Environmental KPC-producing Escherichia coli isolates in Portugal

Tackling Carbapenem Resistance and the Imperative for One Health Strategies-Insights from the Portuguese Perspective

Carbapenemases, a class of enzymes specialized in the hydrolysis of carbapenems, represent a significant threat to global public health. These enzymes are classified into different Ambler's classes based on their active sites, categorized into classes A, D, and B. Among the most prevalent types are IMI/NMC-A, KPC, VIM, IMP, and OXA-48, commonly associated with pathogenic species such as Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The emergence and dissemination of carbapenemase-producing bacteria have raised substantial concerns due to their ability to infect humans and animals (both companion and food-producing) and their presence in environmental reservoirs. Adopting a holistic One Health approach, concerted efforts have been directed toward devising comprehensive strategies to mitigate the impact of antimicrobial resistance dissemination. This entails collaborative interventions, highlighting proactive measures by global organizations like the World Health Organization, the Center for Disease Control and Prevention, and the Food and Agriculture Organization. By synthesizing the evolving landscape of carbapenemase epidemiology in Portugal and tracing the trajectory from initial isolated cases to contemporary reports, this review highlights key factors driving antibiotic resistance, such as antimicrobial use and healthcare practices, and underscores the imperative for sustained vigilance, interdisciplinary collaboration, and innovative interventions to curb the escalating threat posed by antibiotic-resistant pathogens. Finally, it discusses potential alternatives and innovations aimed at tackling carbapenemase-mediated antibiotic resistance, including new therapies, enhanced surveillance, and public awareness campaigns.

Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings

Antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical P. aeruginosa (PAO1) and one clinical K. pneumoniae (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical E. faecium Ef CD1 was extensively drug resistant (XDR); all K. pneumoniae isolates (n = 12) (except K. pneumoniae ATCC 13883) were multidrug resistant (MDR), while the P. aeruginosa (n = 16) isolates exhibited higher susceptibility profiles. The tetM gene (tetracycline resistance) was identified in 47.4 % (n = 6 environmental; n = 3 clinical) of the E. faecium isolates, while the blaKPC gene (carbapenem resistance) was detected in 52.6 % (n = 7 environmental; n = 3 clinical) and 15.4 % (n = 2 environmental) of the E. faecium and K. pneumoniae isolates, respectively. The E. faecium isolates were predominantly poor biofilm formers, the K. pneumoniae isolates were moderate biofilm formers, while the P. aeruginosa isolates were strong biofilm formers. All E. faecium and K. pneumoniae isolates were gamma (γ)-haemolytic, non-gelatinase producing (E. faecium only), and non-hypermucoviscous (K. pneumoniae only), while the P. aeruginosa isolates exhibited beta (β)-haemolysis and produced gelatinase. The fimH (type 1 fimbriae adhesion) and ugE (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the K. pneumoniae isolates, while the P. aeruginosa isolates possessed the phzM (phenazine production) and algD (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical E. faecium, K. pneumoniae, and P. aeruginosa, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.

Freshwater and Marine Environments in California Are a Reservoir of Carbapenem-Resistant Bacteria

Carbapenems are last-resort antibiotics used to treat multidrug-resistant bacterial infections. Resistance to carbapenems has been designated as an urgent threat and is increasing in healthcare settings. However, little is still known about the distribution and characteristics of carbapenem-resistant bacteria (CRB) outside of healthcare settings. Here, we surveyed the distribution of CRB in ten diverse freshwater and seawater environments in California, U.S., ranging from San Luis Obispo County to San Bernardino County, combining both direct isolation and enrichment approaches to increase the diversity of isolated CRB. From the locations surveyed, we selected 30 CRB for further characterization. These isolates were identified as members of the genera Aeromonas, Enterobacter, Enterococcus, Paenibacillus, Pseudomonas, Sphingobacterium, and Stenotrophomonas. These isolates were resistant to carbapenems, other β-lactams, and often to other antibiotics (tetracycline, gentamicin, or ciprofloxacin). We also found that nine isolates belonging to the genera Aeromonas, Enterobacter (blaIMI-2), and Stenotrophomonas (blaL1) produced carbapenemases. Overall, our findings indicate that sampling different types of aquatic environments and combining different isolation approaches increase the diversity of the environmental CRB obtained. Moreover, our study supports the increasingly recognized role of natural water systems as an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including bacteria carrying carbapenemase genes.

A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques

Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.

Carbapenem-resistant Escherichia coli from shrimp and salmon available for purchase by consumers in Canada: a risk profile using the Codex framework

Resistance to carbapenems in human pathogens is a growing clinical and public health concern. The carbapenems are in an antimicrobial class considered last-resort, they are used to treat human infections caused by multidrug-resistant Enterobacterales, and they are classified by the World Health Organization as 'High Priority Critically Important Antimicrobials'. The presence of carbapenem-resistant Enterobacterales (CREs) of animal-origin is of concern because targeted studies of Canadian retail seafood revealed the presence of carbapenem resistance in a small number of Enterobacterales isolates. To further investigate this issue, a risk profile was developed examining shrimp and salmon, the two most important seafood commodities consumed by Canadians and Escherichia coli, a member of the Enterobacterales order. Carbapenem-resistant E. coli (CREc) isolates have been identified in shrimp and other seafood products. Although carbapenem use in aquaculture has not been reported, several classes of antimicrobials are utilised globally and co-selection of antimicrobial-resistant microorganisms in an aquaculture setting is also of concern. CREs have been identified in retail seafood purchased in Canada and are currently thought to be uncommon. However, data concerning CRE or CREc occurrence and distribution in seafood are limited, and argue for implementation of ongoing or periodic surveillance.

KPC-3-, GES-5-, and VIM-1-Producing Enterobacterales Isolated from Urban Ponds

Carbapenems are antibiotics of pivotal importance in human medicine, the efficacy of which is threatened by the increasing prevalence of carbapenem-resistant Enterobacterales (CRE). Urban ponds may be reservoirs of CRE, although this hypothesis has been poorly explored. We assessed the proportion of CRE in urban ponds over a one-year period and retrieved 23 isolates. These were submitted to BOX-PCR, PFGE, 16S rDNA sequencing, antibiotic susceptibility tests, detection of carbapenemase-encoding genes, and conjugation assays. Isolates were affiliated with Klebsiella (n = 1), Raoultella (n = 11), Citrobacter (n = 8), and Enterobacter (n = 3). Carbapenemase-encoding genes were detected in 21 isolates: bla_KPC (n = 20), bla_GES-5 (n = 6), and bla_VIM (n = 1), with 7 isolates carrying two carbapenemase genes. Clonal isolates were collected from different ponds and in different campaigns. Citrobacter F6, Raoultella N9, and Enterobacter N10 were predicted as pathogens from whole-genome sequence analysis, which also revealed the presence of several resistance genes and mobile genetic elements. We found that bla_KPC-3 was located on Tn4401b (Citrobacter F6 and Enterobacter N10) or Tn4401d (Raoultella N9). The former was part of an IncFIA-FII pBK30683-like plasmid. In addition, bla_GES-5 was in a class 3 integron, either chromosomal (Raoultella N9) or plasmidic (Enterobacter N10). Our findings confirmed the role of urban ponds as reservoirs and dispersal sites for CRE.

Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment

The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.

Tracking Klebsiella pneumoniae carbapenemase gene as an indicator of antimicrobial resistance dissemination from a hospital to surface water via a municipal wastewater treatment plant

Antibiotic-resistant bacteria originating from hospitals are ultimately discharged to municipal wastewater treatment plants (WWTP), which may serve as important reservoirs for the spread of antibiotic resistant genes. This study traced and quantified the presence of a rare but clinically relevant antimicrobial resistance gene; Klebsiella pneumoniae carbapenamase (KPC)-and the viable organisms (KPCO) which carried this gene in hospital, non-hospital wastewater discharges, various compartments within a municipal WWTP, receiving water and sediment samples. High concentration of the gene, blaKPC harbored in viable and multispecies KPCO was detected in the hospital wastewater and in the forepart stages of the WWTP, but was not detected in the final effluent following UV disinfection. KPCO were not detected in multiple non-hospital sources of wastewater discharges tested. The treatment train used in the sampled WWTP was found to help remove and reduce KPCO load. Using whole-genome sequencing, a KPC-producing Klebsiella oxytoca strain identical to strains seen in the patients and hospital environment was isolated from the downstream receiving water on one sampling event. KPCO were also found to persist in the biosolids throughout the WWTP, but were not detected in the processed compost-products made from WWTP-biosolids. This study systematically demonstrates dissemination of KPCO from hospital point source to environment via municipal WWTP. Understanding hospitals as the origin and source of spread of some of the most clinically urgent antimicrobial-resistant organisms may help direct interventions that target rate at which antibiotic resistant bacteria evolve and spread via enhancement of wastewater treatment and mitigation of dissemination at source.

Quantitative Risk Assessment for the Introduction of Carbapenem-Resistant Enterobacteriaceae (CPE) into Dutch Livestock Farms

Early detection of emerging carbapenem-resistant Enterobacteriaceae (CPE) in food-producing animals is essential to control the spread of CPE. We assessed the risk of CPE introduction from imported livestock, livestock feed, companion animals, hospital patients, and returning travelers into livestock farms in The Netherlands, including (1) broiler, (2) broiler breeder, (3) fattening pig, (4) breeding pig, (5) farrow-to-finish pig, and (6) veal calf farms. The expected annual number of introductions was calculated from the number of farms exposed to each CPE source and the probability that at least one animal in an exposed farm is colonized. The total number of farms with CPE colonization was estimated to be the highest for fattening pig farms, whereas the probability of introduction for an individual farm was the highest for broiler farms. Livestock feed and imported livestock are the most likely sources of CPE introduction into Dutch livestock farms. Sensitivity analysis indicated that the number of fattening pig farms determined the number of high introductions in fattening pigs from feed, and that uncertainty on CPE prevalence impacted the absolute risk estimate for all farm types. The results of this study can be used to inform risk-based surveillance for CPE in livestock farms.

Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control

Antimicrobial resistant (AMR) bacteria present one of the biggest threats to public health; this must not be forgotten while global attention is focussed on the COVID-19 pandemic. Resistant bacteria have been demonstrated to be transmittable to humans in many different environments, including public settings in urban built environments where high-density human activity can be found, including public transport, sports arenas and schools. However, in comparison to healthcare settings and agriculture, there is very little surveillance of AMR in the built environment outside of healthcare settings and wastewater. In this review, we analyse the existing literature to aid our understanding of what surveillance has been conducted within different public settings and identify what this tells us about the prevalence of AMR. We highlight the challenges that have been reported; and make recommendations for future studies that will help to fill knowledge gaps present in the literature.

Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review

Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.

A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts

E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.

Multidrug-resistant enterobacteriaceae in coastal water: an emerging threat

Background

The environmental role of carbapenemase-producing Enterobacteriaceae (CPE) acquisition and infection in human disease has been described but not thoroughly investigated. We aimed to assess the occurrence of CPE in nearshore aquatic bodies.

Methods

Enterobacteriaceae were cultured from coastal and estuary water near Netanya, Israel in June and July of 2018. Bacteria were identified by VITEK2® and their antimicrobial susceptibility was tested according to the CLSI guidelines. Enterobacteriaceae genomes were sequenced to elucidate their resistome and carbapenemase types.

Results

Among other clinically relevant bacteria, four CPE (three Enterobacter spp and one Escherichia coli isolate) were isolated from two river estuaries (Poleg and Alexander Rivers) and coastal water at a popular recreational beach (Beit Yanai). Molecular analysis and genome sequencing revealed the persistent presence of rare beta-lactamase resistance genes, including bla_IMI-2 and a previously unknown bla_IMI-20 allele, which were not found among the local epidemiological strains. Genome comparisons revealed the high identity of riverine and marine CPE that were cultivated one month apart.

Conclusions

We show that CPE contamination was widespread in nearshore marine and riverine habitats. The high genome-level similarity of riverine and marine CPEs, isolated one month apart, hints at the common source of infection. We discuss the clinical implications of these findings and stress the urgent need to assess the role of the aquatic environment in CPE epidemiology.

The Hydric Environment: A Hub for Clinically Relevant Carbapenemase Encoding Genes

Carbapenems are β-lactams antimicrobials presenting a broad activity spectrum and are considered as last-resort antibiotic. Since the 2000s, carbapenemase producing Enterobacterales (CPE) have emerged and are been quickly globally spreading. The global dissemination of carbapenemase encoding genes (CEG) within clinical relevant bacteria is attributed in part to its location onto mobile genetic elements. During the last decade, carbapenemase producing bacteria have been isolated from non-human sources including the aquatic environment. Aquatic ecosystems are particularly impacted by anthropic activities, which conduce to a bidirectional exchange between aquatic environments and human beings and therefore the aquatic environment may constitute a hub for CPE and CEG. More recently, the isolation of autochtonous aquatic bacteria carrying acquired CEG have been reported and suggest that CEG exchange by horizontal gene transfer occurred between allochtonous and autochtonous bacteria. Hence, aquatic environment plays a central role in persistence, dissemination and emergence of CEG both within environmental ecosystem and human beings, and deserves to be studied with particular attention.

