeromonas punctata and Pseudomonas aeruginosa). Among 64 biochemically identified bacterial isolates tested, 42% were resistant to cefotaxime, 34% to chloramphenicol, 9% to tetracycline, 11% to ciprofloxacin and 9% to gentamicin. Of 27 cefotaxime-resistant isolates, 11 (41%) were ESBL-positive and possessed either bla_CTX-M (n=9), bla_TEM (n=1) or bla_KPC (n=1). Comparative analysis of ESBL gene sequences from Clinton River water bacteria showed 98-100% identity with clinical isolates. ESBL-producing isolates from Clinton River water were found to form biofilms, induced inflammatory cytokines and caused toxicity to epithelial cells.

CONCLUSIONS

Clinton River water contains isolates with ESBL genes identical to clinical isolates and possessing virulence properties, thus it could be a potential reservoir in causing human infections.

Antimicrobial-Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms

Untreated surface waters can be contaminated with a variety of bacteria, including , some of which can be pathogenic for both humans and animals. Therefore, such waters need to be treated before their use in dairy operations to mitigate risks to dairy cow health and milk safety. To understand the molecular ecology of , this study aimed to assess antimicrobial resistance (AMR) in recovered from untreated surface water sources of dairy farms. Untreated surface water samples ( = 240) from 15 dairy farms were collected and processed to isolate . A total of 234 isolates were obtained and further characterized for their serotypes and antimicrobial susceptibility. Of the 234 isolates, 71.4% were pan-susceptible, 23.5% were resistant to one or two antimicrobial classes, and 5.1% were resistant to three or more antimicrobial classes. Whole genome sequence analysis of 11 selected multidrug-resistant isolates revealed AMR genes including and that confer resistance to the critically important extended-spectrum cephalosporins, as well as a variety of plasmids (mainly of the replicon type) and class 1 integrons. Phylogenetic and comparative genome analysis revealed a genetic relationship between some of the sequenced and Shiga toxin-producing O157:H7 (STEC), which warrants further investigation. This study shows that untreated surface water sources contain antimicrobial-resistant which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer. This is another reason why effective water treatment before usage should be routinely done on dairy farm operations.

First detection and genomics analysis of KPC-2-producing Citrobacter isolates from river sediments

The wide spread of carbapenemase-producing Enterobacteriaceae (CPE) in the environment is an emerging environmental issue with potentially-serious public health implications. However, carbapenemase-producing Citrobacter from environment has rarely been investigated. Here we report the isolation and comparative genomics of carbapenemase-producing Citrobacter isolates from river sediment in China. Potential CPE was isolated by selective MacConkey agar plates containing 2 mg/L meropenem. The presence of carbapenemase genes was detected by PCR and sequencing. The clonal relatedness of Klebsiella pneumoniae carbapenemase (KPC-2)-producing Citrobacter isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. Plasmid analysis of KPC-2-producing Citrobacter isolates was performed by S1-PFGE, Southern blotting, and whole genome sequencing. A total of four KPC-2-producing Citrobacter and three Aeromonas isolates were recovered from 54 sediment cultures of Shifeng River. Notably, all KPC-producing isolates were isolated from sampling sites near a waste water treatment plant. Antimicrobial susceptibility testing showed that three of the four sequenced isolates (C1710, C191, and C196) resistant to multiple antibiotics. Genotyping and pan-genome analyses revealed that the C191 and C196 C. freundii isolates exhibited a high level of genetic similarity. Plasmid analysis confirmed that the bla_KPC-2 gene is located on either IncF or IncN3 plasmids in all isolates. The bla_KPC-2 gene of C1710, C181 and C191 was successfully transferred with E. coli EC600 as the recipient strain. In silico analysis further suggested that pKPC-191 is a novel IncF plasmid, with 99% identity to two previously described IncFII plasmids at 71% coverage. We report here the presence of diverse conjugative bla_KPC-2 plasmids from environmental Citrobacter isolates, which poses the possible dissemination of antimicrobial resistance into clinical isolates. To our knowledge, this is the first study to culture and characterize KPC-2-producing Citrobacter isolates from river sediments in China.

