Fecal carriage of multi-drug resistant and extended spectrum β-lactamases producing E. coli in household pigeons, Bangladesh

CTX-M-15/27-positive Escherichia coli and VIM-2-producing Pseudomonas putida in free-living pigeons (Columba livia) in Tunisia

OBJECTIVES

Wild birds are vectors of antimicrobial resistance. Birds living in close contact with humans or other animals, like feral pigeons (Columba livia), might be especially prone to acquire resistance genes such as those encoding extended-spectrum beta-lactamases (ESBLs) and carbapenemases.

METHODS

Cloacal samples (n = 206) of free-living feral pigeons (C. livia) were collected in Sousse and Monastir, Tunisia. Antimicrobial susceptibility profiles were determined by disc-diffusion, and resistant isolates were short- and long-read whole-genome sequenced. Sequence analysis was performed using tools of the Centre for Genomic Epidemiology, and Phylogenetic analysis was performed based on the core-genome MLST.

RESULTS

Fourteen (14/206, 6.8%) pigeons harboured Enterobacterales resistant to last-generations cephalosporins, of which 10 were CTX-M-15- or CTX-M-27-producers, while two (1.0%) carried a VIM-2-producing Pseudomonas putida. Positive pigeons lived on four different livestock farms. Three STs (ST206, ST5584, ST8149) were identified among E. coli, of which ST5584 and ST8149 were found in two different farms. Genetic diversity was also observed in Enterobacter cloacae and P. putida isolates. The blaCTX-M-27 genes were chromosomally encoded, while the blaCTX-M-15 genes were carried on highly similar IncF/F-:A-:B53 plasmids. The blaVIM-2 gene was located on a class 1 integron co-harbouring several resistance genes.

CONCLUSION

Pigeons living on livestock farms carried clinically important resistance genes encoding ESBLs and carbapenemases. Our results evidenced that both clonal (ST8149 and ST5584) and plasmidic (IncF/F-:A-:B53) transfers played a role in the spread of resistance genes among pigeons. Further studies are needed to identify factors favouring the transfer and persistence of resistance genes within the pigeon communities.

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Detection of blaOXA-48 and mcr-1 Genes in Escherichia coli Isolates from Pigeon (Columba livia) in Algeria

The emergence and spread of β-lactams and colistin-resistant Escherichia coli in birds deserve a special concern worldwide. This study aimed to investigate the presence of β-lactams and colistin-resistant Escherichia coli strains isolated from the faeces of urban and rural pigeons in Batna, Algeria, and to characterise their molecular traits of resistance. Between March and April 2019, a total of 276 faecal droppings samples were collected in Batna, Algeria. Samples were subjected to selective isolation of β-lactams and colistin-resistant Escherichia coli. The representative colonies were then identified using Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry. Antimicrobial susceptibility testing was performed using the disc diffusion method. β-lactamases, as well as mcr genes, were screened for by PCR and confirmed by sequencing. Genetic relatedness of the mcr-positive E. coli strains was determined using multi-locus sequence typing analysis. Transferability features of carbapenemase genes were assessed by conjugation experiments. Overall, thirty-five E. coli isolates were obtained only from urban pigeon samples. All carbapenem-resistant isolates harboured the bla_OXA-48 gene as the only carbapenemase gene detected (n = 11), while bla_ESBL genes were detected in eighteen isolates. Out of the thirty-five isolates, four E. coli isolates were positive for the mcr-1 gene. The obtained mcr-1 positive E. coli isolates belonged to four STs, including ST1485, ST224, ST46, and a new ST. This study is the first to report the isolation of E. coli strains carrying the mcr-1 gene from pigeon faeces in Algeria and also the first to report the detection of bla_OXA-48-positive E. coli in pigeons. Close surveillance is, therefore, urgently needed to monitor the dissemination of bla_OXA-48 and mcr-1 producing E. coli strains in wildlife.