High frequency of gram-negative bacilli harboring blaKPC-2 in the different stages of wastewater treatment plant: A successful mechanism of resistance to carbapenems outside the hospital settings

Wastewater treatment plants (WWTPs) are considered to be a reservoir and a source of bacterial resistance. Worryingly, the presence of carbapenem-resistant Gram-negative bacilli (CRGNB) in WWTPs has recently been reported, but there are still many research gaps regarding its emergence and impact. The distribution of CRGNB in the different stages of a WWTP in Colombia and the relationship between the physicochemical factors involved with their presence are described in this paper. Additionally, given the impact on public health, the CRGNB detected were compared with isolates previously found in hospital patients. Residual water samples were taken from five different stages of a WWTP between January and July 2017. A total of 390 GNB were isolated, and a significant frequency of CRGNB harboring bla_KPC-2 (38.2%, n = 149/390) was detected, of which 57% were Enterobacteriaceae, 41.6% Aeromonadaceae, and 1.3% Pseudomonadaceae. The Enterobacteriaceae were more frequent in the raw effluent compared to the Aeromonadaceae, which in turn were more prevalent in the recycled activated sludge and final effluent. Environmental variables such as pH, oxygen, chemical oxygen demand, and temperature were significantly correlated with the quantification of carbapenem-resistant Enterobacteriaceae (CRE) at specific points in the WWTP. Interestingly, isolated K. pneumoniae harboring bla_KPC-2 from the WWTPs were diverse and did not relate genetically to the hospital strains with which they were compared. In conclusion, these results confirm the worrying scenario of the dissemination and persistence of emerging contaminants such as CRGNB harboring bla_KPC-2, and reinforce the need to establish strategies aimed at containing this problem using multifocal interventions.

Environmental dissemination of carbapenemase-producing Enterobacteriaceae in rivers in Switzerland

The aquatic environment takes on a key role in the dissemination of antimicrobial-resistant Enterobacteriaceae. This study assesses the occurrence of carbapenemase-producing Enterobacteriaceae (CPE) in freshwater samples from rivers, inland canals, and streams throughout Switzerland, and characterizes the isolated strains using phenotypic and NGS-based genotypic methods. CPE producing KPC-2 (n = 2), KPC-3 (n = 1), NDM-5 (n = 3), OXA-48 (n = 3), OXA-181 (n = 6), and VIM-1 (n = 2) were detected in 17/164 of the water samples. Seven Escherichia coli had sequence types (STs) that belonged to extra-intestinal pathogenic clonal lineages ST38, ST73, ST167, ST410, and ST648. The majority (16/17) of the carbapenemase genes were located on plasmids, including the widespread IncC (n = 1), IncFIIA (n = 1), and IncFIIB plasmids (n = 4), the epidemic IncL (n = 1) and IncX3 (n = 5) plasmids, a rare Col156 plasmid (n = 1), and the mosaic IncFIB, IncR, and IncQ plasmids (n = 3). Plasmids were composed of elements that were identical to those of resistance plasmids retrieved from clinical and veterinary isolates locally and worldwide. Our data show environmental dissemination of high-risk CPE clones in Switzerland. Epidemic and mosaic-like plasmids carrying clinically relevant carbapenemase genes are replicating and evolving pollutants of river ecosystems, representing a threat to public health and environmental integrity.

The role of the natural aquatic environment in the dissemination of extended spectrum beta-lactamase and carbapenemase encoding genes: A scoping review

The natural aquatic environment is a significant contributor to the development and circulation of clinically significant antibiotic resistance genes (ARGs). The potential for the aquatic environment to act as a reservoir for ARG accumulation in areas receiving anthropogenic contamination has been thoroughly researched. However, the emergence of novel ARGs in the absence of external influences, as well as the capacity of environmental bacteria to disseminate ARGs via mobile genetic elements remain relatively unchallenged. In order to address these knowledge gaps, this scoping literature review was established focusing on the detection of two important and readily mobile ARGs, namely, extended spectrum beta-lactamase (ESBL) and carbapenemase genes. This review included 41 studies from 19 different countries. A range of different water bodies including rivers (n = 26), seawaters (n = 6) and lakes (n = 3), amongst others, were analysed in the included studies. ESBL genes were reported in 29/41 (70.7%) studies, while carbapenemase genes were reported in 13/41 (31.7%), including joint reporting in 9 studies. The occurrence of mobile genetic elements was evaluated, which included the detection of integrons (n = 22), plasmids (n = 18), insertion sequences (n = 4) and transposons (n = 3). The ability of environmental bacteria to successfully transfer resistance genes via conjugation was also examined in 11 of the included studies. The findings of this scoping review expose the presence of clinically significant ARGs in the natural aquatic environment and highlights the potential ability of environmental isolates to disseminate these genes among different bacterial species. As such, the results presented demonstrate how anthropogenic point discharges may not act as the sole contributor to the development and spread of clinically significant antibiotic resistances. A number of critical knowledge gaps in current research were also identified. Key highlights include the limited number of studies focusing on antibiotic resistance in uncontaminated aquatic environments as well as the lack of standardisation among methodologies of reviewed investigations.

Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: blaNDM, blaKPC and blaGES among the detected genes

