Characteristics of extended-spectrum β-lactamase (ESBL)- and pAmpC beta-lactamase-producing Enterobacteriaceae of water samples in Tunisia

Extended-spectrum β-lactamase-producing bacteria and their resistance determinants in different wastewaters and rivers in Nepal

Wastewaters serve as significant reservoirs of antibiotic resistant bacteria. Despite the evidence of antimicrobial resistance in wastewaters and river water in Kathmandu, direct linkage between them is not discussed yet. This study investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing bacteria and associated resistance genes in wastewaters and river water. Out of 246 bacteria from wastewaters, 57.72% were ESBL producers and 77.64% of them were multidrug resistant (MDR). ESBL producing E. coli was dominant in municipal and hospital wastewaters (HWW) as well as in river water while K. pneumoniae was common in pharmaceutical wastewater. The blaSHV and blaTEM genes were prevalent and commonly co-occurred with aac(6')-Ib-cr in K. pneumoniae isolated pharmaceutical wastewater. blaCTX-M carrying E. coli from hospital co-harbored aac(6')-Ib-cr while that from municipal influent and river water co-harbored qnrS. Whole genome sequencing data revealed the presence of diverse ARGs in bacterial isolates against multiple antibiotics. In average, an E. coli and a K. pneumoniae isolate contained 55.75 ± 0.96 and 40.2 ± 5.36 ARGs, respectively. Multi-locus sequence typing showed the presence of globally high-risk clones with wider host range such as E. coli ST10, and K. pneumoniae ST15 and ST307 in HWW and river indicating frequent dissemination of antimicrobial resistance in wastewater of Kathmandu. Whole genome sequence data aligned with phenotypic antibiograms and resistance genes detected by PCR in selected isolates. The presence of significant plasmid replicons (IncF, IncY) and mobile genetic elements (IS903, IS26) indicate high frequency of spreading antibiotic resistance. These findings indicate burden and dissemination of antimicrobial resistance in the environment and highlight the need for effective strategies to mitigate the antibiotic resistance.

Occurrence and persistence of multidrug-resistant Enterobacterales isolated from urban, industrial and surface water in Monastir, Tunisia

The One Health approach of antimicrobial resistance highlighted the role of the aquatic environment as a reservoir and dissemination source of resistance genes and resistant bacteria, especially due to anthropogenic activities. Resistance to extended-spectrum cephalosporins (ESC) conferred by extended-spectrum beta-lactamases (ESBLs) in E. coli has been proposed as the major marker of the AMR burden in cross-sectoral approaches. In this study, we investigated wastewater, surface water and seawater that are subjected to official water quality monitoring in Monastir, Tunisia. While all but one sample were declared compliant according to the official tests, ESC-resistant bacteria were detected in 31 (19.1 %) samples. Thirty-nine isolates, coming from urban, industrial and surface water in Monastir, were collected and characterized using antibiograms and whole-genome sequencing. These isolates were identified as 27 Escherichia coli (69.3 %) belonging to 13 STs, 10 Klebsiella pneumoniae (25.6 %) belonging to six STs, and two Citrobacter freundii (5.1 %). We observed the persistence and dissemination of clones over time and in different sampling sites, and no typically human-associated pathogens could be identified apart from one ST131. All isolates presented a blaCTX-M gene - blaCTX-M-15 (n = 22) and blaCTX-M-55 (n = 8) being the most frequent variants - which were identified on plasmids (n = 20) or on the chromosome (n = 19). In conclusion, we observed ESC resistance in rather ubiquitous bacteria that are capable of surviving in the water environment. This suggests that including the total coliform count and the ESBL count as determined by bacterial growth on selective plates in the official monitoring would greatly improve water quality control in Tunisia.

Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools

BACKGROUND

Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches.

RESULTS

We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome.

CONCLUSIONS

This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.

Wastewater treatment plants, an "escape gate" for ESCAPE pathogens

Antibiotics are an essential tool of modern medicine, contributing to significantly decreasing mortality and morbidity rates from infectious diseases. However, persistent misuse of these drugs has accelerated the evolution of antibiotic resistance, negatively impacting clinical practice. The environment contributes to both the evolution and transmission of resistance. From all anthropically polluted aquatic environments, wastewater treatment plants (WWTPs) are probably the main reservoirs of resistant pathogens. They should be regarded as critical control points for preventing or reducing the release of antibiotics, antibiotic-resistant bacteria (ARB), and antibiotic-resistance genes (ARGs) into the natural environment. This review focuses on the fate of the pathogens Enterococcus faecium, Staphylococcus aureus, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae spp. (ESCAPE) in WWTPs. All ESCAPE pathogen species, including high-risk clones and resistance determinants to last-resort antibiotics such as carbapenems, colistin, and multi-drug resistance platforms, were detected in wastewater. The whole genome sequencing studies demonstrate the clonal relationships and dissemination of Gram-negative ESCAPE species into the wastewater via hospital effluents and the enrichment of virulence and resistance determinants of S. aureus and enterococci in WWTPs. Therefore, the efficiency of different wastewater treatment processes regarding the removal of clinically relevant ARB species and ARGs, as well as the influence of water quality factors on their performance, should be explored and monitored, along with the development of more effective treatments and appropriate indicators (ESCAPE bacteria and/or ARGs). This knowledge will allow the development of quality standards for point sources and effluents to consolidate the WWTP barrier role against the environmental and public health AR threats.

Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France

Antibiotic resistance is a worldwide public health concern and has been associated with reports of elevated mortality. According to the One Health concept, antibiotic resistance genes are transferrable to organisms, and organisms are shared among humans, animals, and the environment. Consequently, aquatic environments are a possible reservoir of bacteria harboring antibiotic resistance genes. In our study, we screened water and wastewater samples for antibiotic resistance genes by culturing samples on different types of agar media. Then, we performed real-time PCR to detect the presence of genes conferring resistance to beta lactams and colistin, followed by standard PCR and gene sequencing for verification. We mainly isolated Enterobacteriaceae from all samples. In water samples, 36 Gram-negative bacterial strains were isolated and identified. We found three extended-spectrum β-lactamase (ESBL)-producing bacteria-Escherichia coli and Enterobacter cloacae strains-harboring the CTX-M and TEM groups. In wastewater samples, we isolated 114 Gram-negative bacterial strains, mainly E. coli, Klebsiella pneumoniae, Citrobacter freundii and Proteus mirabilis strains. Forty-two bacterial strains were ESBL-producing bacteria, and they harbored at least one gene belonging to the CTX-M, SHV, and TEM groups. We also detected carbapenem-resistant genes, including NDM, KPC, and OXA-48, in four isolates of E. coli. This short epidemiological study allowed us to identify new antibiotic resistance genes present in bacterial strains isolated from water in Marseille. This type of surveillance shows the importance of tracking bacterial resistance in aquatic environments. IMPORTANCE Antibiotic-resistant bacteria are involved in serious infections in humans. The dissemination of these bacteria in water, which is in close contact with human activities, is a serious problem, especially under the concept of One Health. This study was done to survey and localize the circulation of bacterial strains, along with their antibiotic resistance genes, in the aquatic environment in Marseille, France. The importance of this study is to monitor the frequency of these circulating bacteria by creating and surveying water treatments.

Xenogenetic evolutionary of integrons promotes the environmental pollution of antibiotic resistance genes - Challenges, progress and prospects

Environmental pollution of antibiotic resistance genes (ARGs) has been a great public concern. Integrons, as mobile genetic elements, with versatile gene acquisition systems facilitate the horizontal gene transfer (HGT) and pollution disseminations of ARGs. However, little is understood about the characteristics of ARGs mediated by integrons, which hampers our monitoring and control of the mobile antimicrobial resistance risks. To address these issues, we reviewed 3,322 publications concerning detection methods and pipeline, ARG diversity and evolutionary progress, environmental and geographical distribution, bacterial hosts, gene cassettes arrangements, and based on which to identify ARGs with high risk levels mediated by integrons. Diverse ARGs of 516 subtypes attributed to 12 types were capable of being carried by integrons, with 62 core ARG subtypes prevalent in pollution source, natural and human-related environments. Hosts of ARG-carrying integrons reached 271 bacterial species, most frequently carried by opportunistic pathogens Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae. Moreover, the observed emergence of ARGs together with their multiple arrangements indicated the accumulation of ARGs mediated by integrons, and thus pose increasing HGT risks under modern selective agents. With the concerns of public health, we urgently call for a better monitoring and control of these high-risk ARGs. Our identified Risk Rank I ARGs (aacA7, blaOXA10, catB3, catB8, dfrA5) with high mobility, reviewed key trends and noteworthy advancements, and proposed future directions could be reference and guidance for standard formulation.

Marine bioactive compounds as antibiofilm agent: a metabolomic approach

The ocean is a treasure trove of both living and nonliving creatures, harboring incredibly diverse group of organisms. A plethora of marine sourced bioactive compounds are discovered over the past few decades, many of which are found to show antibiofilm activity. These are of immense clinical significance since the formation of microbial biofilm is associated with the development of high antibiotic resistance. Biofilms are also responsible to bring about problems associated with industries. In fact, the toilets and wash-basins also show degradation due to development of biofilm on their surfaces. Antimicrobial resistance exhibited by the biofilm can be a potent threat not only for the health care unit along with industries and daily utilities. Various recent studies have shown that the marine members of various kingdom are capable of producing antibiofilm compounds. Many such compounds are with unique structural features and metabolomics approaches are essential to study such large sets of metabolites. Associating holobiome metabolomics with analysis of their chemical attribute may bring new insights on their antibiofilm effect and their applicability as a substitute for conventional antibiotics. The application of computer-aided drug design/discovery (CADD) techniques including neural network approaches and structured-based virtual screening, ligand-based virtual screening in combination with experimental validation techniques may help in the identification of these molecules and evaluation of their drug like properties.

