IncF Plasmids Are Commonly Carried by Antibiotic Resistant Escherichia coli Isolated from Drinking Water Sources in Northern Tanzania

Antibiotic resistance plasmids in Enterobacteriaceae isolated from fresh produce in northern Germany

In this study, the genomes of 22 Enterobacteriaceae isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two Citrobacter isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that Enterobacteriaceae from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for Enterobacteriaceae from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system.

IMPORTANCE

This study showed that Enterobacteriaceae from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.

Systematic review and meta-analyses of the role of drinking water sources in the environmental dissemination of antibiotic-resistant Escherichia coli in Africa

Escherichia coli are pathogenic and antibiotic-resistant organisms that can spread to humans through water. However, there is sparse synthesised information on the dissemination of antibiotic-resistant E. coli through drinking water in Africa. This review provides an overview of the environmental spread of antimicrobial-resistant E. coli through drinking water in Africa. We performed a systematic review based on PRISMA guidelines, and 40 eligible studies from 12 countries were identified until June 2023. Four electronic databases (PubMed, Elsevier, AJOL, and DOAJ) were searched. Studies that employed phenotypic tests (n = 24/40) in identifying the bacterium outstripped those that utilised genome-based methods (n = 13). Of the 40 studies, nine and five, respectively, assessed the bacterium for antimicrobial resistance (AMR) phenotype and genotype. Multiple antibiotic resistance indices of 0.04-0.1 revealed a low level of antibiotic resistance. The detection of multidrug-resistant E. coli carrying resistance genes in certain water sources suggests that AMR-surveillance expansion should include drinking water.

Genomic insights into virulence, antimicrobial resistance, and adaptation acumen of Escherichia coli isolated from an urban environment

Populations of common commensal bacteria such as Escherichia coli undergo genetic changes by the acquisition of certain virulence and antimicrobial resistance (AMR) encoding genetic elements leading to the emergence of pathogenic strains capable of surviving in the previously uninhabited or protected niches. These bacteria are also reported to be prevalent in the environment where they survive by adopting various recombination strategies to counter microflora of the soil and water, under constant selection pressure(s). In this study, we performed molecular characterization, phenotypic AMR analysis, and whole genome sequencing (WGS) of E. coli (n = 37) isolated from soil and surface water representing the urban and peri-urban areas. The primary aim of this study was to understand the genetic architecture and pathogenic acumen exhibited by environmental E. coli. WGS-based analysis entailing resistome and virulome profiling indicated the presence of various virulence (adherence, iron uptake, and toxins) and AMR encoding genes, including blaNDM-5 in the environmental isolates. A majority of our isolates belonged to phylogroup B1 (73%). A few isolates in our collection were of sequence type(s) (ST) 58 and 224 that could have emerged recently as clonal lineages and might pose risk of infection/transmission. Mobile genetic elements (MGEs) such as plasmids (predominantly) of the IncF family, prophages, pipolins, and insertion elements such as IS1 and IS5 were also observed to exist, which may presumably aid in the propagation of genes encoding resistance against antimicrobial drugs. The observed high prevalence of MGEs associated with multidrug resistance in pathogenic E. coli isolates belonging to the phylogroup B1 underscores the need for extended surveillance to keep track of and prevent the transmission of the bacterium to certain vulnerable human and animal populations.

IMPORTANCE

Evolutionary patterns of E. coli bacteria convey that they evolve into highly pathogenic forms by acquiring fitness advantages, such as AMR, and various virulence factors through the horizontal gene transfer (HGT)-mediated acquisition of MGEs. However, limited research on the genetic profiles of environmental E. coli, particularly from India, hinders our understanding of their transition to pathogenic forms and impedes the adoption of a comprehensive approach to address the connection between environmentally dwelling E. coli populations and human and veterinary public health. This study focuses on high-resolution genomic analysis of the environmental E. coli isolates aiming to understand the genetic similarities and differences among isolates from different environmental niches and uncover the survival strategies employed by these bacteria to thrive in their surroundings. Our approach involved molecular characterization of environmental samples using PCR-based DNA fingerprinting and subsequent WGS analysis. This multidisciplinary approach is likely to provide valuable insights into the understanding of any potential spill-over to human and animal populations and locales. Investigating these environmental isolates has significant potential for developing epidemiological strategies against transmission and understanding niche-specific evolutionary patterns.

Antimicrobial resistance in food-associated Escherichia coli in Mexico and Latin America

The World Health Organization (WHO) considers antimicrobial resistance to be one of the critical global public health priorities to address. Escherichia coli is a commensal bacterium of the gut microbiota in humans and animals; however, some strains cause infections and are resistant to antibiotics. One of the most common ways of acquiring pathogenic E. coli strains is through food. This review analyzes multidrug-resistant E. coli isolated from food, emphasizing Latin America and Mexico, and the mobile genetic elements (MGEs) responsible for spreading antibiotic resistance determinants among bacteria in different environments and hosts. We conducted a systematic search of the literature published from 2015 to 2022 in open access databases and electronic repositories. The prevalence of 11 E. coli pathotypes was described, with diarrheagenic E. coli pathotypes being the most frequently associated with foodborne illness in different Latin American countries, highlighting the presence of different antibiotic resistance genes mostly carried by IncF-type plasmids or class 1 integrons. Although the global incidence of foodborne illness is high, there have been few studies in Mexico and Latin America, which highlights the need to generate updated epidemiological data from the "One Health" approach, which allows monitoring of the multidrug-resistance phenomenon in E. coli from a common perspective in the interaction of human, veterinary, and environmental health.

Co-occurrence of antibiotic and disinfectant resistance genes in extensively drug-resistant Escherichia coli isolated from broilers in Ilorin, North Central Nigeria

OBJECTIVES

The occurrence of multidrug-resistant (MDR) bacteria in poultry poses the public health threat of zoonotic transmission to humans. Hence, this study assessed the occurrence of drug-resistant Escherichia coli in broilers in the largest live bird market in Kwara State, Nigeria in December 2020.

METHODS

Presumptive E. coli isolates were isolated using the European Union Reference Laboratory guideline of 2017 and confirmed via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Broth microdilution was performed on confirmed E. coli isolates to determine the minimum inhibitory concentration. Five extensively drug-resistant (XDR) isolates were selected for Illumina whole genome sequencing to predict the resistome, phylotype, sequence type, serotype, and diversity of mobile genetic elements in these isolates.