Genetic Investigation of Beta-Lactam Associated Antibiotic Resistance Among Escherichia Coli Strains Isolated from Water Sources

Background:

Antimicrobial resistance is an important factor threatening human health. It is widely accepted that antibiotic resistant bacteria such as Escherichia coli (E. coli) released from humans and animals into the water sources, can introduce their resistance genes into the natural bacterial community.

Objective:

The aim of this study was to investigate the prevalence of bla_TEM, bla_CTX, bla_SHV, bla_OXA and bla_VEB associated-antibiotic resistance among E. coli bacteria isolated from different water resources in Iran.

Methods:

The study contained all E. coli strains segregated from different surface water sources. The Kirby-Bauer method and combined discs method was determined in this study for testing antimicrobial susceptibility and strains that produced Extended-Spectrum Beta Lactamases (ESBL), respectively. DNA extraction kit was applied for genomic and plasmid DNA derivation. Finally the frequency of resistant genes including bla_TEM, bla_CTX, bla_SHV, bla_OXA and bla_VEB in ESBL producing isolates were studied by PCR.

Results:

One hundred E. coli strains were isolated and entered in the study. The highest antibiotic resistance was observed on clindamycin (96%). Moreover, 38.5% isolates were ESBL producers. The frequency of different ESBLs genes were 37%, 27%, 27%, and 25% for bla_TEM, bla_CTX, bla_SHV, and bla_OXA, respectively. The bla_VEB wasn’t found in any isolates.

Conclusion:

The study revealed a high prevalence of CTX-M, TEM, SHV and OXA genes among E. coli strains in surface water resources. In conclusion, these results raised a concern regarding the presence and distribution of these threatening factors in surface water sources and its subsequent outcomes.

Environmental Escherichia coli: ecology and public health implications-a review

Escherichia coli is classified as a rod-shaped, Gram-negative bacterium in the family Enterobacteriaceae. The bacterium mainly inhabits the lower intestinal tract of warm-blooded animals, including humans, and is often discharged into the environment through faeces or wastewater effluent. The presence of E. coli in environmental waters has long been considered as an indicator of recent faecal pollution. However, numerous recent studies have reported that some specific strains of E. coli can survive for long periods of time, and potentially reproduce, in extraintestinal environments. This indicates that E. coli can be integrated into indigenous microbial communities in the environment. This naturalization phenomenon calls into question the reliability of E. coli as a faecal indicator bacterium (FIB). Recently, many studies reported that E. coli populations in the environment are affected by ambient environmental conditions affecting their long-term survival. Large-scale studies of population genetics revealed the diversity and complexity of E. coli strains in various environments, which are affected by multiple environmental factors. This review examines the current knowledge on the ecology of E. coli strains in various environments with regard to its role as a FIB and as a naturalized member of indigenous microbial communities. Special emphasis is given on the growth of pathogenic E. coli in the environment, and the population genetics of environmental members of the genus Escherichia. The impact of environmental E. coli on water quality and public health is also discussed.

Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n = 66), sequence type 155 (ST155) complex (n = 9), ST10 complex (n = 9), and ST69 complex (n = 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n = 58), clinically important clonal groups, namely, ST95 complex (n = 18), ST127 complex (n = 8), ST12 complex (n = 6), ST14 complex (n = 6), and ST131 complex (n = 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups.IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.

Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater

To assess public health risks from environmental exposure to Extended-Spectrum β-Lactamases (ESBL)-producing bacteria, it is necessary to have insight in the proportion of relative harmless commensal variants and potentially pathogenic ones (which may directly cause disease). In the current study, 170 ESBL-producing E. coli from Dutch wastewater (n = 82) and surface water (n = 88) were characterized with respect to ESBL-genotype, phylogenetic group, resistance phenotype and virulence markers associated with enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), extraintesinal E. coli (ExPEC), and Shiga toxin-producing E. coli (STEC). Overall, 17.1% of all ESBL-producing E. coli were suspected pathogenic variants. Suspected ExPECs constituted 8.8% of all ESBL-producing variants and 8.3% were potential gastrointestinal pathogens (4.1% EAEC, 1.8% EPEC, 1.2% EIEC, 1.2% ETEC, no STEC). Suspected pathogens were significantly associated with ESBL-genotype CTX-M-15 (X² = 14.7, P < 0.001) and phylogenetic group B2 (X² = 23.5, P < 0.001). Finally, 84% of the pathogenic ESBL-producing E. coli isolates were resistant to three or more different classes of antibiotics. In conclusion, this study demonstrates that the aquatic environment is a potential reservoir of E. coli variants that combine ESBL-genes, a high level of multi-drug resistance and virulence factors, and therewith pose a health risk to humans upon exposure.

Characterization of Pathogenic Escherichia coli in River Water by Simultaneous Detection and Sequencing of 14 Virulence Genes

The occurrence of pathogenic Escherichia coli in environmental waters increases the risk of waterborne disease. In this study, 14 virulence genes in 669 E. coli isolates (549 isolates from the Yamato River in Japan, and 30 isolates from each of the following hosts: humans, cows, pigs, and chickens) were simultaneously quantified by multiplex PCR and dual index sequencing to determine the prevalence of potentially pathogenic E. coli. Among the 549 environmental isolates, 64 (12%) were classified as extraintestinal pathogenic E. coli (ExPEC) while eight (1.5%) were classified as intestinal pathogenic E. coli (InPEC). Only ExPEC-associated genes were detected in human isolates and pig isolates, and 11 (37%) and five (17%) isolates were classified as ExPEC, respectively. A high proportion (63%) of cow isolates possessed Shiga-toxin genes (stx1 or stx2) and they were classified as Shiga toxin-producing E. coli (STEC) or enterohemorrhagic E. coli (EHEC). Among the chicken isolates, 14 (47%) possessed iutA, which is an ExPEC-associated gene. This method can determine the sequences as well as the presence/absence of virulence genes. By comparing the sequences of virulence genes, we determined that sequences of iutA were different among sources and may be useful for discriminating isolates, although further studies including larger numbers of isolates are needed. Results indicate that humans are a likely source of ExPEC strains in the river.

Emissions of Escherichia coli carrying extended-spectrum β-lactamase resistance from pig farms to the surrounding environment

The dissemination of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) from food-producing animals to the surrounding environment has attracted much attention. To determine the emissions of ESBL-producing E. coli from pig farms to the surrounding environment, fecal and environmental samples from six pig farms were collected. In total, 119 ESBL-producing E. coli were isolated from feces, air samples, water, sludge and soil samples. Antibiotic susceptibility testing showed that the ESBL-producing isolates were resistant to multiple antibiotics and isolates of different origin within the same farm showed similar resistance phenotypes. Both CTX-M and TEM ESBL-encoding genes were detected in these isolates. CTX-M-14 and CTX-M-15 were the predominant ESBL genes identified. ESBL producers from feces and environmental samples within the same farm carried similar CTX-M types. The results indicated that the ESBL-producing E. coli carrying multidrug resistance could readily disseminate to the surrounding environment.

Distribution and molecular characterization of genes encoding CTX-M and AmpC β-lactamases in Escherichia coli isolated from an Indian urban aquatic environment