Antimicrobial resistance, Extended-Spectrum β-Lactamase production and virulence genes in Salmonella enterica and Escherichia coli isolates from estuarine environment

The impact of antimicrobial resistance (AMR) on global public health has been widely documented. AMR in the environment poses a serious threat to both human and animal health but is frequently overlooked. This study aimed to characterize the association between phenotype and genotype of AMR, virulence genes and Extended-Spectrum β-Lactamase (ESBL) production from estuarine environment. The Salmonella (n = 126) and E. coli (n = 409) were isolated from oysters and estuarine water in Thailand. The isolates of Salmonella (96.9%) and E. coli (91.4%) showed resistance to at least one antimicrobial agent. Multidrug resistance (MDR) was 40.1% of Salmonella and 23.0% of E. coli. Resistance to sulfamethoxazole was most common in Salmonella (95.2%) and E. coli (77.8%). The common resistance genes found in Salmonella were sul3 (14.3%), followed by blaTEM (11.9%), and cmlA (11.9%), while most E. coli were blaTEM (31.5%) and tetA (25.4%). The ESBL production was detected in Salmonella (1.6%, n = 2) of which one isolate was positive to blaTEM-1. Eight E. coli isolates (2.0%) were ESBL producers, of which three isolates carried blaCTX-M-55 and one isolate was blaTEM-1. Predominant virulence genes identified in Salmonella were invA (77.0%), stn (77.0%), and fimA (69.0%), while those in E. coli isolates were stx1 (17.8%), lt (11.7%), and stx2 (1.2%). Logistic regression models showed the statistical association between resistance phenotype, virulence genes and ESBL production (p < 0.05). The findings highlighted that estuarine environment were potential hotspots of resistance. One Health should be implemented to prevent AMR bacteria spreading.

Antibiotic resistomes and their chemical residues in aquatic environments in Africa

The aquatic environment is a hotspot for the transfer of antibiotic resistance to humans and animals. Several reviews have put together research efforts on the presence and distribution of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic chemical residue (ACRs) in food, hospital wastewater, and even in other aquatic environments. However, these reports are largely focused on data from developed countries, while data from developing countries and especially those in Africa, are only marginally discussed. This review is the first effort that distills information on the presence and distribution of ARGs and ACRs in the African aquatic environments (2012-2021). This review provides critical information on efforts put into the study of ARB, ARGs, and ACRs in aquatic environments in Africa through the lens of the different sub-regions in the continent. The picture provided is compared with those from some other continents in the world. It turns out that the large economies in Africa (South Africa, Nigeria, Tunisia, Kenya) all have a few reports of ARB and ARGs in their aquatic environment while smaller economies in the continent could barely provide reports of these in their aquatic environment (in most cases no report was found) even though they have some reports on resistomes from clinical studies. Interestingly, the frequency of these reports of ARB and ARGs in aquatic environments in Africa suggests that the continent is ahead of the South American continent but behind Europe and Asia in relation to providing information on these contaminants. Common ARGs found in African aquatic environment encode resistance to sulfonamide, tetracycline, β-lactam, and macrolide classes of antibiotics. The efforts and studies from African scientists in eliminating ARB and ARGs from the aquatic environment in Africa are also highlighted. Overall, this document is a ready source of credible information for scientists, policy makers, governments, and regional bodies on ARB, ARGs, and ACRs in aquatic environments in Africa. Hopefully, the information provided in this review will inspire some necessary responses from all stakeholders in the water quality sector in Africa to put in more effort into providing more scientific evidence of the presence of ARB, ARGs, and ACRs in their aquatic environment and seek more efficient ways to handle them to curtail the spread of antibiotic resistance among the population in the continent. This will in turn, put the continent on the right path to meeting the United Nations Sustainable Development Goals #3 and #6, which at the moment, appears to be largely missed by most countries in the continent.

Clinically Relevant β-Lactam Resistance Genes in Wastewater Treatment Plants

Antimicrobial resistance (AMR) is one of the largest global concerns due to its influence in multiple areas, which is consistent with One Health's concept of close interconnections between people, animals, plants, and their shared environments. Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) circulate constantly in various niches, sediments, water sources, soil, and wastes of the animal and plant sectors, and is linked to human activities. Sewage of different origins gets to the wastewater treatment plants (WWTPs), where ARB and ARG removal efficiency is still insufficient, leading to their transmission to discharge points and further dissemination. Thus, WWTPs are believed to be reservoirs of ARGs and the source of spreading AMR. According to a World Health Organization report, the most critical pathogens for public health include Gram-negative bacteria resistant to third-generation cephalosporins and carbapenems (last-choice drugs), which represent β-lactams, the most widely used antibiotics. Therefore, this paper aimed to present the available research data for ARGs in WWTPs that confer resistance to β-lactam antibiotics, with a particular emphasis on clinically important life-threatening mechanisms of resistance, including extended-spectrum β-lactamases (ESBLs) and carbapenemases (KPC, NDM).

Occurrence of Extended Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram-Negative Bacteria in Fresh Vegetables, an Increasing Human Health Concern in Algeria

The aim of this study was to screen for extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables in Batna, Algeria. A total of 400 samples of fresh vegetables were collected from different retail stores. Samples were immediately subjected to selective isolation, then the representative colonies were identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF–MS). Phenotypic and genotypic analyses were carried out in terms of species identification and relative antibiotic resistance. Transferability of the carbapenemase and mcr-bearing plasmids was verified by conjugation. The clonal relationships of carbapenemase and mcr-positive Escherichia coli isolates were studied by multi-locus sequence typing (MLST). Sixty-seven isolates were characterised and were mostly isolated from green leafy vegetables, where the dominant species identified included Citrobacter freundii, Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomona maltophilia, E. coli and Citrobacter braakii. PCR and sequencing results showed that E. coli was the bacterial species presenting the highest antibiotic resistance level in parallel to bla_TEM (n = 16) and bla_CTX-M-15 (n = 11), which were the most detected genes. Moreover, five isolates carried carbapenemase genes, including the bla_OXA-48 and/or bla_VIM-4 genes. The mcr-1 gene was detected in two E. coli isolates. MLST analysis revealed three different E. coli sequence types: ST101 (n = 1), ST216 (n = 1) and ST2298 (n = 1). Conjugation assays confirmed the transferability of the bla_OXA-48 and mcr-1 genes. In this study we report, for the first time, the detection of the bla_OXA-48 gene in E. coli and C. braakii isolates and the bla_VIM-4 gene in vegetables. To the best of our knowledge, this is the first report on the detection of mcr-1 genes from vegetables in Algeria.

Characterization of plasmid-mediated quinolone resistance genes and extended-spectrum beta-lactamases in non-typhoidal Salmonella enterica isolated from broiler chickens

Background and Aim:

Antibiotic-resistant Salmonella is a public health concern. Fluoroquinolones and extended-spectrum beta-lactams are widely used for the treatment of Salmonella infections. This study focused on the detection of plasmid-mediated quinolone resistance (PMQR) and extended-spectrum beta-lactamase (ESBL) genes among multidrug-resistant (MDR) Salmonella enterica isolated from broilers.

Materials and Methods:

A total of 40 non-typhoidal S. enterica isolates were collected from 28 broiler chicken farms in four Iraqi Governorates. These isolates were examined for their susceptibility to 10 antimicrobial agents by disk-diffusion method followed by polymerase chain reaction assay for the detection of PMQR determinants and ESBLs genes.

Results:

Salmonella strains revealed high levels of resistance to the following antibiotics: Nalidixic acid 100%, levofloxacin (LEV) 97.5%, amoxicillin-clavulanic acid 95.0%, tetracycline 92.5%, and nitrofurantoin 80.0%. Otherwise, all isolates were susceptible to cefotaxime and ceftriaxone. All isolates were MDR, with 15 different profiles observed. Among 38 amoxicillin/clavulanic acid-resistant Salmonella isolates, 20 (52.6%) had the blaTEM gene, while blaSHV, blaCTX-M, and blaOXA genes were not detected. Only 5 (12.8%) out of 39 LEV-resistant isolates were positive for qnrB, three of which had blaTEM. No qnrC or qnrD, qnrS, aac(6`)-Ib-cr, qunA, and oqxAB genes were found in any of the tested isolates.

Conclusion:

This study demonstrates that broiler chickens may be considered a potential source for spreading MDR non-typhoidal Salmonella and ESBL traits in poultry production. Therefore, it is important to continuously monitor ESBL and PMQR genes to avoid the spread of resistant strains in the food chain and impact public health.

A high level of antibiotic resistance in Klebsiella and Aeromonas isolates from street water sold in Mozambique, associated with the prevalence of extended-spectrum and AmpC ß-lactamases

This study aims to evaluate the resistance profile and the prevalence of antibiotic resistance genes in 30 isolates of Klebsiella spp. and Aeromonas spp. recovered from water sold in the streets of Maputo. Susceptibility profiles to 15 antibiotics were performed according to Clinical Laboratory Standard Institute guidelines with antibiotic disks on Mueller-Hinton agar plates. Multiplex PCRs were performed targeting 10 ß-lactamase genes, five ESBL (bla_TEM-variants, bla_OXA-variants, Bla_SHV-variants, MCTX-_M Group 1 and Group 9 variants) and five AmpC (ACC variants, FOX variants, MOX variants, CIT variants and DHA variants). The results showed a high prevalence of Klebsiella resistance to ß-lactam antibiotics, such as amoxicillin/clavulanic acid (62.5%), amoxicillin (56.3%), ampicillin (50%), cefoxitin (43.8%), and cefotaxime (43.8%). Aeromonas showed resistance to cefoxitin and ampicillin (71.4%), amoxicillin/clavulanic acid (57.1%) and imipenem (42.9%). ESBL bla_OXA-variants, bla_SVH-variants, MCTX-M Group 1 variants, and MCTX-M Group 9 variants were the most prevalent b-lactam genes, followed by the b-lactams AmpC, ACC variants and FOX variants. It is extremely important to improve waterborne disease control strategies, especially in terms of public awareness of the potential health implications of multidrug-resistant strains of Klebsiella and Aeromonas, which are often neglected.