RESULTS

Of the 181 broiler caecal samples, 73 E. coli isolates were obtained, of which 67 (82.0%) and 37 (50.6%) were determined as MDR (resistant to at least three classes of antibiotics) and XDR (resistant to at least five classes of antibiotics), respectively. Whole genome sequencing revealed diverse sequence types, phylogroups, and serotypes (ST165/B1 - O80:H19, ST115/A - Unknown: H7, ST901/B1 - O109:H4, ST4087/F - O117:H42, and ST8324/A - O127:H42). The XDR E. coli isolates encoded resistance to fluoroquinolones, fosfomycin, sulfamethoxazole, ampicillin and cephalosporins, trimethoprim, aminoglycosides, chloramphenicol, tetracycline, and macrolides. Mutations in the gyrA gene conferring resistance to fluoroquinolones were also detected. There was a positive correlation between phenotypic resistance patterns and the antibiotic resistance genes that were detected in the sequenced isolates. The XDR isolates also harbored two disinfectant resistance genes (qacE and sitABCD) that conferred resistance to hydrogen peroxide and quaternary ammonium compounds, respectively. The genome of the XDR isolates harbored several mobile genetic elements and virulence-associated genes, which were conserved in all sequenced XDR isolates.

CONCLUSIONS

This is the first report of co-carriage of antibiotic resistance genes and disinfectant resistance genes in E. coli isolated from broilers in Ilorin, Nigeria. Our findings suggest that poultry are potential carriers of clonally diverse, pathogenic, MDR/XDR E. coli, which may have detrimental zoonotic potentials on human health.

Antimicrobial resistance, virulence associated genes and phylogenetic background versus plasmid replicon types: the possible associations in avian pathogenic Escherichia coli (APEC)

BACKGROUND

Antimicrobial resistance (AMR) in bacterial isolates from food producing animals not only challenges the preventive and therapeutic strategies in veterinary medicine, but also threatens public health. Genetic elements placed on both chromosome and plasmids could be involved in AMR. In the present study, the associations of genomic backbone and plasmids with AMR were evaluated. We also provided some primary evidences that which genetic lineages potentially host certain groups of plasmids.

RESULTS

In the current study, 72 avian pathogenic Escherichia coli (APEC) strains were examined. Isolates resistant to tetracycline and trimethoprim-sulfamethoxazole (87.5%; each), and harboring bla_TEM (61.1%) were dominant. Moreover, phylogroup D was the most prevalent phylogroup in total (23.6%), and among multidrug-resistant (MDR) isolates (14/63). The most prevalent Inc-types were also defined as follows: IncP (65.2%), IncI1 (58.3%), and IncF group (54.1%). Significant associations among phylogroups and AMR were observed such as group C to neomycin (p = 0.002), gentamicin (p = 0.017) and florfenicol (p = 0.036). Furthermore, group D was associated with bla_CTX. In terms of associations among Inc-types and AMR, resistance to aminoglycoside antibiotics was considerably linked with IncP (p = 0.012), IncI1 (p = 0.038) and IncA/C (p = 0.005). The bla_TEM and bla_CTX genes presence were connected with IncI1 (p = 0.003) and IncFIC (p = 0.013), respectively. It was also shown that members of the D phylogroup frequently occured in replicon types FIC (8/20), P (13/47), I1 (13/42), HI2 (5/14) and L/M (3/3).

CONCLUSIONS

Accorging to the results, it seems that group D strains have a great potential to host a variety of plasmids (Inc-types) carrying different AMR genes. Thus, based on the results of the current study, phyogroup D could be a potential challenge in dealing with AMR in poultry. There were more strong correlations among Inc-types and AMR compared to phylotypes and AMR. It is suggested that in epidemiological studies on AMR both genomic backbone and major plasmid types should be investigated.

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.

High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico

The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the bla_CTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.

Identifying the Sources of Intestinal Colonization With Extended-Spectrum β-Lactamase-Producing Escherichia coli in Healthy Infants in the Community

The prevalence of fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) among children in low- and middle-income countries is alarmingly high. This study aimed to identify the sources of ESBL-Ec colonization in children < 1 year old through comparative analysis of E. coli isolates from child stool, child’s mother stool, and point-of-use drinking water from 46 rural households in Bangladesh. The pairwise similarity in antibiotic susceptibility of E. coli from all three sources was evaluated, followed by phylogenetic clustering using enterobacterial repetitive intergenic consensus polymerase chain reaction and whole-genome sequence analysis of the isolates. Matching antibiotic susceptibility and enterobacterial repetitive intergenic consensus polymerase chain reaction patterns were found among ESBL-Ec isolates from child–mother dyads of 24 and 11 households, respectively, from child–water dyads of 5 and 4 households, respectively, and from child–mother–water triads of 3 and 4 households, respectively. Whole-genome sequence analysis of 30 isolates from 10 households revealed that ESBL-Ec from children in five households (50%) was clonally related to ESBL-Ec either from their mothers (2 households), drinking water sources (2 households), or both mother and drinking-water sources (1 household) based on serotype, phylogroup, sequence type, antibiotic resistance genes, mobile genetic elements, core single-nucleotide polymorphisms, and whole-genome multilocus sequence typing. Overall, this study provides empirical evidence that ESBL-Ec colonization in children is linked to the colonization status of mothers and exposure to the household environments contaminated with ESBL-Ec. Interventions such as improved hygiene practices and a safe drinking water supply may help reduce the transmission of ESBL-Ec at the household level.

Association of fluoroquinolone resistance and ESBL production in hypervirulent Klebsiella pneumoniae ST11 and ST893 in Iran

The spread of multidrug resistance in Klebsiella pneumoniae is a serious threat to the public health. In this study, the prevalence of fluoroquinolone resistance and virulence determinants among ESBL-producing K. pneumoniae isolates was investigated. A total of 50 third-generation cephalosporin resistant K. pneumoniae strains were collected from patients' clinical cultures between September 1st, 2019 and February 30th, 2020. Clonal relatedness of clinical isolates was determined by multilocus sequence typing. All 50 isolates were multidrug-resistant (MDR) and carried at least one of the ESBL resistance determinants. The bla CTX-M-15 gene was the major ESBL determinant found in K. pneumoniae (88%), followed by bla SHV (86%) and bla TEM (78%). PMQR was detected in 96% of the isolates and aac(6')-Ib-cr was the most common (78%) as well as multiple mutations in gyrA (S83I, D87G) and parC (S80I) were found. Selected isolates were assigned to seven sequence types (STs) (ST11, ST893, ST147, ST16, ST377, ST13, and ST392). Overall, hypervirulent phenotypes were identified in 26 (52%) of the isolates. Among the 50 isolates, 28 (56%) were positive for ybt, 23 (46%) for rmpA, 17 (34%) for iroB, 15 (30%) for magA, 4 (8%) for alls and 3 (6%) for iucA genes. The K1 capsular type was the most prevalent (11/50; 22%) among isolates. The emergence of hypervirulent K. pneumoniae (hvKp) ST11 and ST893, which co-carried ESBL, PMQR determinants and different virulence genes has become a threat to the treatment of inpatients in the clinical setting.