Carbapenems are used as last-resort drugs to treat infections caused by multidrug-resistant bacteria. Despite the increasing number of reports of carbapenem-resistant Enterobacteriaceae (CRE), there is still limited information on their distribution or prevalence in the environment. Our aim was to assess the occurrence of CRE in the Lis river (Portugal) and to characterize the genetic platforms linked to carbapenemase genes. We collected six water samples from sites near a wastewater treatment plant (n = 4 samples) and livestock farms (n = 2). Twenty-four CRE were characterized by BOX element-polymerase chain reaction (BOX-PCR), and thirteen representative isolates were analysed by Pulsed-Field Gel Electrophoresis (PFGE) and by sequencing the 16S rRNA gene. Antimicrobial susceptibility testing, PCR screening for carbapenemase-encoding genes, conjugation experiments and plasmid analysis were performed. Four isolates were chosen for whole-genome sequencing. All water samples contained CRE (4.0 CFU/mL on average). Representative isolates were multidrug-resistant (resistant to ciprofloxacin, trimethoprim-sulfamethoxazole and to all β-lactams tested) and were identified as K. pneumoniae, Enterobacter and Citrobacter. Isolates carried plasmids and harboured carbapenemase-encoding genes: bla_KPC-3 in K. pneumoniae (n = 9), bla_NDM-1 in Enterobacter (n = 3) and bla_GES-5 in Citrobacter (n = 1). Conjugation experiments were successful in two Klebsiella isolates. Enterobacter PFGE profiles grouped in one cluster while Klebsiella were divided in three clusters and a singleton. Whole-genome sequencing analysis revealed bla_GES-5 within a novel class 3 integron (In3-16) located on an IncQ/pQ7-like plasmid in Citrobacter freundii CR16. bla_KPC-3 was present on IncFIA-FII pBK30683-like plasmids, which were subsequently confirmed in all K. pneumoniae (n = 9). Furthermore, bla_KPC-3 was part of a genomic island in K. pneumoniae CR12. In E. roggenkampii CR11, bla_NDM-1 was on an IncA/C₂ plasmid. The carbapenemase-encoding plasmids harboured other resistance determinants and mobile genetic elements. Our results demonstrate that Lis river is contaminated with CRE, highlighting the need for monitoring antibiotic resistance in aquatic environments, especially to last-resort drugs.

Urban and agricultural soils in Southern California are a reservoir of carbapenem-resistant bacteria

Carbapenems are last‐resort β‐lactam antibiotics used in healthcare facilities to treat multidrug‐resistant infections. Thus, most studies on identifying and characterizing carbapenem‐resistant bacteria (CRB) have focused on clinical settings. Relatively, little is still known about the distribution and characteristics of CRBs in the environment, and the role of soil as a potential reservoir of CRB in the United States remains unknown. Here, we have surveyed 11 soil samples from 9 different urban or agricultural locations in the Los Angeles–Southern California area to determine the prevalence and characteristics of CRB in these soils. All samples tested contained CRB with a frequency of <10 to 1.3 × 10⁴ cfu per gram of soil, with most agricultural soil samples having a much higher relative frequency of CRB than urban soil samples. Identification and characterization of 40 CRB from these soil samples revealed that most of them were members of the genera Cupriavidus, Pseudomonas, and Stenotrophomonas. Other less prevalent genera identified among our isolated CRB, especially from agricultural soils, included the genera Enterococcus, Bradyrhizobium, Achromobacter, and Planomicrobium. Interestingly, all of these carbapenem‐resistant isolates were also intermediate or resistant to at least 1 noncarbapenem antibiotic. Further characterization of our isolated CRB revealed that 11 Stenotrophomonas, 3 Pseudomonas, 1 Enterococcus, and 1 Bradyrhizobium isolates were carbapenemase producers. Our findings show for the first time that both urban and agricultural soils in Southern California are an underappreciated reservoir of bacteria resistant to carbapenems and other antibiotics, including carbapenemase‐producing CRB.

Environmental Prevalence of Carbapenem Resistance Enterobacteriaceae (CRE) in a Tropical Ecosystem in India: Human Health Perspectives and Future Directives

In the past few decades, infectious diseases have become increasingly challenging to treat, which is explained by the growing number of antibiotic-resistant bacteria. Notably, carbapenem-resistant Enterobacteriaceae (CRE) infections at global level attribute a vast, dangerous clinical threat. In most cases, there are enormous difficulties for CRE infection except a few last resort toxic drugs such as tigecycline and colistin (polymyxin E). Due to this, CRE has now been categorized as one among the three most dangerous multidrug resistance (MDR) pathogens by the US Centres for Disease Control and Prevention (CDC). Considering this, the study of the frequency of CRE infections and the characterization of CRE is an important area of research in clinical settings. However, MDR bacteria are not only present in hospitals but are spreading more and more into the environment, thereby increasing the risk of infection with resistant bacteria outside the hospital. In this context, developing countries are a global concern where environmental regulations are often insufficient. It seems likely that overcrowding, poor sanitation, socioeconomic status, and limited infrastructures contribute to the rapid spread of MDR bacteria, becoming their reservoirs in the environment. Thus, in this review, we present the occurrence of CRE and their resistance determinants in different environmental compartments in India.

Carbapenemase-producing Enterobacteriaceae and Aeromonas spp. present in wastewater treatment plant effluent and nearby surface waters in the US

Carbapenemase-producing bacteria (CPB) are rare, multidrug resistant organisms most commonly associated with hospitalized patients. Metropolitan wastewater treatment plants (WWTP) treat wastewater from large geographic areas which include hospitals and may serve as epidemiologic reservoirs for the maintenance or expansion of CPB that originate from hospitals and are ultimately discharged in treated effluent. However, little is known about the potential impact of these WWTP CPB on the local surface water and their risk to the public health. In addition, CPB that are present in surface water may ultimately disseminate to intensively-managed animal agriculture facilities where there is potential for amplification by extended-spectrum cephalosporins. To better understand the role of WWTPs in the dissemination of CPB in surface waters, we obtained samples of treated effluent, and both upstream and downstream nearby surface water from 50 WWTPs throughout the US. A total of 30 CPB with clinically-relevant genotypes were recovered from 15 WWTPs (30%) of which 13 (50%) serviced large metropolitan areas and 2 (8.3%) represented small rural populations (P < 0.05). Recovery of CPB was lowest among WWTPs that utilized ultraviolet radiation for primary disinfection (12%), and higher (P = 0.11) for WWTPs that used chlorination (42%) or that did not utilize disinfection (50%). We did not detect a difference in CPB recovery by sampling site, although fewer CPB were detected in upstream (8%) compared to effluent (20%) and downstream (18%) samples. Our results indicate that WWTP effluent and nearby surface waters in the US are routinely contaminated with CPB with clinically important genotypes including those producing Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM). This is a concern for both public health and animal agriculture because introduction of CPB into intensively managed livestock populations could lead to their amplification and foodborne dissemination.