A rich mosaic of resistance in extended-spectrum β-lactamase-producing Escherichia coli isolated from red foxes (Vulpes vulpes) in Poland as a potential effect of increasing synanthropization

In our research, we analyzed the resistance of cephalosporin-resistant E. coli strains to antimicrobial agents. The strains were collected during five years from wild animal species commonly inhabiting Poland. We have identified the type of β-lactamases produced and the multidrug-resistance profile. Most strains (73.8%) had genes encoding ESBL enzymes, mainly CTX-M-1 and TEM. Almost all AmpC-β-lactamase-producing isolates had the bla_CMY-2 gene. Almost 70% of the strains tested showed a multi-drug resistance profile. The dominant phenotype was resistance to tetracycline (69.05%), and/or sulfamethoxazole (57.1%). We also found high resistance to quinolones: ciprofloxacin 35.7% and nalidixic acid 52.4%. The phenotypic resistance of the strains was in most cases confirmed by the presence of corresponding genes. Among strains, 26.2% were carriers of plasmid-mediated quinolone resistance genes (PMQR). MLST analysis revealed a large clonal variation of the strains, which was reflected in 28 different sequence types. More than half of the strains (54.7%) were classified into the following sequence complexes: 10, 23, 69, 101, 155, 156, 168, 354, 398, 446, and 648. Only one strain in the studied group was assigned to the ExPEC pathotype and represented sequence type 117. The results of our research have confirmed that isolates obtained from wild animals possess many resistance determinants and sequence types, which are also found in food-producing animals and humans. This reflects the doctrine of "One health", which clearly indicates that human health is inextricably linked with animal health as well as degree of environmental contamination. We conclude that the resistance and virulence profiles of strains isolated from wildlife animals may be a resultant of various sources encountered by animals, creating a rich and varied mosaic of genes, which is very often unpredictable and not reflected in the correlation between the sequence type and the gene profile of resistance or virulence observed in epidemic clones.

A role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58

Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.

Detection of AmpC and ESBL-producing Enterobacterales isolated from urinary tract infections in Tunisia

Urinary tract infections (UTIs) are the most frequent human infections in community and hospitals. This study aimed to determine the distribution of bacterial uropathogens among urinary tract infections diagnosed within the regional hospital Houcine Bouzaiene (Gafsa, South West Tunisia) during a survey of 54 days from the 8th of November to the 31st of December 2017. Enterobacterales strains were tested for antimicrobial resistance by disk diffusion method and extended-spectrum β-lactamase (ESBL) production was tested by double-disc synergy test. Strains were further subjected to a molecular assessment of ESBL and AmpC β-lactamase production by PCR. Overall, 173 bacterial isolates were studied, out of which 91.3% were Enterobacterales. Escherichia coli was the dominant pathogen, followed by Klebsiella pneumoniae. High to moderate resistance rates were observed, ranging from 66% to 90.7% for penicillins, from 6.7% to 18.6% for cephalosporins and from 16.2% to 25.4% for fluoroquinolones. Enterobacterales with decreased susceptibility to third-generation cephalosporins (3rd GC) carried several resistance genes: blaCTX-M group 1 and group 9, and ACC and FOX AmpC β-lactamase genes. Overall, ESBLs and AmpC β-lactamases were detected in 57% and 14% of the 3rd GC-resistant isolates, respectively. This study proved the high potential of K. pneumaniae species to develop resistance against commonly used antibiotics. Thus, rigorous monitoring of the antibiotic resistance of clinical pathogens have to be implemented in Tunisia. Our results are very relevant to evaluate efficiency of the Tunisian therapeutic strategies against UTIs and adapt them to the emerging problem of antimicrobial resistance.

Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli

With the emergence of multiresistant bacteria, the use of bacteriophages is gaining renewed interest as potential antimicrobial agents. The aim of this study was to analyze the structure of three lytic bacteriophages infecting Escherichia coli (SD1, SD2, and SD3) using a gel-based proteomics approach and the cellular response of this bacterium to phage SD1 infection at the proteome level. The combination of the results of 1-DE and 2-DE followed by mass spectrometry led to the identification of 3, 14, and 9 structure proteins for SD1, SD2, and SD3 phages, respectively. Different protein profiles with common proteins were noticed. We also analyzed phage-induced effects by comparing samples from infected cells to those of noninfected cells. We verified important changes in E. coli proteins expression during phage SD1 infection, where there was an overexpression of proteins involved in stress response. Our results indicated that viral infection caused bacterial oxidative stress and bacterial cells response to stress was orchestrated by antioxidant defense mechanisms. This article makes an empirical scientific contribution toward the concept of bacteriophages as potential antimicrobial agents. With converging ecological threats in the 21st century, novel approaches to address the innovation gaps in antimicrobial development are more essential than ever. Further research on bacteriophages is called for in this broader context of planetary health and integrative biology.

Exploring Phytochemicals for Combating Antibiotic Resistance in Microbial Pathogens

Antibiotic resistance or microbial drug resistance is emerging as a serious threat to human healthcare globally, and the multidrug-resistant (MDR) strains are imposing major hurdles to the progression of drug discovery programs. Newer antibiotic-resistance mechanisms in microbes contribute to the inefficacy of the existing drugs along with the prolonged illness and escalating expenditures. The injudicious usage of the conventional and commonly available antibiotics in human health, hygiene, veterinary and agricultural practices is proving to be a major driver for evolution, persistence and spread of antibiotic-resistance at a frightening rate. The drying pipeline of new and potent antibiotics is adding to the severity. Therefore, novel and effective new drugs and innovative therapies to treat MDR infections are urgently needed. Apart from the different natural and synthetic drugs being tested, plant secondary metabolites or phytochemicals are proving efficient in combating the drug-resistant strains. Various phytochemicals from classes including alkaloids, phenols, coumarins, terpenes have been successfully demonstrated their inhibitory potential against the drug-resistant pathogens. Several phytochemicals have proved effective against the molecular determinants responsible for attaining the drug resistance in pathogens like membrane proteins, biofilms, efflux pumps and bacterial cell communications. However, translational success rate needs to be improved, but the trends are encouraging. This review highlights current knowledge and developments associated challenges and future prospects for the successful application of phytochemicals in combating antibiotic resistance and the resistant microbial pathogens.

Antimicrobial Susceptibility Profiles of Escherichia Coli Isolates from Diarrheic Dogs in Maiduguri, Borno State, Nigeria

Diarrhea caused by multidrug-resistant Escherichia coli (E. coli) is an important and common problem in companion animals, especially dogs. Moreover, these dogs may serve as a reservoir of pathogenic strains of E. coli that may cause enteric and extra-intestinal infections in humans and other animals. This study was conducted to investigate the antibiotic susceptibility pattern of E. coli isolates from diarrheic dogs in Maiduguri Metropolis, Borno State, Nigeria. In fecal samples of 200 dogs with diarrhea, 147 E. coli strains (73.5%) were isolated and characterized by the standard bacteriological techniques (culture, biochemical tests, and antimicrobial susceptibility testing). Out of the 147 positive isolates, 45, 50, and 52 were from Elkanemi Park, Magaram, and Sabon gari wards respectively. The isolates show 100% resistance to chloramphenicol, cefuroxime, and ceftriaxone, 96.6% to amoxicillin, and 95.9% to gentamicin, while all (100%) were susceptible to ciprofloxacin. All the isolates showed multiple antimicrobial resistance. The result of the current study showed that dogs in Maiduguri are important reservoirs of multidrug-resistant E. coli. Therefore, it is important to adopt and apply guidelines for the correct use of antimicrobials in small animal practice to reduce the emergence of multidrug resistance among E. coli in companion animals.

Genetic diversity and co-prevalence of ESBLs and PMQR genes among plasmid-mediated AmpC β-lactamase-producing Klebsiella pneumoniae isolates causing urinary tract infection

Klebsiella pneumoniae is an opportunistic pathogen that frequently causes nosocomial urinary tract infection (UTI). The aim of this study was to investigate the prevalence of extended-spectrum β-lactamases (ESBL), plasmid-mediated quinolone resistance (PMQR) genes, in acquired AmpC (ac-AmpC) β‑lactamase‑producing K. pneumoniae isolates from patients with nosocomial UTI and to characterize the transmissibility of plasmids harbouring multiple resistance genes. From January 2017 to June 2018, we collected 46 ac-AmpC-producing K. pneumoniae isolates causing UTI from a tertiary care hospital in China. Antimicrobial susceptibility assays showed that non-susceptibility of all isolates to third-generation cephalosporin and fluoroquinolone was very high (>80%). Diverse types of ESBLs and PMQR genes, including bla_SHV-12 (n = 23), bla_SHV-27 (n = 1)_, bla_SHV-28 (n = 2)_, bla_SHV-33 (n = 4), bla_CTX-M-3 (n = 24)_, bla_CTX-M-14 (n = 6)_, bla_CTX-M-15 (n = 6)_, bla_CTX-M-22 (n = 1) and bla_OXA-10 (n = 26)_, as well as qnrA (n = 2), qnrB (n = 39) and qnrS (n = 2) genes were identified amongst AmpC-producing K. pneumoniae isolates. The bla_AmpC, qnrB and several ESBLs genes from six strains harbouring multiple AmpC (at least two ampC) were co-transferrable to recipients via conjugation or electroporation, with IncFIA, IncFIB and IncA/C being the dominant replicons. Conserved genetic context associated with the mobilization of bla_ampC genes was detected. Forty-six isolates were categorized into 25 enterobacterial repetitive intergenic consensus (ERIC) types, and the 6 isolates harbouring multiple AmpC genes belonged to ST1 lineage. This work reports that the emergence of plasmids co-harbouring multiple resistance determinants and mediating the local prevalence in K. pneumoniae causing UTI in China.