Insights and genetic features of extended-spectrum beta-lactamase producing Escherichia coli isolates from two hospitals in Ghana

Recently, the emergence and rapid dissemination of extended-spectrum beta-lactamase (ESBL)-producing bacteria, particularly of the family Enterobacteriaceae, has posed serious healthcare challenges. Here, we determined the antimicrobial susceptibility and genetic characteristics of 164 Escherichia coli strains isolated from infected patients in two hospitals in Ghana. In total, 102 cefotaxime-resistant isolates (62.2%) were identified as ESBL-producers. Multilocus sequence typing of the ESBL-producers identified 20 different sequence types (STs) with ST131 (n = 25, 24.5%) as the dominant group. Other detected STs included ST410 (n = 21, 20.6%) and ST617 (n = 19, 18.6%). All identified ESBL-producers harbored bla_CTX-M-14, bla_CTX-M-15, or bla_CTX-M-27, with bla_CTX-M-15 (n = 96, 94.1%) being the most predominant ESBL allele. Further analysis showed that the immediate genetic environment around bla_CTX-M-15 is conserved within bla_CTX-M-15 containing strains. Five of the 25 ST131 isolates were clustered with clade A, one with sub-clade C1, and 19 with the dominant sub-clade C2. The results show that fluoroquinolone-resistant, bla_CTX-M-14- and bla_{CTX- M-15}-producing ESBL E. coli ST131 strains belonging to clade A and sub-clades C1 and C2 are disseminating in Ghanaian hospitals. To the best of our knowledge, this is the first report of the ST131 phylogeny in Ghana.

Prevalence, Risk Factors, and Genetic Characterization of Extended-Spectrum Beta-Lactamase Escherichia coli Isolated From Healthy Pregnant Women in Madagascar

Antimicrobial resistance is a major public health concern worldwide affecting humans, animals and the environment. However, data is lacking especially in developing countries. Thus, the World Health Organization developed a One-Health surveillance project called Tricycle focusing on the prevalence of ESBL-producing Escherichia coli in humans, animals, and the environment. Here we present the first results of the human community component of Tricycle in Madagascar. From July 2018 to April 2019, rectal swabs from 492 pregnant women from Antananarivo, Mahajanga, Ambatondrazaka, and Toamasina were tested for ESBL-E. coli carriage. Demographic, sociological and environmental risk factors were investigated, and E. coli isolates were characterized (antibiotic susceptibility, resistance and virulence genes, plasmids, and genomic diversity). ESBL-E. coli prevalence carriage in pregnant women was 34% varying from 12% (Toamasina) to 65% (Ambatondrazaka). The main risk factor associated with ESBL-E. coli carriage was the rainy season (OR = 2.9, 95% CI 1.3-5.6, p = 0.009). Whole genome sequencing was performed on 168 isolates from 144 participants. bla CTX-M-15 was the most frequent ESBL gene (86%). One isolate was resistant to carbapenems and carried the bla NDM-5 gene. Most isolates belonged to commensalism associated phylogenetic groups A, B1, and C (90%) and marginally to extra-intestinal virulence associated phylogenetic groups B2, D and F (10%). Multi locus sequence typing showed 67 different sequence types gathered in 17 clonal complexes (STc), the most frequent being STc10/phylogroup A (35%), followed distantly by the emerging STc155/phylogroup B1 (7%), STc38/phylogroup D (4%) and STc131/phylogroup B2 (3%). While a wide diversity of clones has been observed, SNP analysis revealed several genetically close isolates (n = 34/168) which suggests human-to-human transmissions. IncY plasmids were found with an unusual prevalence (23%), all carrying a bla CTX-M-15. Most of them (85%) showed substantial homology (≥85%) suggesting a dissemination of IncY ESBL plasmids in Madagascar. This large-scale study reveals a high prevalence of ESBL-E. coli among pregnant women in four cities in Madagascar associated with warmth and rainfall. It shows the great diversity of E. coli disseminating throughout the country but also transmission of specific clones and spread of plasmids. This highlights the urgent need of public-health interventions to control antibiotic resistance in the country.

Conjugative Plasmids Disseminating CTX-M-15 among Human, Animals and the Environment in Mwanza Tanzania: A Need to Intensify One Health Approach

Background: Globally, bla_CTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying bla_CTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying bla_CTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying bla_CTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10⁻¹ to 10⁻⁹ and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying bla_CTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat.

Myths and misconceptions in the management of Helicobacter pylori infection

The discovery of Helicobacter pylori infection in 1984 revolutionised the management of several common upper gastrointestinal diseases. However, some of the clinical practices that were adopted following discovery of this organism have become less appropriate over the intervening years. This article discusses five 'myths and misconceptions' that we believe have now emerged and which we argue need re-evaluation. Although the prevalence of H. pylori infection is decreasing in some developed countries, it remains a huge global problem and the most serious consequence of infection, gastric adenocarcinoma, is still a major cause of mortality. The epidemiology of H. pylori-related diseases is also changing and careful testing remains crucially important, especially in patients with peptic ulceration. Eradication of H. pylori infection has also become much more difficult over recent years as a result of the widespread acquisition of antibiotic resistance. Routine assessment of the success of eradication should therefore now be performed. Finally, there has been increased awareness about the role of H. pylori in the multistep pathway of gastric carcinogenesis, about the opportunities to prevent cancer development by eradicating this infection in some individuals and about detecting high-risk preneoplastic changes via endoscopic surveillance. The discovery of H. pylori was rightly honoured by the award of the Nobel prize for Physiology and Medicine in 2005. However, unless we re-evaluate and update the ways in which we manage H. pylori infection, much of the fantastic progress that has been made in this field of medicine may tragically be lost once again.

Cost-effectiveness modelling of use of urea breath test for the management of Helicobacter pylori-related dyspepsia and peptic ulcer in the UK

OBJECTIVE

Clinical data comparing diagnostic strategies in the management of Helicobacter pylori-associated diseases are limited. Invasive and noninvasive diagnostic tests for detecting H. pylori infection are used in the clinical care of patients with dyspeptic symptoms. Modelling studies might help to identify the most cost-effective strategies. The objective of the study is to assess the cost-effectiveness of a 'test-and-treat' strategy with the urea breath test (UBT) compared with other strategies, in managing patients with H. pylori-associated dyspepsia and preventing peptic ulcer in the UK.

DESIGN

Cost-effectiveness models compared four strategies: 'test-and-treat' with either UBT or faecal antigen test (FAT), 'endoscopy-based strategy' and 'symptomatic treatment'. A probabilistic cost-effectiveness analysis was performed using a simulation model in order to identify probabilities and costs associated with relief of dyspepsia symptoms (over a 4-week time horizon) and with prevention of peptic ulcers (over a 10-year time horizon). Clinical and cost inputs to the model were derived from routine medical practice in the UK.