Prevalence and characterization of carbapenem-resistant bacteria in water bodies in the Los Angeles-Southern California area

Carbapenems are β-lactam antibiotics used in healthcare settings as last resort drugs to treat infections caused by antibiotic-resistant bacteria. Carbapenem-resistant bacteria are increasingly being isolated from healthcare facilities; however, little is known about their distribution or prevalence in the environment, especially in the United States, where their distribution in water environments from the West Coast has not been studied before. The aim of this study was to determine the prevalence of carbapenem-resistant bacteria and carbapenemase genes in water bodies from the Los Angeles area (California, USA). All samples that were analyzed contained carbapenem-resistant bacteria with a frequency of between 0.1 and 324 carbapenem-resistant cfu per 100 mls of water. We identified 76 carbapenem-resistant or -intermediate isolates, most of which were also resistant to noncarbapenem antibiotics, as different strains of Enterobacter asburiae, Aeromonas veronii, Cupriavidus gilardii, Pseudomonas, and Stenotrophomonas species. Of them, 52 isolates were carbapenemase-producers. Furthermore, PCR and sequence analysis to identify the carbapenemase gene of these carbapenemase-producing isolates revealed that all Enterobacter asburiae isolates had a blaIMI-2 gene 100% identical to the reference sequence, and all Stenotrophomonas maltophlia isolates had a blaL1 gene 83%-99% identical to the reference blaL1 . Our findings indicate that water environments in Southern California are an important reservoir of bacteria-resistant to carbapenems and other antibiotics, including bacteria carrying intrinsic and acquired carbapenemase genes.

River water analysis using a multiparametric approach: Portuguese river as a case study

The Ave River in northern Portugal has a history of riverbanks and water quality degradation. The river water quality was assessed by physicochemical, biological (macroinvertebrates) and microbiological (Enterococcus spp. and Escherichia coli) parameters in six locations (A-F, point A being the nearest to the source) throughout its course during a year. Epilithic biofilms were studied through polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE). Antimicrobial susceptibility testing helped with selecting isolates (n = 149 E. coli and n = 86 enterococci) for further genetic characterization. Pursuant to physicochemical and macroinvertebrates-based parameters, the river water was of reasonable quality according to European legislation (Directive 2000/60/EC). However, the microbiological analysis showed increased fecal contamination downstream from point C. At point D, four carbapenem-resistant E. coli isolates were recovered. Paradoxically, point D was classified as a point of 'Good Water Quality' according to macroinvertebrates results. Point F presented the highest contamination level and incidence of multidrug-resistant (MDR) isolates in the water column (13 MDR enterococci out of 39 and 33 MDR E. coli out of 97). Epilithic biofilms showed higher diversity in pristine points (A and B). Thus, biological and microbiological parameters used to assess the water quality led to divergent results; an outcome that reinforces the need for a holistic evaluation.

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.

Occurrence and persistence of carbapenemases genes in hospital and wastewater treatment plants and propagation in the receiving river

This study aims to investigate the prevalence of clinically relevant carbapenemases genes (bla_KPC, bla_NDM and bla_OXA-48) in water samples collected over one-year period from hospital (H), raw and treated wastewater of two wastewater treatment plants (WWTPs) as well as along the Zenne River (Belgium). The genes were quantified in both particle-attached (PAB) and free-living (FLB) bacteria. Our results showed that absolute abundances were the highest in H waters. Although absolute abundances were significantly reduced in WWTP effluents, the relative abundance (normalized per 16S rRNA) was never lowered through wastewater treatment. Particularly, for the PAB the relative abundances were significantly higher in the effluents respect to the influents of both WWTPs for all the genes. The absolute abundances along the Zenne River increased from upstream to downstream, peaking after the release of WWTPs effluents, in both fractions. Our results demonstrated that bla_KPC, bla_NDM and bla_OXA-48 are widely distributed in the Zenne as a consequence of chronic discharge from WWTPs. To conclude, the levels of carbapenemases genes are significantly lower than other genes conferring resistance to more widely used antibiotics (analyzed in previous studies carried out at the same sites), but could raise up to the levels of high prevalent resistance genes.

VIM-1 carbapenemase-producing Escherichia coli isolated from retail seafood, Germany 2016

Carbapenems belong to the group of last resort antibiotics in human medicine. Therefore, the emergence of growing numbers of carbapenemase-producing bacteria in food-producing animals or the environment is worrying and an important concern for the public health sector. In the present study, a set of 45 Enterobacteriaceae isolated from German retail seafood (clams and shrimps), sampled in 2016, were investigated by real-time PCR for the presence of carbapenemase-producing bacteria. One Escherichia coli (ST10), isolated from a Venus clam (Ruditapes philippinarum) harvested in the Mediterranean Sea (Italy), contained the carbapenemase gene bla_VIM-1 as part of the variable region of a class I integron. Whole-genome sequencing indicated that the integron was embedded in a Tn3-like transposon that also contained the fluoroquinolone resistance gene qnrS1. Additional resistance genes such as the extended-spectrum beta-lactamase bla_SHV-12 and the AmpC gene bla_ACC-1 were also present in this isolate. Except bla_ACC-1, all resistance genes were located on an IncY plasmid. These results confirm previous observations that carbapenemase-producing bacteria have reached the food chain and are of increasing concern for public health.

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.

Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon

Extended-spectrum beta-lactamases (ESBLs) have been recurrently reported in both human and veterinary medicine, and carbapenemases have also emerged in these two sectors. Such resistance phenotypes were increasingly reported in the environment, which both receives and further disseminates multidrug-resistant (MDR) bacteria. Here, we report the high contamination of water samples (68.2%; 15/22) collected in estuaries in Lebanon. From these 15 contaminated sites, a total of 21 ESBL-producing (mostly harbouring the bla_CTX-M-15 gene) and four carbapenemase-producing (two bla_OXA-48 and two bla_OXA-244) Enterobacteriaceae were recovered. ESBL contamination was also identified in water samples collected from rural wells and spring water, although at a lower frequency. Indeed, 1.9% (3/155) and 6.1% (7/115) of the wells and springs were contaminated, respectively, and all identified isolates were CTX-M-15-producing E. coli. Interestingly, sequence types (STs) previously associated both with animal and human reservoirs were detected (ST38, ST10 and ST131), suggesting a complex source of contamination. This situation is alarming since water drawn from wells or springs is directly intended for human consumption in Lebanon without any further treatment. Moreover, even though water from estuaries is not intended for human consumption, it is used to water animals and irrigate crops. Consequently, water contamination by ESBLs and carbapenemases in Lebanon is potentially a major risk to public health. Part of this work was presented at the 7th Symposium on Antimicrobial Resistance in Animals and the Environment (ARAE).

Indistinguishable NDM-producing Escherichia coli isolated from recreational waters, sewage, and a clinical specimen in Ireland, 2016 to 2017

In this study, New Delhi metallo-beta-lactamase (NDM)-producing Enterobacteriaceae were identified in Irish recreational waters and sewage. Indistinguishable NDM-producing Escherichia coli by pulsed-field gel electrophoresis were isolated from sewage, a fresh water stream and a human source. NDM-producing Klebsiella pneumoniae isolated from sewage and seawater in the same area were closely related to each other and to a human isolate. This raises concerns regarding the potential for sewage discharges to contribute to the spread of carbapenemase-producing Enterobacteriaceae.