High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of bla_CTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, bla_TEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), bla_CTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where bla_CTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of bla_CTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of bla_CTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.

Characterization of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolates from Jurong Lake, Singapore with Whole-Genome-Sequencing

Background: The fast-spreading of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli (ESBL-producing E. coli) and ESBL genes has become a big challenge to public health. The risk of spreading ESBL genes and pathogens in the environment and community has raised public health concern. The characterizing and whole-genome sequencing studies of ESBL-producing bacteria from reservoir water in Singapore is still limited. Materials and methods: The reservoir water sample was taken from two randomly selected sampling points of the Chinese Garden (Jurong river reservoir), which is a popular reservoir park in Singapore. The bacteria of the water sample were collected with 0.45 µm filter membranes and enriched before processing with ESBL-producing E. coli screening. The collected ESBL positive isolates were further characterized by both phenotypic tests including disc diffusion and microdilution Minimum Inhibitory Concentration (MIC) test, and also genotypic test as whole-genome sequencing analysis. Besides, to investigate the transferability of the resistance gene, a conjugation test was performed with the J53 E. coli strain as the gene receptor. Result: Nine ESBL-producing E. coli isolates were collected and confirmed as ESBL-producing with both phenotypic and genotypic tests. A potential pathogen as ST131 clade A isolate was identified, and all isolates were determined to harbor a bla_CTX-M gene. Among them, strain J1E4 was resistant to polymyxin E and confirmed to harboring a conjugatable mcr-1 gene. Further genetic environment analysis has reflected a conversed gene cluster formed by insert sequence (IS), bla_CTX-M-15, and WbuC family cupin-fold metalloprotein, which may potentially jump from the plasmids to the chromosome. Conclusion: The first time we reported the whole genome sequencing (WGS) data of ESBL-producing E. coli including potential pathogen (ST131) present in reservoir water in Singapore. The ESBL-producing E. coli from reservoir water also carrying conjugatable colistin resistance genes which may become a risk to human health.

Prevalence of ESBL-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae in treated wastewater: a comparison with nosocomial infection surveillance

The increasing prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae (CRE) is a worldwide health threat. Monitoring of these resistant bacteria in the environment can provide regional prevalence reflecting both healthy and infected populations, although the quantitative monitoring of those resistant bacteria, especially CRE, is difficult due to their low proportion in the total Enterobacteriaceae population and the possible interference by autochthonous species with intrinsic resistance. In this study, these resistant bacteria in treated wastewater were quantified at 12 different treatment plants. The proportions of cefotaxime-resistant and ESBL-producing E. coli in the total E. coli population in the chlorinated effluents in Tokyo were 5.7 and 5.3%, respectively. The estimated proportion of CRE was 0.007% with the constituting species of Klebsiella spp. and Enterobacter spp., although the conditions during the first incubation may have affected the estimation even after the correction by the proportion of resistant population in the isolates. The observed resistant proportions in this study were lower than those in the surveillance on nosocomial infection not only for inpatients but also for outpatients, and higher than those in the veterinary monitoring.

Co-occurrence of multidrug resistance, β-lactamase and plasmid mediated AmpC genes in bacteria isolated from river Ganga, northern India

Wastewater effluents released in surface water provides suitable nutrient rich environment for the growth and proliferation of antibiotic resistant bacteria (ARB) and genes (ARG). Consequently, bacterial resistance has highly evolved over the recent years and diversified that each antibiotic class is inhibited by a distinct mechanism. In the present study, the prevalence of Multidrug resistant (MDR), extended spectrum β-lactamases (ESBL) and plasmid mediated Amp-C producing strains was analyzed in 28 surface water samples collected near domestic effluent discharge sites in river Ganga located across 11 different geographical indices of Uttar Pradesh, India. A total of 243 bacterial strains with different phenotypes were isolated. Among 243 isolates, 206 (84.77%) exhibited MDR trait displaying maximum resistance towards β-lactams (P = 78.19%; AMX = 72.84%), glycopeptides (VAN = 32.92%; TEI = 79.42%), cephalosporins (CF = 67.90%; CFX = 38.27%), and lincosamides (CD = 78.18%) followed by sulfonamide, macrolide and tetracycline. ESBL production was confirmed in 126 (51.85%) isolates that harbored the genes: blaTEM (95.24%), blaSHV (22.22%), blaOXA (11.90%) and blaCTX-M group (14.28%). The presence of plasmid mediated AmpC was detected only in 6.17% of isolates. The existence of such pathogenic strains in the open environment generates an urgent need for incorporating stringent measures to reduce the antibiotic consumption and hence its release.

Genomic insights into multidrug-resistant and hypervirulent Klebsiella pneumoniae co-harboring metal resistance genes in aquatic environments

Klebsiella pneumoniae is one of the most important pathogens related to hospital-acquired infections. The incidence of infections by hypervirulent K. pneumoniae (hvKp), especially community-acquired infections, has been increasing in recent decades. The occurrence of multidrug-resistant (MDR) hvKp has been increasingly reported worldwide decreasing the treatment options, which is a concern. Aquatic environments have been considered a reservoir of MDR pathogens, which contribute to the spread of MDR pathogens. Therefore, this study aimed to characterize MDR-hvKp strains obtained from public aquatic environments using whole genome sequencing in Brazil. Resistome analysis showed ARGs to β-lactams, quinolones, tetracyclines, sulfonamides, and fosfomycin as well as several metal resistance genes. Virulome analysis showed several virulence genes. Besides, genomic islands, CRISPR and prophage-related sequences were also detected. MLST analysis revealed the presence of two novel sequences types (STs) belonging to different clonal complexes (CCs) [ST4415 (CC515) and ST4416 (CC2654)], and one already described [ST661 (CC661)]. The presence of MDR-hvKp lineages in water sources belonging to STs and CCs associated with humans and animals shows the ability of these pathogens to spread to different aquatic environments. This study reports for the first time two novel STs of MDR-hvKp as well as the presence of a rare ST661 closely related to outbreaks in aquatic environments, and contributes to surveillance studies and MDR-hvKp monitoring worldwide.

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.

Detection of Extended-Spectrum β-Lactamases (ESBL) Producing Enterobacteriaceae from Fish Trapped in the Lagoon Area of Bizerte, Tunisia

Extended-spectrum β-lactamase and their molecular mechanism in Enterobacteriaceae were analyzed in 126 fish samples of 9 various wild species, living in the lagoon of Bizerte in Tunisia. Fifty-nine (59) Gram-negative strains were isolated and identified as Escherichia coli (n = 24), Klebsiella pneumonia (n = 21), Citrobacter freundii (n = 8), and Shigella boydii (n = 6). Forty-seven ESBL producers were identified using the synergic test. β-Lactamase genes detected were bla_CTX-M-1 (E. coli/15; K. pneumonia/8; C. freundii/1; Sh. boydii/1), bla_CTX-M-1+ bla_OXA-1 (E. coli/4; K. pneumonia/3), bla_CTX-M-1+ bla_TEM-1-a (K. pneumonia/2), bla_CTX-M-15+ bla_TEM-1-a (K. pneumonia/1; Sh. boydii/1), bla_CTX-M-15+ bla_OXA-1 (K. pneumonia/1), bla_CTX-M-15 (E. coli/3; K. pneumonia/1; Sh. boydii/3), and bla_CTX-M-9 (C. freundii/3). Most strains (84.7%) showed a multiresistant phenotype. qnrA and qnrB genes were identified in six E. coli and in ten E. coli+one K. pneumonia isolates, respectively. The resistance to tetracycline and sulfonamide was conferred by the tet and sul genes. Characterization of phylogenic groups in E. coli isolates revealed phylogroups D (n = 20 strains), B2 (n = 2), and A (n = 2). The studied virulence factor showed prevalence of fimA genes in 9 E. coli isolates (37.5%). Similarly, no strain revealed the three other virulence factors tested (eae, aer, and cnf1). Our findings confirmed that the lagoons of Bizerte may be a reservoir of multidrug resistance/ESBL-producing Enterobacteriaceae. This could lead to indisputable impacts on human and animal health, through the food chain.