RESULTS

For relief of dyspepsia symptoms, 'test-and-treat' strategies with either UBT (€526/success) and FAT (€518/success) were the most cost-effective strategies compared with 'endoscopy-based strategy' (€1317/success) and 'symptomatic treatment' (€1 029/success). For the prevention of peptic ulcers, 'test-and-treat' strategies with either UBT (€208/ulcer avoided/year) or FAT (€191/ulcer avoided/year) were the most cost-effective strategies compared with 'endoscopy-based strategy' (€717/ulcer avoided/year) and 'symptomatic treatment' (€651/ulcer avoided/year) (1 EUR=0,871487 GBP at the time of the study).

CONCLUSION

'Test-and-treat' strategies with either UBT or FAT are the most cost-effective medical approaches for the management of H. pylori-associated dyspepsia and the prevention of peptic ulcer in the UK. A 'test-and-treat' strategy with UBT has comparable cost-effectiveness outcomes to the current standard of care using FAT in the UK.

Molecular Mechanisms Influencing Bacterial Conjugation in the Intestinal Microbiota

Bacterial conjugation is a widespread and particularly efficient strategy to horizontally disseminate genes in microbial populations. With a rich and dense population of microorganisms, the intestinal microbiota is often considered a fertile environment for conjugative transfer and a major reservoir of antibiotic resistance genes. In this mini-review, we summarize recent findings suggesting that few conjugative plasmid families present in Enterobacteriaceae transfer at high rates in the gut microbiota. We discuss the importance of mating pair stabilization as well as additional factors influencing DNA transfer efficiency and conjugative host range in this environment. Finally, we examine the potential repurposing of bacterial conjugation for microbiome editing.

Distribution of Beta-Lactamase Producing Gram-Negative Bacterial Isolates in Isabela River of Santo Domingo, Dominican Republic

Bacteria carrying antibiotic resistance genes (ARGs) are naturally prevalent in lotic ecosystems such as rivers. Their ability to spread in anthropogenic waters could lead to the emergence of multidrug-resistant bacteria of clinical importance. For this study, three regions of the Isabela river, an important urban river in the city of Santo Domingo, were evaluated for the presence of ARGs. The Isabela river is surrounded by communities that do not have access to proper sewage systems; furthermore, water from this river is consumed daily for many activities, including recreation and sanitation. To assess the state of antibiotic resistance dissemination in the Isabela river, nine samples were collected from these three bluedistinct sites in June 2019 and isolates obtained from these sites were selected based on resistance to beta-lactams. Physico-chemical and microbiological parameters were in accordance with the Dominican legislation. Matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses of ribosomal protein composition revealed a total of 8 different genera. Most common genera were as follows: Acinetobacter (44.6%) and Escherichia (18%). Twenty clinically important bacterial isolates were identified from urban regions of the river; these belonged to genera Escherichia (n = 9), Acinetobacter (n = 8), Enterobacter (n = 2), and Klebsiella (n = 1). Clinically important multi-resistant isolates were not obtained from rural areas. Fifteen isolates were selected for genome sequencing and analysis. Most isolates were resistant to at least three different families of antibiotics. Among beta-lactamase genes encountered, we found the presence of blaTEM, blaOXA, blaSHV, and blaKPC through both deep sequencing and PCR amplification. Bacteria found from genus Klebsiella and Enterobacter demonstrated ample repertoire of antibiotic resistance genes, including resistance from a family of last resort antibiotics reserved for dire infections: carbapenems. Some of the alleles found were KPC-3, OXA-1, OXA-72, OXA-132, CTX-M-55, CTX-M-15, and TEM-1.

Plasmid Identification and Plasmid-Mediated Antimicrobial Gene Detection in Norwegian Isolates

Norway is known for being one of the countries with the lowest levels of antimicrobial resistance (AMR). AMR, through acquired genes located on transposons or conjugative plasmids, is the horizontal transmission of genes required for a given bacteria to withstand antibiotics. In this work, bioinformatic analysis of whole-genome sequences and hybrid assembled data from Escherichia coli, and Klebsiella pneumoniae isolates from Norwegian patients was performed. For detection of putative plasmids in isolates, the plasmid assembly mode in SPAdes was used, followed by annotation of resulting contigs using PlasmidFinder and two curated plasmid databases (Brooks and PLSDB). Furthermore, ResFinder and Comprehensive Antibiotic Resistance Database (CARD) were used for the identification of antibiotic resistance genes (ARGs). The IncFIB plasmid was detected as the most prevalent plasmid in both E. coli, and K. pneumoniae isolates. Furthermore, ARGs such as aph(3″)-Ib, aph(6)-Id, sul1, sul2, tet(D), and qnrS1 were identified as the most abundant plasmid-mediated ARGs in Norwegian E. coli and K. pneumoniae isolates, respectively. Using hybrid assembly, we were able to locate plasmids and predict ARGs more confidently. In conclusion, plasmid identification and ARG detection using whole-genome sequencing data are heavily dependent on the database of choice; therefore, it is best to use several tools and/or hybrid assembly for obtaining reliable identification results.

American Crows as Carriers of Extra Intestinal Pathogenic E. coli and Avian Pathogenic-Like E. coli and Their Potential Impact on a Constructed Wetland

The study examines whether crows are carriers of extraintestinal pathogenic E. coli (ExPEC) and avian pathogenic E. coli (APEC)-like strains, and if wetland roost areas contribute to their spread. A total of 10 crow feces (n = 71) and 15 water E. coli isolates (n = 134) from a wetland area could be characterized as potentially ExPEC based on the presence of ≥2 of the five cardinal genes iutA, kpsMT2, papEF, pap A/C, papG, sfa/foc, and afa/dra, while six fecal and 14 water isolates could be characterized as potentially APEC-like based on the presence of plasmid associated genes: iutA, episomal iss, ompT, hlyF and iroN. A total of 32 fecal and 27 water isolates tested carried plasmids based on incompatibility typing. Plasmids from 34 of 38 isolates tested could be transferred to another E. coli strain by conjugation with the antibiotic resistance (AR) profile being transferred, indicating their potential to be transferred to indigenous and non-pathogenic strains in the wetland. APEC-like plasmids could be transferred in six of eight isolates tested. Pathogenic E. coli of importance to the medical community and poultry industry may be detected in high levels in surface water due to corvid activity. Regardless of their role in health or disease, water in wetlands and streams can serve as a media for the dissemination of AR and virulence traits of bacteria, with corvids acting as potential vectors for farther dissemination.