Aquatic environments harboring antibiotic resistant Escherichia coli constitute an important public health concern. Thus, it is important to characterize the resistance genetic elements of waterborne E. coli. It is also important to identify the predominant clonal groups/phylogroups represented by resistant strains to understand the epidemiology of antibiotic resistant E. coli in natural environments, and to identify the role of well-established genotypes in the spread of resistance in a particular geographical area through natural environments. In the present investigation, E. coli strains (n=126) isolated from various points along the river Yamuna traversing through the National Capital Territory of Delhi (India) were grouped phylogenetically. A collection of 61 strains representing all phylogroups was investigated for extended-spectrum β-lactamase (ESBL) and AmpC production. blaTEM, blaSHV and blaCTX-M genes were detected and analyzed, promoter/attenuator mutations associated with chromosomally-mediated AmpC overexpression were identified, and plasmid-mediated ampC was determined. blaTEM was the most widespread (100%) gene followed by bla(CTX-M) (16%), and plasmid-mediated ampC (3%). bla(CTX-M-15) and bla(CMY-42) were identified as the genes encoding CTX-M type ESBL and CIT type AmpC β-lactamases, respectively. CTX-M-15 ESBL phenotype was most common in phylogroup D (50%), followed by phylogroups B1 (30%), and A (20%). E. coli that produce plasmid-mediated AmpC were rare and present only in phylogroup D. Presence of multi β-lactam resistance, bla(CTX-M-15) and bla(CMY-42) in waterborne E. coli belonging to virulence-associated phylogroup D highlights the need for routine surveillance of resistance determinants in aquatic environments. This is also the first report for the presence of bla(CMY-42) in waterborne E. coli.

Dissemination of ESBL-producing Escherichia coli of chicken origin to the nearby river water

The dissemination of drug-resistant bacteria from animal farms to aquatic environments can pose a potential threat to public health. In this study, antimicrobial resistance, resistance genes, and genetic similarity of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli of different origins (chicken feces and upstream and downstream river waters) were analyzed to track the spread of drug-resistant bacteria of animals. The results showed that a total of 29 ESBL-producing E. coli were obtained from 258 samples, and isolation rates of the ESBL-producing E. coli from chicken feces and upstream and downstream waters were 10.7% (16/150), 3.7% (1/27), and 14.8% (12/81), respectively. The ESBL-producing E. coli from upstream water was resistant to 7 antibiotics, but isolates from feces and downstream water had a higher resistance rate. In 29 ESBL-producing E. coli, the most common gene was CTX-M and the SHV gene was not detected. Five ESBL-producing isolates from downstream water showed >90% similarity with the fecal isolates, while the only one isolate from upstream water had <70% similarity with fecal isolates. The results suggest that animal farms' effluent, especially the untreated wastewater, could contribute to the spread of resistance genes.

Presence of multi-drug resistant pathogenic Escherichia coli in the San Pedro River located in the State of Aguascalientes, Mexico

Contamination of surface waters in developing countries is a great concern. Treated and untreated wastewaters have been discharged into rivers and streams, leading to possible waterborne infection outbreaks and may represent a significant dissemination mechanism of antibiotic resistance genes. In this study, the water quality of San Pedro River, the main river and pluvial collector of the Aguascalientes State, Mexico was assessed. Thirty sample locations were tested throughout the River. The main physicochemical parameters of water were evaluated. Results showed high levels of fecal pollution as well as inorganic and organic matter abundant enough to support the heterotrophic growth of microorganisms. These results indicate poor water quality in samples from different locations. One hundred and fifty Escherichia coli were collected and screened by PCR for several virulence genes. Isolates were classified as either pathogenic (n = 91) or commensal (n = 59). The disc diffusion method was used to determine antimicrobial susceptibility to 13 antibiotics. Fifty-two percent of the isolates were resistant to at least one antimicrobial agent and 30.6% were multi-resistant. Eighteen E. coli strains were quinolone resistant of which 16 were multi-resistant. Plasmid-mediated quinolone resistance (PMQR) genes were detected in 12 isolates. Mutations at the Ser-83→Leu and/or Asp-87→Asn in the gyrA gene were detected as well as mutations at the Ser-80→Ile in parC. An E. coli microarray (Maxivirulence V 3.1) was used to characterize the virulence and antimicrobial resistance genes profiles of the fluoroquinolone-resistant isolates. Antimicrobial resistance genes such as bla TEM, sulI, sulII, dhfrIX, aph3 (strA), and tet (B) as well as integrons were found in fluoroquinolone (FQ) resistance E. coli strains. The presence of potential pathogenic E. coli and antibiotic resistance in San Pedro River such as FQ resistant E. coli could pose a potential threat to human and animal health.