Widespread high-risk clones of multidrug-resistant extended-spectrum β-lactamase-producing Escherichia coli B2-ST131 and F-ST648 in public aquatic environments

Aquatic environments are considered a reservoir for the dissemination of multidrug-resistant (MDR) bacteria, principally Escherichia coli, with the consequent spread of acquired antimicrobial resistance genes (ARGs). Widespread high-risk clones of MDR E. coli are responsible for human infections worldwide. This study aimed to characterise, through whole-genome sequencing (WGS), isolates of MDR E. coli harbouring ARGs obtained from public aquatic environments in Brazil. MDR E. coli isolates were obtained from rivers, streams and lakes that presented different Water Quality Index records and were submitted to WGS. The resistome, mobilome and virulome showed a great diversity of ARGs, plasmids and virulence genes, respectively. In addition, mutations in the quinolone resistance-determining regions of GyrA, ParC and ParE as well as several metal resistance genes (MRGs) and antibacterial biocide resistance genes (ABGs) were detected. Typing and subtyping of MDR E. coli revealed different lineages, with two belonging to widespread high-risk clones (i.e. B2-ST131-fimH30 and F-ST648-fimH27), which are grouped by core genome multilocus sequence typing (cgMLST) in clusters with E. coli lineages obtained from different sources distributed worldwide. MDR bacteria carrying MRGs and ABGs have emerged as a global human and environmental health problem. Detection of widespread high-risk clones calls for attention to the dissemination of fluoroquinolone-resistant QnrS1- and CTX-M-producing E. coli lineages associated with human infections in public aquatic environments.

Antibiotic resistant Klebsiella spp. from a hospital, hospital effluents and wastewater treatment plants in the uMgungundlovu District, KwaZulu-Natal, South Africa

Hospital effluents are crucial hotspots for the dissemination of antibiotic resistant microorganisms. This study analysed hospital effluent and proximate wastewater treatment plants for the presence of antibiotic resistant Klebsiella spp. Water samples were obtained twice over a three-month period from an urban and rural hospital at three effluent points each, and from two proximate wastewater treatment plants (WWTPs) comprising influent and effluent and river water samples up/downstream the WWTPs. Presumptive Klebsiella spp. were enumerated, isolated, and phenotypically confirmed using a well-established commercial test system for Enterobacteriaceae (API20E). Clinical Klebsiella pneumoniae isolates were provided by a hospital for comparison. The antibiotic resistance profiles of Klebsiella spp. isolates to 16 selected antibiotics were established according to EUCAST (European Committee on Antimicrobial Susceptibility Testing). In addition, extended spectrum β-lactamase (ESBL) and carbapenemase production was analysed. A total of 93 confirmed Klebsiella spp. isolates from hospital effluents and 37 from WWTPs were obtained, comprising K. pneumoniae and K. oxytoca. The viable counts for confirmed Klebsiella spp. for hospital effluents ranged from 1.38 × 10² to 1.03 × 10⁴, while those for WWTP influent were in a range of 1.76 × 10³ to 5.10 × 10³ CFU/ml. A higher proportion of Klebsiella spp. from urban hospital effluent was categorized as multidrug-resistant (MDR) (23%) compared to rural hospital effluent (9%). Resistance was observed to all antibiotic classes tested. Several clinical isolates presented resistance to four carbapenem antibiotics, while certain isolates from hospital effluent and WWTPs exhibited ertapenem and doripenem resistance. Fifteen Klebsiella spp. isolates (clinical and from urban hospital effluent) produced carbapenemases. Hospital effluents in South Africa contain antibiotic resistant Klebsiella spp. and may pose a risk to proximate informal communities if inadequately treated. Moreover, common phenotypic resistance profiles among isolates from the clinical-hospital effluent-wastewater works continuum suggest a need for further treatment of such effluent.

Acquired AmpC β-Lactamases among Enterobacteriaceae from Healthy Humans and Animals, Food, Aquatic and Trout Aquaculture Environments in Portugal

We aimed to investigate the occurrence of acquired AmpC β-lactamases (qAmpC), and characterize qAmpC-producing Enterobacteriaceae from different non-clinical environments in Portugal. We analysed 880 Enterobacteriaceae resistant to third-generation cephalosporins recovered from 632 non-clinical samples [healthy human and healthy animal (swine, chickens) faeces; uncooked chicken carcasses; aquatic and trout aquaculture samples]. Bacterial and qAmpC identification, antibiotic susceptibility, clonal (PFGE, MLST) and plasmid (S1-/I-CeuI-PFGE, replicon typing, hybridization) analysis were performed using standard methods. The occurrence of qAmpC among Enterobacteriaceae from non-clinical origins was low (0.6%; n = 4/628 samples), corresponding to CMY-2-producing Escherichia coli from three healthy humans (HH) and one uncooked chicken carcass (UCC). We highlight a slight increase in CMY-2 human faecal carriage in the two periods sampled [1.0% in 2013–2014 versus 0% in 2001–2004], which is in accordance with the trend observed in other European countries. CMY-2-producing E. coli belonged to B2₂-ST4953 (n = 2, HH), A₀-ST665 (n = 1, HH) or A₁-ST48 (n = 1, UCC) clones. bla_CMY-2 was identified in non-typeable and IncA/C₂ plasmids. This study is one of the few providing an integrated evaluation of the qAmpC-producing Enterobacteriaceae occurrence, which was low, from a very large collection of different non-clinical origins. Further surveillance in contemporary collections can provide an integrated epidemiological information of potential shifts in reservoirs, transmission routes and mechanisms of dissemination of bla_qAmpC in non-clinical settings.

Antimicrobial use and resistance in food-producing animals and the environment: an African perspective

BACKGROUND

The overuse of antimicrobials in food animals and the subsequent contamination of the environment have been associated with development and spread of antimicrobial resistance. This review presents information on antimicrobial use, resistance and status of surveillance systems in food animals and the environment in Africa.

METHODS

Information was searched through PubMed, Google Scholar, Web of Science, and African Journal Online databases. Full-length original research and review articles on antimicrobial use, prevalence of AMR from Africa covering a period from 2005 to 2018 were examined. The articles were scrutinized to extract information on the antimicrobial use, resistance and surveillance systems.

RESULTS

A total of 200 articles were recovered. Of these, 176 studies were included in the review while 24 articles were excluded because they were not relevant to antimicrobial use and/or resistance in food animals and the environment. The percentage of farms using antimicrobials in animal production ranged from 77.6% in Nigeria to 100% in Tanzania, Cameroon, Zambia, Ghana and Egypt. The most antibiotics used were tetracycline, aminoglycoside and penicillin groups. The percentage of multi drug resistant isolates ranged from 20% in Nigeria to 100% in South Africa, Zimbabwe and Tunisia. In the environment, percentage of multi drug resistant isolates ranged from 33.3% in South Africa to 100% in Algeria. None of the countries documented national antimicrobial use and resistance surveillance system in animals.

CONCLUSION

There is high level of antimicrobial use, especially tetracycline, aminoglycoside and penicillin in animal production systems in Africa. This is likely to escalate the already high prevalence of antimicrobial resistance and multi drug resistance in the continent. This, coupled with weak antimicrobial resistance surveillance systems in the region is a great concern to the animals, environment and humans as well.

Metagenomic analysis of β-lactamase and carbapenemase genes in the wastewater resistome

The emergence and spread of resistance to antibiotics among bacteria is the most serious global threat to public health in recent and coming decades. In this study, we characterized qualitatively and quantitatively β-lactamase and carbapenemase genes in the wastewater resistome of Central Wastewater Treatment Plant in Koziegłowy, Poland. The research concerns determination of the frequency of genes conferring resistance to β-lactam and carbapenem antibiotics in the genomes of culturable bacteria, as well as in the wastewater metagenome at three stages of treatment: raw sewage, aeration tank, and final effluent. In the final effluent we found bacteria with genes that pose the greatest threat to public health, including genes of extended spectrum β-lactamases - bla_CTX-M, carbapenemases - bla_NDM, bla_VIM, bla_GES, bla_OXA-48, and showed that during the wastewater treatment their frequency increased. Moreover, the wastewater treatment process leads to significant increase in the relative abundance of bla_TEM and bla_GES genes and tend to increase the relative abundance of bla_CTX-M, bla_SHV and bla_OXA-48 genes in the effluent metagenome. The biodiversity of bacterial populations increased during the wastewater treatment and there was a correlation between the change in the composition of bacterial populations and the variation of relative abundance of β-lactamase and carbapenemase genes. PCR-based quantitative metagenomic analysis combined with analyses based on culture methods provided significant information on the routes of ARBs and ARGs spread through WWTP. The limited effectiveness of wastewater treatment processes in the elimination of antibiotic-resistant bacteria and resistance genes impose the need to develop an effective strategy and implement additional methods of wastewater disinfection, in order to limit the increase and the spread of antibiotic resistance in the environment.