Virulence and resistance properties of E. coli isolated from urine samples of hospitalized patients in Rio de Janeiro, Brazil - The role of mobile genetic elements

Extraintestinal pathogenic E. coli (ExPEC) is the most frequent etiological agent of urinary tract infections (UTIs). Particular evolutionary successful lineages are associated with severe UTIs and higher incidences of multidrug resistance. Most of the resistance genes are acquired by horizontal transfer of plasmids and other mobile genetic elements (MGEs), and this process has been associated with the successful dissemination of particular lineages. Here, we identified the presence of MGEs and their role in virulence and resistance profiles of isolates obtained from the urine of hospitalized patients in Brazil. Isolates belonging to the successful evolutionary lineages of sequence type (ST) 131, ST405, and ST648 were found to be multidrug-resistant, while those belonging to ST69 and ST73 were often not. Among the ST131, ST405, and ST648 isolates with a resistant phenotype, a high number of mainly IncFII plasmids was identified. The plasmids contained resistance cassettes, and these were also found within phage-related sequences and the chromosome of the isolates. The resistance cassettes were found to harbor several resistance genes, including bla_CTX-M-15. In addition, in ST131 isolates, diverse pathogenicity islands similar to those found in highly virulent ST73 isolates were detected. Also, a new genomic island associated with several virulence genes was identified in ST69 and ST131 isolates. In addition, several other MGEs present in the ST131 reference strain EC958 were identified in our isolates, most of them exclusively in ST131 isolates. In contrast, genomic islands present in this reference strain were only partially present or completely absent in our ST131 isolates. Of all isolates studied, ST73 and ST131 isolates had the most similar virulence profile. Overall, no clear association was found between the presence of specific MGEs and virulence profiles. Furthermore, the interplay between virulence and resistance by acquiring MGEs seemed to be lineage dependent. Although the acquisition of IncF plasmids, specific PAIs, GIs, and other MGEs seemed to be involved in the success of some lineages, it cannot explain the success of different lineages, also indicating other (host) factors are involved in this process. Nevertheless, the detection, identification, and surveillance of lineage-specific MGEs may be useful to monitor (new) emerging clones.

Genetic Characterization of Fluoroquinolone Resistance in Salmonella enterica Serovar Gallinarum Isolates from Chicken in Korea

Salmonella enterica serovar Gallinarum is a nonmotile host-adapted Salmonella that causes fowl typhoid (FT), and an outbreak of FT is characterized by anorexia, greenish-yellow diarrhea, paleness, and sudden death with high mortality in poultry. To control and treat FT in commercial chickens, fluoroquinolones are widely used in Korea. This study aimed to investigate the genetic characteristics of fluoroquinolone-resistant Salmonella Gallinarum isolates from 2014-18 from chicken in Korea. A total of 35 ciprofloxacin (CIP)-resistant Salmonella Gallinarum was tested, and 22 (62.9%) isolates were observed to have multidrug resistance. All isolates had a mutation at the Ser83 or Asp87 codon in the gyrA gene, whereas three isolates had only double mutations at Ser83 → Phe and Asp87 → Asn or Ser83 → Phe and Asp87 → Gly. Minimum inhibitory concentrations of isolates with double mutations were relatively higher (≥8 mg/L for CIP and ≥16 mg/L for enrofloxacin) than those of other isolates with a single mutation in gyrA. Among 35 CIP-resistant Salmonella Gallinarum, plasmid-mediated quinolone resistance genes were detected in six (17.1%) isolates, and qnrB and qnrS were detected in four and two isolates, respectively. In the distribution of antimicrobial resistance genes in 35 CIP-resistant Salmonella Gallinarum, ant(2″)-I (54.3%) was the most prevalent gene, followed by TEM-1 (14.3%), sul1 (11.4%), and cmlA (5.7%). Fifteen (42.9%) of the 35 CIP-resistant Salmonella Gallinarum also carried class 1 integrons, which showed five types of resistance gene cassettes: aadA2 (7 isolates), aadA2 + dfrA12 (5 isolates), and aadA1 + aad A2 (3 isolates). Among plasmid replicons, 23 isolates (65.7%) carried five different plasmid replicons: Frep (9 isolates), FIB (7 isolates), FIIA (6 isolates), B/O (4 isolates), and I1 (3 isolates). These results suggest that continued monitoring of fluoroquinolone resistance is necessary to preserve the effectiveness of fluoroquinolones in poultry and to surveil the transmission to humans through the food chain.

Molecular Epidemiology of OXA-48 and NDM-1 Producing Enterobacterales Species at a University Hospital in Tehran, Iran, Between 2015 and 2016

Carbapenem-resistant Enterobacterales (CRE) is an increasing problem worldwide. Here, we examined the clonal relatedness of 71 non-repetitive CRE isolates collected in a university hospital in Tehran, Iran, between February 2015 and March 2016. Pulsed-field gel electrophoresis (PFGE) and MLST were used for epidemiological analysis. Screening for antibiotic resistance genes, PCR-based replicon typing, conjugation experiments, and optical DNA mapping were also performed. Among all 71 isolates, 47 isolates of Klebsiella pneumoniae (66.2%), eight Escherichia coli (11.2%), five Serratia marcescens (7%), and two Enterobacter cloacae (2.8%) harbored bla_NDM–1 and bla_OXA–48 genes together or alone. PFGE analysis revealed that most of the OXA-48- and NDM-1-producing K. pneumoniae and all of OXA-48-producing S. marcescens were clonally related, while all eight E. coli and two E. cloacae isolates were clonally unrelated. The predominant clones of carbapenemase-producing K. pneumoniae associated with outbreaks within the hospital were ST147 (n = 13) and ST893 (n = 10). Plasmids carrying bla_NDM–1 and bla_OXA–48 were successfully transferred to an E. coli K12-recipient strain. The bla_OXA–48 gene was located on an IncL/M conjugative plasmid, while the bla_NDM–1 gene was located on both IncFII ∼86-kb to ∼140-kb and IncA/C conjugative plasmids. Our findings provide novel epidemiologic data on carbapenemase-producing Enterobacterales (CPE) in Iran and highlight the importance of horizontal gene transfer in the dissemination of bla_NDM–1 and bla_OXA–48 genes. The occurrence and transmission of distinct K. pneumoniae clones call for improved infection control to prevent further spread of these pathogens in Iran.

An African perspective on the prevalence, fate and effects of carbapenem resistance genes in hospital effluents and wastewater treatment plant (WWTP) final effluents: A critical review

This article provides an overview of the antibiotic era and discovery of earliest antibiotics until the present day state of affairs, coupled with the emergence of carbapenem-resistant bacteria. The ways of response to challenges of antibiotic resistance (AR) such as the development of novel strategies in the search of new antibiotics, designing more effective preventive measures as well as the ecology of AR have been discussed. The applications of plant extract and chemical compounds like nanomaterials which are based on recent developments in the field of antimicrobials, antimicrobial resistance (AMR), and chemotherapy were briefly discussed. The agencies responsible for environmental protection have a role to play in dealing with the climate crisis which poses an existential threat to the planet, and contributes to ecological support towards pathogenic microorganisms. The environment serves as a reservoir and also a vehicle for transmission of antimicrobial resistance genes hence, as dominant inhabitants we have to gain a competitive advantage in the battle against AMR.

Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes

Antimicrobial resistance has become a global threat to public health since multidrug-resistant (MDR) bacteria have been reported worldwide carrying different antimicrobial resistance genes (ARGs), and animals have been described as a reservoir of ARGs. The presence of antimicrobial-resistant bacteria and ARGs in the food matrix is a risk to public health. This study aimed to research the presence of clinically relevant ARGs for important antimicrobials and genetic elements in fecal samples from dairy cows and calves on a Brazilian farm. In this study, a total of 21 fecal samples were collected, and then, the DNA of cultivable aerobic bacteria was extracted. Fifty-seven ARGs and twenty-three genetic elements were researched by PCR and confirmed by sequencing. Several ARGs that confer resistance to β-lactams, tetracyclines, fluoroquinolones, sulphonamides, phenicols, aminoglycoside, glycopeptides, and macrolides were detected. A total of 200 amplicons from 23 ARGs (bla_CTX-M-Gp2, bla_CMY, bla_SHV, tetA, tetB, tetC, qepA, qnrB, qnrS, oqxA, oqxB, vanC1, vanC2/3, aadA, sul1, sul2, sul3, ermB, mefAE, floR, cmlA, aadA, aph(3')-Ia, aac(3')-Ia), and 145 amplicons from 12 genetic elements (IncF, IncFIA, IncFIB, IncI1, IncY, IncU, IncK, IncP, IncR, IncHI1, ColE-like, intI1) were detected. The results presented in this study call attention to the monitoring of antimicrobial resistance in dairy farms worldwide. MDR bacteria and ARGs can spread to different sources, including milk products, which are one of the most consumed products worldwide, representing a potential risk to human health.

First Report of Extended-Spectrum Betalactamase-Producing Klebsiella pneumoniae Among Fecal Carriage in Iran: High Diversity of Clonal Relatedness and Virulence Factor Profiles

Increasing rate of silent intestinal carriers with extended-spectrum betalactamase (ESBL)-producing Klebsiella pneumonia (ESBL-KP) has given rise to a serious healthcare problem in clinical settings. Various epidemiological studies are being conducted to determine clonal relatedness among carriers. In this study, we investigated the intestinal carriage of ESBL-KP and clonal relatedness among ESBL-KP isolated from fecal carriage in Iran for the first time. A total of 120 rectal swabs (RSs) were collected including 61 from inpatients of intensive care unit and 59 from outpatients. ESBL-KP screening was performed using MacConkey agar supplemented with cefotaxime. PCR was done for detection of ESBL, carbapenemase, and virulence factor genes. Conjugation experiments and PCR-based replicon typing were performed. Clonal relatedness was investigated by multilocus sequence typing (MLST) and multiple locus variable number tandem repeat analysis (MLVA). Out of a total of 120 RSs, 18.3% (22/120) ESBL-KP were isolated. The rate of bla_CTXM-15 was 81%. ompk35 was the most prevalent virulence gene detected in 86.3% of the isolates. In conjugation experiments, three out of five tested isolates had conjugative plasmids. The most prevalent plasmid types belonged to IncL/M, IncA/C, and Inc FII. The MLST analysis showed that the main sequence types (STs) identified among ESBL-KP isolates were ST147, ST15, and ST16. The isolates were characterized into 4 miniclusters and 11 singletons using MLVA. High heterogeneity among ESBL-KP isolates indicated that this bacterium could be colonized in different sites and easily transferred. Screening of carriers in hospitals and community could help in controlling of infection in the healthcare and community settings.

IncI1 Plasmid Associated with blaCTX-M-2 Transmission in ESBL-Producing Escherichia coli Isolated from Healthy Thoroughbred Racehorse, Japan

In our previous study, extended spectrum β-lactamase (ESBL)-producing Escherichia coli (ESBLEC) were isolated from healthy Thoroughbred racehorse feces samples in Japan. Some ESBL genes were predicted to be located on the conjugative plasmid. PCR-based replicon typing (PBRT) is a useful method to monitor and detect the association of replicons with specific plasmid-borne resistant genes. This study aimed to evaluate the plasmid replicon associated with ESBLEC isolated from healthy Thoroughbred racehorses at Japan Racing Association Training Centers in Japan. A total of 24 ESBLECs isolated from 23 (10.8%) individual Thoroughbred racehorse feces samples were used in this study. ESBL gene transfer was performed using a conjugation assay. Then, replicon types of ESBLEC isolates and their transconjugants were determined using PBRT. Pulsed-field gel electrophoresis (PFGE) was performed to look at the clonality of the ESBLECs isolates. ESBLECs were detected from 10.8% of healthy Thoroughbred racehorses. The bla_CTX-M-2 was identified as the dominant type of ESBL gene, followed by bla_CTX-M-1 and bla_TEM-116. In this study, only the bla_CTX-M-2 and the IncI1 plasmid were transferred to transconjugants. The PFGE results showed that ESBL genes were distributed in diversity of ESBLECs. This finding suggested that the IncI1 plasmid was associated with the dissemination of bla_CTX-M-2 in Thoroughbred racehorses in Japan.

Plasmid profiles among some ESKAPE pathogens in a tertiary care centre in south India

Background & objectives

Plasmid has led to increase in resistant bacterial pathogens through the exchange of antimicrobial resistance (AMR) genetic determinants through horizontal gene transfer. Baseline data on the occurrence of plasmids carrying AMR genes are lacking in India. This study was aimed to identify the plasmids associated with AMR genetic determinants in ESKAPE pathogens.

Methods

A total of 112 ESKAPE isolates including Escherichia coli (n=37), Klebsiella pneumoniae (n=48, including 7 pan-drug susceptible isolates), Acinetobacter baumannii (n=8), Pseudomonas aeruginosa (n=1) and Staphylococcus aureus (n=18) were analyzed in the study. Isolates were screened for antimicrobial susceptibility and whole genome sequencing of isolates was performed using Ion Torrent (PGM) sequencer. Downstream data analysis was done using PATRIC, ResFinder, PlasmidFinder and MLSTFinder databases. All 88 whole genome sequences (WGS) were deposited at GenBank.

Results

Most of the study isolates showed resistant phenotypes. As analyzed from WGS, the isolates included both known and unknown sequence types. The plasmid analysis revealed the presence of single or multiple plasmids in the isolates. Plasmid types such as IncHI1B(pNDM-MAR), IncFII(pRSB107), IncFIB(Mar), IncFIB(pQil), IncFIA, IncFII(K), IncR, ColKP3 and ColpVC were present in K. pneumoniae. In E. coli, IncFIA, IncFII, IncFIB, Col(BS512), IncL1, IncX3 and IncH were present along with other types. S. aureus harboured seven different plasmid groups pMW2 (rep 5), pSAS1 (rep 7), pDLK1 (rep 10), pUB110 (rep US12), Saa6159 (rep 16), pKH12 (rep 21) and pSA1308 (rep 21). The overall incidence of IncF type plasmids was 56.5 per cent followed by Col type plasmids 18.3 per cent and IncX 5.3 per cent. Other plasmid types identified were <5 per cent.