Carbapenem Resistance: A Review

Carbapenem resistance is a major and an on-going public health problem globally. It occurs mainly among Gram-negative pathogens such as Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, and may be intrinsic or mediated by transferable carbapenemase-encoding genes. This type of resistance genes are already widespread in certain parts of the world, particularly Europe, Asia and South America, while the situation in other places such as sub-Saharan Africa is not well documented. In this paper, we provide an in-depth review of carbapenem resistance providing up-to-date information on the subject.

Troubled water under the bridge: Screening of River Mur water reveals dominance of CTX-M harboring Escherichia coli and for the first time an environmental VIM-1 producer in Austria

Antibiotic resistant bacteria (ARB) in the aquatic environment are reported from all over the world and their presence in the environment has become quite common. The current most prominent example is the presence of beta-lactamases harboring Enterobacteriaceae. The aim of this study was to investigate the presence and diversity (on the genetic and phenotypic levels) of extended spectrum beta-lactamases (ESBL) and carbapenemases harboring Enterobacteriaceae from the River Mur in the center of Graz, Austria's second largest city. Thus over a period of four months water samples were taken, filtrated and screened for these bacteria. All samples revealed ESBL harboring Enterobacteriaceae, of which all with only one exception were Escherichia coli. Dominant ESBL gene family was CTX-M, represented by subgroups CTX-M-1 group, CTX-M-2 group and CTX-M-9 group. Surprisingly co-resistances to non-beta-lactam antibiotics were low, only resistance to trimethoprim was detected in 50% of all (70) isolates. One Klebsiella oxytoca with GES-1 was isolated. To date, GES ESBL has never been reported from Austria before and only rarely from other European countries. Screening for carbapenemase harboring Enterobacteriaceae revealed one Enterobacter cloacae with the gene for VIM-1. Members sharing the same multi-locus-sequence-type (MLST) as well as members of the same rep PCR clusters occurred at different sampling time points. ESBL-harboring Enterobacteriaceae are common in Austrian river water, is dominated by Escherichia coli and CTX-M enzymes. Furthermore, some of the isolates could be linked to different origins.

Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements. We hypothesized that wastewater contributes to the dissemination of carbapenemase-producing Enterobacteriaceae (CPE), and studied this through a cross-sectional observational study of wastewater in the East of England. We isolated clinically relevant species of CPE in untreated and treated wastewater, confirming that waste treatment does not prevent release of CPE into the environment. We observed that CPE-positive plants were restricted to those in direct receipt of hospital waste, suggesting that hospital effluent may play a role in disseminating carbapenem resistance. We postulated that plasmids carrying carbapenemase genes were exchanged between bacterial hosts in sewage, and used short-read (Illumina) and long-read (MinION) technologies to characterize plasmids encoding resistance to antimicrobials and heavy metals. We demonstrated that different CPE species (Enterobacter kobei and Raoultella ornithinolytica) isolated from wastewater from the same treatment plant shared two plasmids of 63 and 280 kb. The former plasmid conferred resistance to carbapenems (bla_OXA-48), and the latter to numerous drug classes and heavy metals. We also report the complete genome sequence for Enterobacter kobei. Small, portable sequencing instruments such as the MinION have the potential to improve the quality of information gathered on antimicrobial resistance in the environment.

Carbapenemase-producing enterobacteriaceae recovered from a Spanish river ecosystem

The increasing resistance to carbapenems is an alarming threat in the fight against multiresistant bacteria. The dissemination properties of antimicrobial resistance genes are supported by their detection in a diverse population of bacteria, including strains isolated from the environment. The objective of this study was to investigate the presence of carbapenemase-producing Enterobacteriaceae (CPE) collected from a river ecosystem in the Barcelona metropolitan area (Spain). Identification of β-lactamases and other resistance determinants was determined as was the antimicrobial susceptibility profile. Moreover, screening of virulence factors, plasmid addiction systems, plasmid partition systems and replicon typing was performed. The results identified 8 isolates belonging to different species (Escherichia coli, Enterobacter cloacae, Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica). The most prevalent enzyme was KPC-2 (n = 6), followed by VIM-1 (n = 2) and IMI-2 (n = 1), whereas no OXA-48-type was detected. In addition, one strain was positive for both KPC-2 and VIM-1 enzymes. All the carbapenemase-encoding plasmids carried at least one plasmid addiction or partition system, being vagCD and parAB the most frequently detected, respectively. E. coli and K. pneumoniae isolates carried a low number of virulence-associated factors and none of the detected clones has previously been identified in the clinical setting. These findings support the high dissemination potential of the carbapanemase-encoding genes and reinforce the idea that the environment is another reservoir that may play an important role in the capture, selection and dissemination of carbapenem resistance genes.

Discharge of KPC-2 genes from the WWTPs contributed to their enriched abundance in the receiving river

At present, very little is known about the persistence and spread pathway of KPC-2 genes in the environment. Our previous study reported the prevalence and persistence of KPC-2 genes in wastewater treatment plants (WWTPs). In the present work, we investigated the occurrence and fate of KPC-2 genes in a WWTP discharge-receiving river and studied the effect of WWTP discharges on the prevalence of KPC-2 genes and host bacteria in the receiving river. It is observed that a considerable level of KPC-2 genes occurred in the receiving river, and a significant increase of bla_KPC-2 abundance in the downstream following WWTP discharge was observed compared to the upstream. Furthermore, opportunistic pathogens with 100% identical bla_KPC-2 sequence, like Escherichia coli and Kluyvera georgiana, were isolated from both WWTP and its receiving water, whereas no bla_KPC-2 carrying bacteria was detected in the upstream. These findings indicated that the treated wastewater discharges have a considerable influence on bla_KPC-2 levels in the receiving river. Interestingly, there is no correlation between concentrations of antibiotics and bla_KPC-2 concentrations, demonstrating that the increase of KPC-2 genes in the receiving river is mainly due to WWTP release. This finding is important because it illustrates a significant pathway for KPC-2 gene proliferation to the environment.

Genetically unrelated multidrug- and carbapenem-resistant Citrobacter freundii detected in outpatients admitted to a Portuguese hospital

OBJECTIVES

Non-clonal, carbapenem- and multidrug-resistant Citrobacter freundii isolates were collected from unrelated outpatients admitted to a Portuguese hospital emergency department. One patient lived in a nursing home and was never hospitalised, whereas the other patient was repeatedly hospitalised in this hospital. The aim of this study was to unveil the molecular mechanisms associated with the carbapenem resistance of these isolates and to assess its potential dissemination.