Whole genome sequencing snapshot of multi-drug resistant Klebsiella pneumoniae strains from hospitals and receiving wastewater treatment plants in Southern Romania

We report on the genomic characterization of 47 multi-drug resistant, carbapenem resistant and ESBL-producing K. pneumoniae isolates from the influent (I) and effluent (E) of three wastewater treatment plants (WWTPs) and from Romanian hospital units which are discharging the wastewater in the sampled WWTPs. The K. pneumoniae whole genome sequences were analyzed for antibiotic resistance genes (ARGs), virulence genes and sequence types (STs) in order to compare their distribution in C, I and E samples. Both clinical and environmental samples harbored prevalent and widely distributed ESBL genes, i.e. bla_SHV, bla_OXA, bla_TEM and bla_{CTX M}. The most prevalent carbapenemase genes were bla_NDM-1, bla_OXA-48 and bla_KPC-2. They were found in all types of isolates, while bla_OXA-162, a rare bla_OXA-48 variant, was found exclusively in water samples. A higher diversity of carbapenemases genes was seen in wastewater isolates. The aminoglycoside modifying enzymes (AME) genes found in all types of samples were aac(6’), ant(2'')Ia, aph(3'), aaD, aac(3) and aph(6). Quinolone resistance gene qnrS1 and the multi-drug resistance oqxA/B pump gene were found in all samples, while qnrD and qnrB were associated to aquatic isolates. The antiseptics resistance gene qacEdelta1 was found in all samples, while qacE was detected exclusively in the clinical ones. Trimethroprim-sulfamethoxazole (dfrA, sul1 and sul2), tetracyclines (tetA and tetD) and fosfomycin (fosA6, known to be located on a transpozon) resistance genes were found in all samples, while for choramphenicol and macrolides some ARGs were detected in all samples (catA1 and catB3 / mphA), while other (catA2, cmIA5 and aac(6’)Ib / mphE and msrE) only in wastewater samples. The rifampin resistance genes arr2 and 3 (both carried by class I integrons) were detected only in water samples. The highly prevalent ARGs preferentially associating with aquatic versus clinical samples could ascribe potential markers for the aquatic (bla_SHV-145, qacEdelta1, sul1, aadA1, aadA2) and clinical (bla_OXA-1, bla_SHV-106,bla_TEM-150, aac(3)Iia, dfrA14, oqxA10; oqxB17,catB3, tetD) reservoirs of AR. Moreover, some ARGs (oqxA10; bla_SHV-145; bla_SHV-100, aac(6')Il, aph(3')VI, armA, arr2, cmlA5, bla_CMY-4, mphE, msrE, oqxB13, bla_OXA-10) showing decreased prevalence in influent versus effluent wastewater samples could be used as markers for the efficiency of the WWTPs in eliminating AR bacteria and ARGs. The highest number of virulence genes (75) was recorded for the I samples, while for E and C samples it was reduced to half. The most prevalent belong to three functional groups: adherence (fim genes), iron acquisition (ent, fep, fyu, irp and ybt genes) and the secretion system (omp genes). However, none of the genes associated with hypervirulent K. pneumoniae have been found. A total of 14 STs were identified. The most prevalent clones were ST101, ST219 in clinical samples and ST258, ST395 in aquatic isolates. These STs were also the most frequently associated with integrons. ST45 and ST485 were exclusively associated with I samples, ST11, ST35, ST364 with E and ST1564 with C samples. The less frequent ST17 and ST307 aquatic isolates harbored bla_OXA-162, which was co-expressed in our strains with bla_CTX-M-15 and bla_OXA-1.

Prevalence of extended-spectrum β-lactamases in the local farm environment and livestock: challenges to mitigate antimicrobial resistance

The effectiveness of antibiotics has been challenged by the increasing frequency of antimicrobial resistance (AR), which has emerged as a major threat to global health. Despite the negative impact of AR on health, there are few effective strategies for reducing AR in food-producing animals. Of the antimicrobial resistant microorganisms (ARMs), extended-spectrum β-lactamases (ESBLs)-producing Enterobacteriaceae are an emerging global threat due to their increasing prevalence in livestock, even in animals raised without antibiotics. Many reviews are available for the positive selection of AR associated with antibiotic use in livestock, but less attention has been given to how other factors including soil, water, manure, wildlife, and farm workers, are associated with the emergence of ESBL-producing bacteria. Understanding of antibiotic resistance genes and bacteria transfer at the interfaces of livestock and other potential reservoirs will provide insights for the development of mitigation strategies for AR.

Increasing Prevalence of ESBL-Producing Multidrug Resistance Escherichia coli From Diseased Pets in Beijing, China From 2012 to 2017

We investigated antimicrobial resistance trends and characteristics of ESBL-producing Escherichia coli isolates from pets and whether this correlates with antibiotic usage in the clinic. Clinical samples containing E. coli from diseased cats and dogs were screened for antibiotic sensitivity and associated genotypic features. We identified 127 E. coli isolates from 1886 samples from dogs (n = 1565) and cats (n = 321) with the majority from urinary tract infections (n = 108, 85%). High rates of resistance were observed for β-lactams and fluoroquinolones and resistance to > 3 antibiotic classes (MDR) increased from 67% in 2012 to 75% in 2017 (P < 0.0001). This was especially true for strains resistant to 6-9 antibiotics that increased from 26.67 to 60.71%. Increased rates in β-lactam use for clinical treatment accompanied these increasing resistance rates. Accordingly, the most frequently encountered subtypes were bla _CTX-M (n = 44, 34.65%), bla _CTX-M-65 (n = 19) and bla _CTX-M-15 (n = 18) and qnrB (n = 119, 93.70%). The bla _CTX-M-isolates possessed 36 unique pulsed field electrophoretic types (PFGEs) and 28 different sequence types (STs) in ST405 (7, 15.9%), ST131 (3, 6.8%), ST73, ST101, ST372, and ST827 (2, 4.5% each) were the most prevalent. This data demonstrated a high level of diversity for the bla _CTX-M-positive E. coli isolates. Additionally, bla _NDM-5 was detected in three isolates (n = 3, 2.36%), comprised of two ST101 and one ST405 isolates, and mcr-1 was also observed in three colistin-resistant E. coli with three different STs (ST6316, ST405, and ST46). Our study demonstrates an increasing trend in MDR and ESBL-producing E. coli and this correlated with β-lactam antibiotic usage for treatment of these animals. This data indicates that there is significant risk for the spread of resistant bacteria from pets to humans and antibiotic use for pets should be more strictly regulated.

Antimicrobial resistance genes and virulence gene encoding intimin in Escherichia coli and Enterococcus isolated from wild rabbits (Oryctolagus cuniculus) in Tunisia

The spread of antimicrobial-resistant bacteria in wildlife must be viewed as a major concern with serious implications for human and animal health. Escherichia coli and enterococcal isolates were recovered from faecal samples of 49 wild rabbits (Oryctolagus cuniculus) on specific media and were characterised using biochemical and molecular tests. For all isolates, antimicrobial susceptibility testing was performed, and resistance genes were detected by PCR. Molecular typing of isolates was carried out by pulsed-field gel-electrophoresis, and E. coli strains were also tested for the presence of intimin (eae) gene characteristic of rabbit enteropathogenic E. coli. A total of 34 E. coli and 36 enterococci [E. hirae (52.8%) and E. faecalis (47.2%)] were obtained. For E. coli, resistance to tetracycline (94%), streptomycin (62%), ciprofloxacin (47%), trimethoprim-sulphamethoxazole (35%) and chloramphenicol (6%) was observed. Resistance to third-generation cephalosporins was detected in one E. coli strain that carried the bla_CMY-2 and bla_TEM-1 genes. Class 1 integrons were detected in eight isolates. For enterococci, resistance to tetracycline (63.9%), erythromycin (30.5%), streptomycin (18.2%), and chloramphenicol (5.5%) was detected. The tet(M)+tet(L), erm(B) and ant (6)-Ia genes were identified in thirteen, seven and three resistant Enterococcus strains, respectively. Molecular typing showed a high diversity among our strains. Wild rabbits could represent a reservoir of E. coli, and enterococci carrying antimicrobial resistance genes and E. coli additionally carrying the eae gene of enteropathogenic pathotypes could both contaminate the environment. our finding seems to represent the first report of eae-positive E. coli in wild rabbits.

Emergence of Escherichia coli harbouring mcr-1 and mcr-3 genes in North West Algerian farmlands

OBJECTIVES

Colistin resistance has emerged worldwide, threatening the efficacy of colistin treatment of Gram-negative bacterial infections. Farms have been recognised as an important reservoir of genes conferring resistance to colistin. This study aimed to isolate and characterise colistin-resistant bacteria in farmlands located in the region of Oran, northwest Algeria.

METHODS

Forty environmental samples were collected between May 2016 and March 2018 at eight agricultural sites in the Oran region.

RESULTS

From the 40 samples, 103 colistin-resistant isolates were isolated from agricultural soil (n = 52), irrigation water (n = 31) and manure (n = 20). Eight isolates were identified as Escherichia coli, including six and two isolates carrying the mcr-1 and mcr-3 gene, respectively. All eight E. coli isolates were non-susceptible to amoxicillin, amoxicillin/clavulanic acid, ticarcillin, nalidixic acid, ciprofloxacin, gentamicin, trimethoprim/sulfamethoxazole and rifamycin; two were also non-susceptible to cefotaxime, cefepime and aztreonam and carried the bla_TEM-12 gene in addition to mcr-1. The six mcr-1-carrying E. coli isolates (MIC ≥ 2 μg/mL) belonged to three sequences types, including ST10 (n = 3), ST405 (n = 2) and ST345 (n = 1), whereas the two mcr-3-carrying isolates were assigned to ST155. The conjugation assay was positive only for two mcr-1-positive isolates.

CONCLUSION

These results show that farms are an important reservoir of colistin-resistant E. coli as well as other antimicrobial resistance genes such as ESBL genes. Transfer of manure from animals to soil and irrigation water might be disseminating a mix of multiple resistances, posing a worrying threat to human health.

mcr-1 encoding colistin resistance in CTX-M-1/CTX-M-15- producing Escherichia coli isolates of bovine and caprine origins in Tunisia. First report of CTX-M-15-ST394/D E. coli from goats

The objective of this study was to isolate and characterize ESBL-producing Escherichia coli (ESBL-EC) from raw bovine and caprine milk samples, as well as from bovine faeces in Tunisia. Therefore, 120 bovine faecal samples and 9 caprine raw milk samples were collected from 2 extensive dairy-cow-farms and 5 ovine farms, respectively. In addition, 94 raw bovine milk samples, from containers and holding tanks from 50 small public-markets in the North of Tunisia, were processed for the isolation of cefotaxime-resistant E. coli (CTX^R). Antimicrobial susceptibility testing was carried out by disc-diffusion/broth-microdilution methods. The presence of genes encoding ESBL, as well as those encoding colistin (mcr-1 to 5 genes)- sulfonamide-, tetracycline-, gentamicin-, quinolone and chloramphenicol-resistance and class 1 integrons were tested by PCR (and sequencing in some cases). ESBL-EC isolates were further characterized by phylogrouping and MLST/PFGE typing. Eight samples (3.6%) contained ESBL-EC isolates (3/2 from raw bovine/goat milk and 3 from cattle faeces) and one isolate/sample was characterized. Four ESBL-EC isolates, all of bovine origin (3 faeces/1 milk), were resistant to colistin (MIC: 8-16 μg/ml), harboured the mcr-1 gene and carried IncP- and IncFIB-type plasmids. The 8 ESBL-EC strains had the following characteristics: a) bovine faeces: mcr-1/CTX-M-1/D-ST1642 (3 strains); b) raw milk: mcr-1/CTX-M-1/A-ST10 (1 strain); CTX-M-15/B1-ST394 (3 strains), and CTX-M-15/A-ST46 (1 strain). Most of bovine ESBL-EC isolates were multidrug-resistant (4/5). Our results showed that ESBL-EC were detected in bovine and caprine samples (CTX-M-1/CTX-M-15 producers), being some of them colistin-resistant (associated with mcr-1 gene), and they belonged to international clonal lineages.