Interpretation & conclusions

Results from the study may serve as a baseline data for the occurrence of AMR genes and plasmids in India. Information on the association between phenotypic and genotypic expression of AMR was deciphered from the data. Further studies on the mechanism of antibiotic resistance dissemination are essential for enhancing clinical lifetime of antibiotics.

Analysis of virulence potential of Escherichia coli O145 isolated from cattle feces and hide samples based on whole genome sequencing

Escherichia coli O145 serogroup is one of the big six non-O157 Shiga toxin producing E. coli (STEC) that causes foodborne illnesses in the United States and other countries. Cattle are a major reservoir of STEC, which harbor them in their hindgut and shed in the feces. Cattle feces is the main source of hide and subsequent carcass contaminations during harvest leading to foodborne illnesses in humans. The objective of our study was to determine the virulence potential of STEC O145 strains isolated from cattle feces and hide samples. A total of 71 STEC O145 strains isolated from cattle feces (n = 16), hide (n = 53), and human clinical samples (n = 2) were used in the study. The strains were subjected to whole genome sequencing using Illumina MiSeq platform. The average draft genome size of the fecal, hide, and human clinical strains were 5.41, 5.28, and 5.29 Mb, respectively. The average number of genes associated with mobile genetic elements was 260, 238, and 259, in cattle fecal, hide, and human clinical strains, respectively. All strains belonged to O145:H28 serotype and carried eae subtype γ. Shiga toxin 1a was the most common Shiga toxin gene subtype among the strains, followed by stx2a and stx2c. The strains also carried genes encoding type III secretory system proteins, nle, and plasmid-encoded virulence genes. Phylogenetic analysis revealed clustering of cattle fecal strains separately from hide strains, and the human clinical strains were more closely related to the hide strains. All the strains belonged to sequence type (ST)-32. The virulence gene profile of STEC O145 strains isolated from cattle sources was similar to that of human clinical strains and were phylogenetically closely related to human clinical strains. The genetic analysis suggests the potential of cattle STEC O145 strains to cause human illnesses. Inclusion of more strains from cattle and their environment in the analysis will help in further elucidation of the genetic diversity and virulence potential of cattle O145 strains.

Characterization of non-O157 Shiga toxin-producing Escherichia coli (STEC) obtained from feces of sheep in Brazil

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens and may induce severe diarrheagenic diseases in humans and other animals. Non-O157 STEC have been emerging as important pathogens causing outbreaks worldwide. Bacterial resistance to antimicrobials has become a global public health problem, which involves different ecological spheres, including animals. This study aimed to characterize the resistance to antimicrobials, plasmids and virulence, as well as the serotypes and phylogenetic groups in E. coli isolated from sheep in Brazil. A total of 57 isolates were obtained and showed different antimicrobial resistance profiles. Nineteen isolates presented acquired antimicrobial resistance genes (ARGs) (bla_CTX-M-Gp9, qnrB, qnrS, oqxB, oqxA, tetA, tetB, tetC, sul1 and sul2) and plasmid families (F, FIA, FIB, I1, K, HI1 and ColE-like). The stx1, stx2 and ehxA virulence genes were detected by PCR, being 50 isolates (87.7%) classified as STEC. A great diversity of serotypes was detected, being O176:HNM the most predominant. Phylogenetic group E was the most prevalent, followed by B1, A and B2. To the best of our knowledge, this is the first report in the world of bla_CTX-M-Gp9 (O75, O114, O100, O128ac and O176 serogroups), qnrB and oqxB genes in non-O157 STEC in healthy sheep. The results obtained in the present study call attention to the monitoring of antimicrobial-resistant non-O157 STEC harboring acquired ARGs worldwide and indicate a zoonotic risk due to the profile of virulence, resistance and serotype found.

Plasmid profiling and incompatibility grouping of multidrug resistant Salmonella enterica serovar Typhi isolates in Nairobi, Kenya

OBJECTIVES

Plasmids harbour antibiotic resistance genes which contribute to the emergence of multidrug resistant pathogens. We detected the presence of plasmids in multidrug resistant Salmonella enterica serovar Typhi (S. Typhi) isolates from our previous study and consequently determined their incompatibility groups and possibility of conjugation transmission. Plasmids were extracted from 98 multidrug resistant S. Typhi isolates based on alkaline lysis technique. Plasmid incompatibility grouping was established by PCR replicon typing using 18 pairs of primers to amplify FIA, FIB, FIC, HI1, HI2, I1-Iγ, L/M, N, P, W, T, A/C, K, B/O, X, Y, F and FIIA replicons. Antibiotic resistance phenotypes were conjugally transferred from S. Typhi isolates with plasmids to Escherichia coli K12F strain devoid of plasmids.

RESULTS

Approximately 79.6% of the MDR S. Typhi isolates were related to the existence of plasmids. We detected 93.6% of plasmids belonging to incompatibility (Inc) group HI1. The other incompatibility groups identified included IncFIC (16.7%), IncP (1.3%), and IncI1 (1.3%) which appeared together with Inc HI1. MDR S. Typhi isolated carried a homologous plasmid of incompatibility group HI1 most of which transferred the resistance phenotypes of ampicillin, tetracycline and chloramphenicol to the transconjugants.

Molecular Characterization of Multidrug-Resistant Escherichia coli Isolates from Edible Offal in Korea

HIGHLIGHTS

Edible offal is significantly contaminated by antimicrobial-resistant Escherichia coli. E. coli from edible offal is harboring various antimicrobial resistance and virulence genes. Improvements in hygienic conditions of edible offal production is required.

Considerable rate of putative virulent phylo-groups in fecal carriage of extended-spectrum β-lactamase producing Escherichia coli

Extended-Spectrum Beta-lactamase producing Enterobacteriales (ESBL-PE) in fecal carriage have become a global health concern. Detection of putative virulent ESBL-producing E.coli (ESBL-EC) isolates among asymptomatic carriers is a threatening issue in public health. The aim of this study was to investigate the intestinal carriage of ESBL-EC, phylo-groups and clonal relatedness among putative virulent groups of ESBL-EC isolated from fecal carriages. A total of 120 rectal swabs; 50.8% (61/120) from inpatients of intensive care unit (ICU) and 49.2% (59/120) from outpatients were collected. The ESBL-EC screening was performed by using MacConkey agar supplemented with cefotaxime. PCR assays were applied for determination of phylo-groups, detection of ESBL and carbapenemase genes. Conjugation experiment, plasmid replicon typing and Multilocus Sequence Typing (MLST) were performed for putative virulent phylo-groups. Totally, of 120 studied individuals, 60.0% (72/120) were carrier for ESBL-EC. The rate of bla_CTX-M-15, bla_TEM, bla_SHV was 90.2% (65/72), 50.0% (36/72) and 5.5% (4/72), respectively. The frequency of phylo-groups A, B1, B2, C, D, and F were 20.8% (15/72), 6.9% (5/72), 20.8% (15/72), 2.7% (2/72), 13.8 (10/72) and 12.5% (9/72), respectively. In conjugation experiments, of 6 tested isolates, 5 had conjugative plasmids. The most prevalent plasmid types belonged to IncF incompatibility groups. The MLST analysis showed that the main sequence types among ESBL-EC isolates were ST769 and ST472. The current study provides novel information about the presence of the ESBL-EC isolates, particularly putative virulent phylo-groups among fecal carriages in Iran. Our data revealed that there was almost high ST heterogeneity among putative ESBL-EC isolates. In order to implementation of effective infection control program, detection of fecal carriage in appropriate time typically at the beginning of admission to the hospital is recommended.