METHODS

Isolate identification was performed by VITEK^®2 and was confirmed by 16S rDNA sequencing. The clonal relationship of the isolates was evaluated by repetitive element palindromic PCR (rep-PCR). Antibiotic susceptibility was determined using the automatic VITEK^®2 AES system and disk diffusion assay. β-Lactamases, porins and mobile genetic elements were characterised by PCR and sequencing. Pulsed-field gel electrophoresis (PFGE) and Southern blot hybridisation were used to determine the genetic location of integrons, and their transferability was tested by conjugation.

RESULTS

No genetic relatedness was found, suggesting different origins of the isolates. In isolate Cf254 a VIM-2 carbapenemase integrated in In58 was detected, located in a high-frequency conjugative IncL/M plasmid that also carried CTX-M-15 and CMY-39 genes. VIM-1 in isolate Cf872 was chromosomal. This is the first description in Portugal of VIM carbapenemases in C. freundii. Loss/alteration of porins was also detected.

CONCLUSIONS

Emergence of carbapenem-resistant Enterobacteria is not confined to the nosocomial environment. Community-acquired strains appear to be in circulation between inpatients and outpatients, spreading carbapenem resistance genes by horizontal gene transfer.

Enterobacteriaceae Isolated from the River Danube: Antibiotic Resistances, with a Focus on the Presence of ESBL and Carbapenemases

In a clinical setting it seems to be normal these days that a relevant proportion or even the majority of different bacterial species has already one or more acquired antibiotic resistances. Unfortunately, the overuse of antibiotics for livestock breeding and medicine has also altered the wild-type resistance profiles of many bacterial species in different environmental settings. As a matter of fact, getting in contact with resistant bacteria is no longer restricted to hospitals. Beside food and food production, the aquatic environment might also play an important role as reservoir and carrier. The aim of this study was the assessment of the resistance patterns of Escherichia coli and Klebsiella spp. out of surface water without prior enrichment and under non-selective culture conditions (for antibiotic resistance). In addition, the presence of clinically important extended spectrum beta lactamase (ESBL) and carbapenmase harboring Enterobacteriaceae should be investigated. During Joint Danube Survey 3 (2013), water samples were taken over the total course of the River Danube. Resistance testing was performed for 21 different antibiotics. Samples were additionally screened for ESBL or carbapenmase harboring Enterobacteriaceae. 39% of all isolated Escherichia coli and 15% of all Klebsiella spp. from the river Danube had at least one acquired resistance. Resistance was found against all tested antibiotics except tigecycline. Taking a look on the whole stretch of the River Danube the proportion of multiresistances did not differ significantly. In total, 35 ESBL harboring Enterobacteriaceae, 17 Escherichia coli, 13 Klebsiella pneumoniae and five Enterobacter spp. were isolated. One Klebsiella pneumoniae harboring NMD-1 carbapenmases and two Enterobacteriaceae with KPC-2 could be identified. Human generated antibiotic resistance is very common in E. coli and Klebsiella spp. in the River Danube. Even isolates with resistance patterns normally associated with intensive care units are present.

Outbreak of KPC-3-producing ST15 and ST348 Klebsiella pneumoniae in a Portuguese hospital

To date, only a few sporadic cases of infections due to Klebsiella pneumoniae carbapenemase (KPC) producers have been reported in Portugal. Here, we report for the first time an outbreak of K. pneumoniae KPC-3 producers in a tertiary-care hospital during 2013. Twenty-seven ertapenem-resistant K. pneumoniae were identified in patients at a tertiary-care hospital during 2013 isolated predominantly from urine (48·1%) and blood (25·9%) cultures. All isolates were highly resistant to β-lactam antibiotics and most showed intermediate resistance to imipenem. The more frequent β-lactamases were TEM- (77·7%), CTX-M- (70·3%) and KPC-type (66·6%). KPC-3 was identified by sequencing. The bla KPC-3 gene was associated with an IncF plasmid, and efficiently transferred to E. coli J53. Pulsed-field gel electrophoresis typing revealed three clusters of isolates which were further characterized by multi-locus sequence typing as ST11, ST15 and ST348. Ertapenem-resistant ST15 was already in circulation in the hospital, related to expression of OmpK36 modified porin, but the other two sequence types had not been previously found in the hospital. We conclude that the IncF plasmid mediated transfer of KPC-3 in the outbreak and that implementation of carbapenemase gene screening in isolates from patients on admission to hospital is advisable in order to control dissemination of these antimicrobial resistance elements.

KPC-3-Producing Klebsiella pneumoniae in Portugal Linked to Previously Circulating Non-CG258 Lineages and Uncommon Genetic Platforms (Tn4401d-IncFIA and Tn4401d-IncN)

KPC-3-producing bacteria are endemic in many countries but only recently became apparent their wide distribution in different Portuguese hospitals. The aim of this study is to characterize genetic backgrounds associated with bla KPC-3 among Klebsiella pneumoniae isolates recently identified on non-hospitalized patients in Portugal. Twenty KPC-producing K. pneumoniae identified between October 2014 and November 2015 in three different community laboratories were characterized. Isolates were mainly from patients from long-term care facilities (n = 11) or nursing homes (n = 6), most of them (75%) previously hospitalized in different Portuguese hospitals. Standard methods were used for bacterial identification and antibiotic susceptibility testing. Carbapenemase production was assessed by the Blue-Carba test, and identification of bla genes was performed by PCR and sequencing. Epidemiological features of KPC-producing K. pneumoniae included population structure (XbaI-PFGE, MLST and wzi sequencing), genetic context (mapping of Tn4401), and plasmid (replicon typing, S1-PFGE, and hybridization) analysis. All K. pneumoniae isolates produced KPC-3, with two MDR K. pneumoniae epidemic clones representing 75% of the isolates, namely ST147 (wzi64/K14.64, February-November 2015) and ST15 (two lineages exhibiting capsular types wzi19/K19 or wzi93/K60, July-November 2015). Other sporadic clones were detected: ST231 (n = 3; wzi104), ST348 (n = 1; wzi94) and ST109 (n = 1, wzi22/K22.37). bla KPC-3 was identified within Tn4401d in all isolates, located in most cases (80%) on cointegrated plasmids (repA FIA+repA FII+ori ColE1;105-250 kb) or in 50 kb IncN plasmids. In conclusion, this study highlights a polyclonal structure of KPC-3-producing K. pneumoniae and the predominance of the ST147 clone among non-hospitalized patients in Portugal, linked to platforms still unnoticed in Europe (bla KPC-3-Tn4401d-IncFIA) or firstly reported (bla KPC-3-Tn4401d-IncN). This scenario underlines the recent penetration of successful mobile genetic elements in previously circulating MDR K. pneumoniae lineages (mainly ST147 and ST15) in Portugal, rather than the importation of the global lineages from clonal group 258.