Global distribution and current research of AmpC beta-lactamase genes in aquatic environments: A systematic review

AmpC beta-lactamase genes are some of the most common antibiotic resistance genes and require special attention once they have become mobilised. The detection of these genes is well documented in clinical settings. However, there is insufficient knowledge of both plasmid and genomic AmpC genes in aquatic environments. This systematic review aimed to determine the extent of the knowledge gap in the literature regarding the prevalence of AmpC beta-lactamase genes in aquatic systems. Using selected criteria, a total of 27 databases were searched for applicable peer-reviewed journal articles. No date and language restrictions were applied. Journal articles that highlighted the detection of AmpC beta-lactamase genes in environmental aquatic systems, including wastewater treatment plants, were included. Of the 950 literature sources that were identified, 50 were selected for full text analysis based on predetermined criteria. Studies on AmpC genes detection were traced in 23 countries. These studies focused on surface water (24), wastewater (17), sea water (4) and both surface and wastewater (5). Most studies did not specifically aim to detect AmpC genes, but to detect antibiotic resistance genes in general. Presently no surveillance protocols, standardised detection methods or environmental limits exist for these genes and, due to a paucity of research in this field, it is unlikely that such systems will be implemented in the near future. The implications and dynamics of AmpC genes in aquatic systems remain unclear and require intense research to ensure the sustainability of environmental systems and human health.

High clonal diversity of multidrug-resistant and extended spectrum beta-lactamase-producing Escherichia coli in a wastewater treatment plant

Increasing beta-lactam resistance has led to the exploration of different places, such as wastewater treatment plants (WWTPs) which have been considered to be reservoirs and sources of bacterial resistance. This work aims to determine the presence of beta-lactamase-producing-Enterobacteriaceae in different points of a WWTP in Colombia. Six samplings were carried out in 2017 in the raw influent, aeration tanks, recycled sludge and final effluent of a WWTP. The beta-lactamase-producing-Enterobacteriaceae were detected and identified using phenotypic and molecular methods. Of the 353 isolates included, 28.3% corresponded to enterobacteria. The most frequent microorganisms were Escherichia coli (83%), Citrobacter freundii (11%) and Enterobacter cloacae complex (4%). The 97% of enterobacteriaceae had at least one beta-lactamase, and the most prevalent were the bla_TEM (43.8%) and bla_CTX-M-1group (35.8%) which were detected specially in recycled sludge and final effluent sample points. High percentage of multidrug resistance (to beta-lactams and non-beta-lactam antibiotics) was detected in E. coli (63.2%). Additionally, the typing by PFGE and MLST showed high genotypic diversity and the presence of the successful ST131 clone, globally spread. This work highlights the strong role of E. coli as a vector for the dissemination of resistance and the beta-lactamases in aquatic environments.

Draft genome sequencing and annotation of a low-virulence Morganella morganii strain CQ-M7, a multidrug-resistant isolate from the giant salamander in China

OBJECTIVES

A multidrug-resistant Morganella morganii strain (CQ-M7), isolated from the kidney of a diseased Chinese giant salamander in China, was examined with whole genome sequencing to better understand drug tolerance and its pathogenicity.

METHODS

The draft genome of the investigated strain was assembled using HGA assembler and annotated using Rapid Annotations Subsystems Technology (RAST) server. The contigs were annotated by the appropriate bioinformatics tools available on the National Center for Biotechnology Information (NCBI) website. Antibiotic resistance genes were detected by PCR. Pathogenicity of the isolate was performed on 30 healthy Chinese giant salamanders with different infection dosages.

RESULTS

The CQ-M7 strain showed resistance to multiple antimicrobials, especially to aminoglycoside and β-lactam antibiotics. Seventeen drug-resistance genes were detected, which were related to β-lactams, aminoglycosides, fluoroquinolones, tetracyclines, peptide antibiotic, and fosfomycin resistance. Sequence analysis showed the assembled genome size to be 4 966 326bp with 51.16% of GC content, containing 4587 protein-coding genes, 71 pseudogenes, five rRNAs, 80 tRNAs, and five noncoding RNAs. The genome sequence was deposited in GenBank under accession number RQIJ00000000. Artificial infection results indicated that the CQ-M7 strain was a low-virulence strain for the Chinese giant salamander.

CONCLUSION

It is believed that this is the first draft genome of Chinese giant salamander original Morganella morganii strain harbouring multiple antibiotic resistance genes in China. The reported genome sequence could provide insights into antibiotic resistance mechanisms and control strategies of Morganella morganii.

The Role of Plasmids in the Multiple Antibiotic Resistance Transfer in ESBLs-Producing Escherichia coli Isolated From Wastewater Treatment Plants

We compared the diversity of extended-spectrum β-lactamases (ESBLs) producing Escherichia coli (E. coli) in wastewater of a municipal wastewater treatment plant. This was done by analyzing multiple antibiotic resistant phenotypes and genotypes. Also, we investigated the antibiotic resistance transfer mechanism of the plasmid by comparing the antibiotic resistance gene linked transfer using a conjugative test, and by analyzing the full-length DNA sequence of one plasmid. The results showed that 50 ESBLs-producing E. coli isolates were isolated from 80 wastewater samples at the rate of 62.5% (50/80), out of which 35 transconjugants were obtained with the multiple antibiotic resistant transfer rate as high as 70.0% (35/50). Multiple antibiotic resistance was shown in all transconjugants and donor bacteria, which were capable of resistance to 11 out of 15 kinds of antibiotics. Both transconjugants and donors were capable of resistance to the Ampicillin and Cefalotin at a rate of 100.00% (35/35), while the total antibiotic resistant spectrum of transconjugants narrowed at the rate of 94.29% (33/35) and broadened at the rate of 5.71% (2/35) after conjugate to the donor bacteria. PCR showed that the resistant genotypes decreased or remained unchanged when compared to donor bacteria with transconjugants while the blaTEM and blaCTX-M genes were transferred and linked at a rate of 100.00% (35/35) and the blaSHV gene was at the rate as high as 94.29% (33/35). However, the qnrS gene was transferred at a low rate of 4.17% (1/24). In addition, the major resistance gene subtypes were blaTEM- 1, blaSHV -11 , and blaCTX-M-15 according to sequencing and Blast comparison. Plasmid wwA8 is a closed-loop DNA molecule with 83157 bp, and contains 45 predicted genes, including three antibiotic resistant resistance genes, blaCTX-M-15 , blaTEM-1 and qnrS1, which can be transferred with E. coli in vitro. This study shows that E. coli isolated from wastewater was capable of transferring resistance genes and producing antibiotic resistant phenotypes. The plasmids containing different resistance genes in E. coli play an important role in the multiple antibiotic resistant transfer. Most importantly, antibiotic resistant resistance genes have different transfer efficiencies, the blaTEM and blaCTX-M genes transferred at a rate of 100.00% and linked transfer in all 35 transconjugants.

A survey of extended-spectrum β-lactamase-producing Enterobacteriaceae in environmental water in Okinawa Prefecture of Japan and relationship with indicator organisms

Surveys of extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-pE) in stream water and untreated wastewater were carried out in Okinawa Prefecture, Japan. Thirty-six samples of water were collected from 18 streams in Okinawa Prefecture, as well as ten samples of wastewater flowing into four wastewater treatment plants (WWTPs). We investigated bacterial species, Escherichia coli O antigen, ESBL phenotype, ESBL genotype, and pulsed-field gel electrophoresis (PFGE) type of isolates, and total viable count and fecal coliforms as indicator organisms. The relation between indicator organisms and ESBL-pE was also validated using the same samples. A total of 141 ESBL-pE including 107 E. coli, 15 Klebsiella pneumoniae, 2 Proteus mirabilis, and 17 other species was isolated from stream water and wastewater. Of the 141 ESBL-pE, 14.9% and 54.6% were found to be blaCTX-M-15 and blaCTX-M-14-like types, respectively, which have been found in hospital isolates in Okinawa. Two pairs of possibly related patterns according to PFGE criteria were isolated from stream water and wastewater in two districts. When ESBL-pE was significantly isolated, total viable count and fecal coliform boundaries were ≥ 6.0 × 10³ CFU/ml and ≥ 4.3 × 10² most probable number/100 ml, respectively. These results suggested that ESBL-pE isolated from stream water is human derived, and that total viable count and fecal coliforms will be useful as indicators for confirming the spread of ESBL-pE to the environment by means of simple hygiene surveys.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.