Detection of multidrug-resistant Enterobacteriaceae isolated from river waters flowing to the Guanabara Bay and from clinical samples of hospitals in Rio de Janeiro, Brazil

INTRODUCTION

The use of antibiotics in humans, animal husbandry and veterinary activities induces selective pressure leading to the colonization and infection by resistant strains.

OBJECTIVE

We evaluated water samples collected from rivers of the Guanabara Bay, which have suffered minor and major environmental degradation, and clinical samples of hospital origin to detect evidence of the presence of resistance genes to aminoglycosides, beta-lactam antibiotics and fluoroquinolones in strains of Klebsiella pneumoniae subsp. pneumoniae, K. pneumoniae subsp. ozaenae and Escherichia coli.

MATERIALS AND METHODS

For isolation of the water strains we employed culture media containing 32 μg/ml cephalotin and 8 μg/ml gentamicin. The strains from clinical materials were selected using culture media containing 8 μg/ml gentamicin. The strains were identified and subjected to antimicrobial susceptibility testing (AST), plasmid DNA extraction and polymerase chain reaction (PCR) to detect genes encoding enzymes modifying aminoglycosides (EMA), extended-spectrum beta-lactamases (ESBL) and plasmid mechanisms of quinolone resistance (PMQR).

RESULTS

The AST of the isolates recovered from water samples showed multidrugresistance profiles similar to those found in isolates recovered from clinical materials. All isolates from water samples and 90% of the isolates from clinical samples showed at least one plasmid band. In the PCR assays, 7.4% of the isolates recovered from water samples and 20% of those from clinical materials showed amplification products for the three antimicrobial classes.

CONCLUSION

We believe that the detection of microorganisms presenting genetic elements in environments such as water is necessary for the prevention and control of their dissemination with potential to infect humans and other animals in eventual contact with these environments.

The Transferable Resistome of Produce

Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.

Characterization of Cefotaxime- and Ciprofloxacin-Resistant Commensal Escherichia coli Originating from Belgian Farm Animals Indicates High Antibiotic Resistance Transfer Rates

Food-producing animals represent one of the sources of antibiotic resistant commensal bacteria. There is an increasing awareness that these bacteria might have the potential to transfer their resistance genes to other (pathogenic) bacteria. In this study, 50 commensal Escherichia coli strains originating from food-producing animals and resistant to the "highest priority, critically important antibiotics" cefotaxime and/or ciprofloxacin, were selected for further characterization. For each strain (i) an antibiogram, (ii) the phylogenetic group, (iii) plasmid replicon type, (iv) presence and identification of integrons, and (v) antibiotic resistance transfer ratios were determined. Forty-five of these strains were resistant to 5 or more antibiotics, and 6 strains were resistant to 10 or more antibiotics. Resistance was most common to ampicillin (100%), sulfamethoxazole, ciprofloxacin (82%), trimethoprim, tetracycline (74%), cefotaxime, (70%) and ceftazidime (62%). Phylogenetic groups A (62%) and B1 (26%) were most common, followed by C (8%) and E (4%). In 43 strains, more than 1 replicon type was detected, with FII (88%), FIB (70%), and I1 (48%) being the most encountered types. Forty strains, positive for integrons, all harbored a class I integron and seven of them contained an additional class II integron. No class III integrons were detected. The antibiotic resistance transfer was assessed by liquid mating experiments. The transfer ratio, expressed as the number of transconjugants per recipient, was between 10^-5 and 10⁰ for cefotaxime resistance and between 10^-7 and 10^-1 for ciprofloxacin resistance. The results of the current study prove that commensal E. coli in food-production animals can be a source of multiple resistance genes and that these bacteria can easily spread their ciprofloxacin and cefotaxime resistance.

Effect of antibiotics on bacterial populations: a multi-hierachical selection process

Antibiotics have been widely used for a number of decades for human therapy and farming production. Since a high percentage of antibiotics are discharged from the human or animal body without degradation, this means that different habitats, from the human body to river water or soils, are polluted with antibiotics. In this situation, it is expected that the variable concentration of this type of microbial inhibitor present in different ecosystems may affect the structure and the productivity of the microbiota colonizing such habitats. This effect can occur at different levels, including changes in the overall structure of the population, selection of resistant organisms, or alterations in bacterial physiology. In this review, I discuss the available information on how the presence of antibiotics may alter the microbiota and the consequences of such alterations for human health and for the activity of microbiota from different habitats.

Comparison of antibiotic resistant Escherichia coli obtained from drinking water sources in northern Tanzania: a cross-sectional study

Background

Antimicrobial resistance (AMR) is a growing and significant threat to public health on a global scale. Escherichia coli comprises Gram-negative, fecal-borne pathogenic and commensal bacteria that are frequently associated with antibiotic resistance. AMR E. coli can be ingested via food, water and direct contact with fecal contamination.

Methods

We estimated the prevalence of AMR Escherichia coli from select drinking water sources in northern Tanzania. Water samples (n = 155) were collected and plated onto Hi-Crome E. coli and MacConkey agar. Presumptive E. coli were confirmed by using a uidA PCR assay. Antibiotic susceptibility breakpoint assays were used to determine the resistance patterns of each isolate for 10 antibiotics. Isolates were also characterized by select PCR genotyping and macro-restriction digest assays.

Results

E. coli was isolated from 71 % of the water samples, and of the 1819 E. coli tested, 46.9 % were resistant to one or more antibiotics. Resistance to ampicillin, streptomycin, sulfamethoxazole, tetracycline, and trimethoprim was significantly higher (15–30 %) compared to other tested antibiotics (0–6 %; P < 0.05). Of the β-lactam-resistant isolates, bla_TEM-1 was predominant (67 %) followed by bla_CTX-M (17.7 %) and bla_SHV-1 (6.0 %). Among the tetracycline-resistant isolates, tet(A) was predominant (57.4 %) followed by tet(B) (24.0 %). E. coli isolates obtained from these water sources were genetically diverse with few matching macro-restriction digest patterns.

Conclusion

Water supplies in northern Tanzania may be a source of AMR E. coli for people and animals. Further studies are needed to identify the source of these contaminants and devise effective intervention strategies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0870-9) contains supplementary material, which is available to authorized users.