Prevalence and Fate of Carbapenemase Genes in a Wastewater Treatment Plant in Northern China

Carbapenemase-producing strains of bacteria, which were primarily found in the medical field, have increasingly been found in the environment, thus posing potential risks to public health. One possible way for carbapenemase genes to enter the environment is via wastewater. Therefore, the goal of this study was to determine the occurrence and fate of five high-risk carbapenemase genes in a wastewater treatment plant (WWTP) in northern China using real-time qPCR. Results showed that the bla_KPC-2, bla_GES-1, and bla_IMP-1 genes prevailed throughout all processing stages (even in the chlorination disinfection unit) in the WWTP, whereas the bla_VIM-2 and bla_OXA-48 genes were not detected in all samples. Worryingly, considerable amounts of carbapenemase genes ((1.54 ± 0.61) × 10³ copies/mL to (2.14± 0.41) × 10⁵ copies/mL) were detected in WWTP effluent samples, while the majority of the carbapenemase genes were transported to the dewatered sludge with concentrations from (6.51 ± 0.14) × 10⁹ copies/g to (6.18 ± 0.63) × 10¹⁰ copies/g dry weight. Furthermore, a total of 97 KPC-2-producing strains, belonging to 8 bacterial genera, were isolated from the WWTP. Sequencing of 16S rRNA revealed that most of KPC-2 producing isolates were opportunistic pathogens, including Klebsiella spp. (10.3%), Enterococcus spp. (11.3%), Acinetobacter spp. (19.6%), Escherichia spp. (12.4%), Shigella spp. (17.5%), Stenotrophomonas spp. (10.3%) and Wautersiella spp. (9.3%). Moreover, bla_KPC-2 genes were identified for the first time in Paenibacillus spp. isolates (an indigenous bacteria), indicating an increased risk of horizontal transfer between clinical pathogens and environmental bacteria. Indeed, a conjugation experiment demonstrated transfer of the bla_KPC-2 gene to an E.coli J53 strain from a Klebsiella strain isolated from the WWTP. To our knowledge, this is the first study to obtain Paenibacillus spp. isolates carrying the carbapenemase gene and to quantify the abundance of carbapenemase genes in the environment.

Structural and Functional Aspects of Class A Carbapenemases

The fight against infectious diseases is probably one of the greatest public health challenges faced by our society, especially with the emergence of carbapenem-resistant gram-negatives that are in some cases pan-drug resistant. Currently,β-lactamase-mediated resistance does not spare even the newest and most powerful β-lactams (carbapenems), whose activity is challenged by carbapenemases. The worldwide dissemination of carbapenemases in gram-negative organisms threatens to take medicine back into the pre-antibiotic era since the mortality associated with infections caused by these "superbugs" is very high, due to limited treatment options. Clinically-relevant carbapenemases belong either to metallo-β- lactamases (MBLs) of Ambler class B or to serine-β-lactamases (SBLs) of Ambler class A and D enzymes. Class A carbapenemases may be chromosomally-encoded (SME, NmcA, SFC-1, BIC-1, PenA, FPH-1, SHV-38), plasmid-encoded (KPC, GES, FRI-1) or both (IMI). The plasmid-encoded enzymes are often associated with mobile elements responsible for their mobilization. These enzymes, even though weakly related in terms of sequence identities, share structural features and a common mechanism of action. They variably hydrolyse penicillins, cephalosporins, monobactams, carbapenems, and are inhibited by clavulanate and tazobactam. Three-dimensional structures of class A carbapenemases, in the apo form or in complex with substrates/inhibitors, together with site-directed mutagenesis studies, provide essential input for identifying the structural factors and subtle conformational changes that influence the hydrolytic profile and inhibition of these enzymes. Overall, these data represent the building blocks for understanding the structure-function relationships that define the phenotypes of class A carbapenemases and can guide the design of new molecules of therapeutic interest.

Emergence of KPC-2-producing Escherichia coli isolates in an urban river in Harbin, China

Three KPC-2-producing Escherichia coli (E1, E2, and E3) were recovered from water samples of an urban river in the city of Harbin, China. Antimicrobial susceptibility was determined by broth microdilution. Molecular characterization and genetic relatedness of the isolates were determined by polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and PCR-directed phylotyping. Plasmids were analyzed by conjugation, S1-PFGE, Southern blotting and PCR-based replicon typing (PBRT). The genetic environment of the bla KPC-2 gene was determined using PCR and sequencing. PCR analyses revealed that the E1 isolate carried the bla KPC-2, bla CMY-2, bla TEM-1, bla CTX-M-14, and qnrB2 genes and belonged to sequence type ST410, phylogenetic type A; the E2 isolate was assigned to ST131-B2 and carried the bla KPC-2, bla TEM-1, bla CTX-M-3, bla DHA-1, aac(6')-Ib-cr, and qnrS1 genes; while the E3 isolate was of ST648-D and possessed bla KPC-2, bla TEM-1, bla OXA-1, bla CTX-M-15, armA, and aac(6')-Ib-cr genes. PFGE demonstrated that each of the three KPC-2-producing E. coli isolates exhibited an individual XbaI patterns. The bla KPC-2 gene was located on plasmids of 60-140 kb with IncA/C, IncN, or non-typeable replicon types. The genetic environment of bla KPC-2 of the three strains was consistent with the genetic structure of bla KPC-2 on the plasmid pKP048.

Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases

Klebsiella pneumoniae carbapenemases (KPCs) were originally identified in the USA in 1996. Since then, these versatile β-lactamases have spread internationally among Gram-negative bacteria, especially K pneumoniae, although their precise epidemiology is diverse across countries and regions. The mortality described among patients infected with organisms positive for KPC is high, perhaps as a result of the limited antibiotic options remaining (often colistin, tigecycline, or aminoglycosides). Triple drug combinations using colistin, tigecycline, and imipenem have recently been associated with improved survival among patients with bacteraemia. In this Review, we summarise the epidemiology of KPCs across continents, and discuss issues around detection, present antibiotic options and those in development, treatment outcome and mortality, and infection control. In view of the limitations of present treatments and the paucity of new drugs in the pipeline, infection control must be our primary defence for now.