Emergence of mcr-1 plasmid-mediated colistin-resistant Escherichia coli isolates from seawater

Colistin is currently regarded as one of the 'last-resort' antibiotics used for the treatment of critical infections caused by multidrug-resistant Gram-negative pathogens. Recently, there have been numerous reports of the emergence of a transferable plasmid-mediated colistin resistance gene, mcr-1 in patients, animals, food, and environment. Here, we characterize the support of colistin resistance among environmental isolates collected from seawater of Algiers coast. Our study was carried out on 246 isolates resistant to colistin (MIC > 2 μg/L). The mcr-1 gene was identified in only two isolates; M49 and M78. The two strains were identified as Escherichia coli and were non-susceptible to amoxicillin, ticarcillin, piperacillin, gentamicin, nalidixic acid, tigecycline, tetracycline, trimethoprim-sulfamethoxazole and colistin. For the latter, isolates M49 and M78 showed MIC values of 4 μg/mL and 8 μg/mL, respectively. Only the strain M78 was intermediary resistant to tobramycin. The two E. coli strains belonged to two different sequence types (STs): ST23 for M49 and ST115 for M78. The mcr-1 gene was present on a non-conjugative plasmid in the two strains.

Highly Prevalent Multidrug-Resistant Salmonella From Chicken and Pork Meat at Retail Markets in Guangdong, China

This study aimed to investigate the prevalence, serotype distribution, and antibiotic resistance, and to characterize the extended spectrum β-lactamases (ESBLs) producing Salmonella isolates from chicken and pork meats from retail markets in Guangdong province, China. A total of 903 retail meat samples (475 chicken and 428 pork meats) were obtained from six cities (Guangzhou, Shenzhen, Heyuan, Shaoguan, Foshan, and Yunfu) of Guangdong province between May 2016 and April 2017. High levels of Salmonella contamination were detected in chicken (302/475, 63.6%) and pork (313/428, 73.1%). Thirty-eight serotypes were identified in 615 detected Salmonella, and the serotypes varied greatly between chicken and pork samples. Agona (55/302, 18.2%), Corvallis (45/302, 14.9%), Kentucky (38/302, 12.6%), Mbandaka (32/302, 10.6%) was the dominant serotypes in chicken samples. However, Typhimurium (78/313, 24.9%), Rissen (67/313, 24.1%), Derby (66/313, 21.1%), and London (48, 15.3%) were the most common in pork samples. High rates of antibiotic resistance were found to sulfisoxazole (468/615, 76.1%), tetracycline (463/615, 75.3%), ampicillin (295/615, 48.0%), and ofloxacin (275/615, 44.7%). Notably, antimicrobial susceptibility tests identified resistance to polymyxin B (12/615, 2.0%) and imipenem (3/615, 0.5%). Multidrug-resistance (MDR) was detected in Salmonella isolated from chicken (245/302, 81.1%) and pork (229/313, 73.2%). The resistance rate of different Salmonella serotypes varied widely. Especially, isolates such as Typhimurium, Agona, Corvallis and Kentucky exhibited highly resistance to antibiotics. The MDR rate of Salmonella isolates from chicken was significantly higher than that from pork isolates (P < 0.05). Twenty-one Salmonella isolates were identified as ESBLs-producing, covering six Salmonella serotypes and displaying different pulse field gel electrophoresis (PFGE) genotypes. Bla_OXA-1 was the dominant ESBLs gene (9/21, 42.9%), followed by bla_CTX-M-55 (5/21, 23.8%). This study indicated that Salmonella was widespread in chicken and pork from retail markets in Guangdong province and the isolates showed high multidrug-resistance, especially the known multidrug-resistant Salmonella serotypes. Therefore, it is important to focus on Salmonella serotypes and strengthen the long-term monitoring of MDR Salmonella serotypes in animal-derived foods.

Detection of CTX-M-15 harboring Escherichia coli isolated from wild birds in Tunisia

Background

The spreading of antibiotic resistant bacteria is becoming nowadays an alarming threat to human and animal health. There is increasing evidence showing that wild birds could significantly contribute to the transmission and spreading of drug-resistant bacteria. However, data for antimicrobial resistance in wild birds remain scarce, especially throughout Africa. The aims of this investigation were to analyze the prevalence of ESBL-producing E. coli in faecal samples of wild birds in Tunisia and to characterize the recovered isolates.

Results

One hundred and eleven samples were inoculated on MacConkey agar plates supplemented with cefotaxime (2 μg/ml). ESBL-producing E. coli isolates were detected in 12 of 111 faecal samples (10.81%) and one isolate per sample was further characterized. β-lactamase detected genes were as follows: bla_CTX-M-15 (8 isolates), bla_CTX-M-15 + bla_TEM-1b (4 isolates). The ISEcp1 and orf477 sequences were found respectively in the regions upstream and downstream of all bla_CTX-M-15 genes. Seven different plasmid profiles were observed among the isolates. IncF (FII, FIA, FIB) and IncW replicons were identified in 11 CTX-M-15 producing isolates, and mostly, other replicons were also identified: IncHI2, IncA/C, IncP, IncI1 and IncX. All ESBL-producing E. coli isolates were integron positive and possessed “empty” integron structures with no inserted region of DNA. The following detected virulence genes were: (number of isolates in parentheses): fimA (ten); papC (seven); aer (five); eae (one); and papGIII, hly, cnf, and bfp (none). Molecular typing using pulsed-field gel electrophoresis and multilocus sequence typing showed a low genetic heterogeneity among the 12 ESBL-producing strains with five unrelated PFGE types and five different sequence types (STs) respectively. CTX-M-15-producing isolates were ascribed to phylogroup A (eleven isolates) and B2 (one isolate).

Conclusion

To our knowledge, this study provides the first insight into the contribution of wild birds to the dynamics of ESBL-producing E. coli in Tunisia.

Molecular Epidemiology of Dairy Cattle-Associated Escherichia coli Carrying blaCTX-M Genes in Washington State

An increase in the prevalence of commensal Escherichia coli carrying bla_CTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 bla_CTX-M-positive and 126 bla_CTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes from E. coli obtained during a previous study. For 99 isolates, we also determined the bla_CTX-M alleles using PCR and sequencing and identified the replicon types of bla_CTX-M-carrying plasmids. The bla_CTX-M-negative E. coli isolates comprised 76 sequence types (STs) compared with 32 STs in bla_CTX-M-positive E. coli isolates. The bla_CTX-M-positive E. coli isolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% of bla_CTX-M-negative E. coli isolates clustered into 10 clonal complexes, and the remainder were singletons. Overall, bla_CTX-M-negative E. coli isolates had more diverse genotypes that were distinct to farms, whereas bla_CTX-M-positive E. coli isolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB. bla_CTX-M-15 was the predominant CTX-M gene allele, followed by bla_CTX-M-27 and bla_CTX-M-14 There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCE Infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli occur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producing Enterobacteriaceae, and so understanding the causes of successful dissemination of bla_CTX-M genes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.

Culture-based study on the development of antibiotic resistance in a biological wastewater system treating stepwise increasing doses of streptomycin

The effects of streptomycin (STM) on the development of antibiotic resistance in an aerobic-biofilm reactor was explored by stepwise increases in STM doses (0-50 mg L^-1), over a period of 618 days. Totally 191 bacterial isolates affiliated with 90 different species were harvested from the reactor exposed to six STM exposures. Gammaproteobacteria (20-31.8%), Bacilli (20-35.7%), Betaproteobacteria (4.5-21%) and Actinobacteria (0-18.2%) were dominant, and their diversity was not affected over the whole period. Thirteen dominant isolates from each STM exposures (78 isolates) were applied to determine their resistance prevalence against eight classes of antibiotics. Increased STM resistance (53.8-69.2%) and multi-drug resistance (MDR) (46.2-61.5%) were observed in the STM exposures (0.1-50 mg L^-1), compared to exposure without STM (15.3 and 0%, respectively). Based on their variable minimum inhibitory concentration results, 40 differentiated isolates from various STM exposures were selected to check the prevalence of nine aminoglycoside resistance genes (aac(3)-II, aacA4, aadA, aadB, aadE, aphA1, aphA2, strA and strB) and two class I integron genes (3'-CS and IntI). STM resistance genes (aadA, strA and strB), a non-STM resistance gene (aacA4) and integron genes (3'-CS and Int1) were distributed widely in all STM exposures, compared to the exposure without STM. This new culture-based stepwise increasing antibiotic approach reveals that biological systems treating wastewater with lower STM dose (0.1 mg L^-1) could lead to notably increased levels of STM resistance, MDR, and resistant gene determinants, which were sustainable even under higher STM doses (> 25 mg L^-1).

Detection of β-lactamase encoding genes in feces, soil and water from a Brazilian pig farm

β-lactam antibiotics are widely used for the treatment of different types of infections worldwide and the resistance to these antibiotics has grown sharply, which is of great concern. Resistance to β-lactams in gram-negative bacteria is mainly due to the production of β-lactamases, which are classified according to their functional activities. The aim of this study was to verify the presence of β-lactamases encoding genes in feces, soil, and water from a Brazilian pig farm. Different β-lactamases encoding genes were found, including bla_CTX-M-Gp1, bla_CTX-M-Gp9, bla_SHV, bla_OXA-1-like, bla_GES, and bla_VEB. The bla_SHV and bla_CTX-M-Gp1 genes have been detected in all types of samples, indicating the spread of β-lactam resistant bacteria among farm pigs and the environment around them. These results indicate that β-lactamase encoding genes belonging to the cloxacillinase, ESBL, and carbapenemase and they have high potential to spread in different sources, due to the fact that genes are closely related to mobile genetic elements, especially plasmids.