Pigeons as Carriers of Clinically Relevant Multidrug-Resistant Pathogens-A Clinical Case Report and Literature Review

Pigeons are widespread bird species in urban regions (Columba livia forma urbana) and may carry pathogens with zoonotic potential. In recent years, more and more data indicate that these zoonotic pathogens are multidrug resistant. Our results confirmed that global trend. Three different multidrug-resistant pathogens were isolated from an oral cavity of a racing pigeon with lesions typical for pigeon pox virus infection. Staphylococcus aureus was recognized as methicillin resistant, thus resistant to all beta-lactams. Additionally, it was also resistant to many other classes of antibiotics, namely: aminoglycosides, tetracyclines, phenicols, lincosamides, and macrolides. Escherichia coli showed resistance to all antimicrobials tested, and it was classified as intermediate to amikacin. Moreover, Candida albicans resistant to clotrimazole, natamycin, flucytosine, and amphotericin and intermediate to ketoconazole, nystatin, and econazole was also isolated. This raises the question how pigeons acquire such highly resistant strains. Therefore, more data are needed concerning the resistance to antibiotics in strains from domestic and wild pigeons in Poland. Until the problem is fully understood, it will be challenging to implement adequate planning of any control measures and check their effectiveness.

Antimicrobial resistance pattern in domestic animal - wildlife - environmental niche via the food chain to humans with a Bangladesh perspective; a systematic review

BACKGROUND

Antimicrobial resistance (AMR) is a growing concern globally, but the impact is very deleterious in the context of Bangladesh. Recent review article on the AMR issue demonstrates the scenario in human medicine; unfortunately, no attempt was taken to address this as One Health issue. The antimicrobial resistance bacteria or genes are circulating in the fragile ecosystems and disseminate into human food chain through direct or indirect ways. In this systematic review we are exploring the mechanism or the process of development of resistance pathogen into human food chain via the domestic animal, wildlife and environmental sources in the context of One Health and future recommendation to mitigate this issue in Bangladesh.

RESULTS

Tetracycline resistance genes were presenting in almost all sample sources in higher concentrations against enteric pathogen Escherichia coli. The second most significant antibiotics are amino-penicillin that showed resistant pattern across different source of samples. It is a matter of concerns that cephalosporin tends to acquire resistance in wildlife species that might be an indication of this antibiotic resistance gene or the pathogen been circulating in our surrounding environment though the mechanism is still unclear.

CONCLUSIONS

Steps to control antibiotic release and environmental disposal from all uses should be immediate and obligatory. There is a need for detailed system biology analysis of resistance development in-situ.

Extended-Spectrum Beta-Lactamase-Producing Escherichia coli in Drinking Water Samples From a Forcibly Displaced, Densely Populated Community Setting in Bangladesh

Introduction: Community-acquired infections due to extended-spectrum beta-lactamase (ESBL) producing Escherichia coli are rising worldwide, resulting in increased morbidity, mortality, and healthcare costs, especially where poor sanitation and inadequate hygienic practices are very common.

Objective: This study was conducted to investigate the prevalence and characterization of multidrug-resistant (MDR) and ESBL-producing E. coli in drinking water samples collected from Rohingya camps, Bangladesh.

Methods: A total of 384 E. coli isolates were analyzed in this study, of which 203 were from household or point-of-use (POU) water samples, and 181 were from source water samples. The isolates were tested for virulence genes, ESBL-producing genes, antimicrobial susceptibility by VITEK 2 assay, plasmid profiling, and conjugal transfer of AMR genes.

Results: Of the 384 E. coli isolates tested, 17% (66/384) were found to be ESBL producers. The abundance of ESBL-producers in source water contaminated with E. coli was observed to be 14% (27/181), whereas, 19% (39/203) ESBL producers was found in household POU water samples contaminated with E. coli. We detected 71% (47/66) ESBL-E. coli to be MDR. Among these 47 MDR isolates, 20 were resistant to three classes, and 27 were resistant to four different classes of antibiotics. Sixty-four percent (42/66) of the ESBL producing E. coli carried 1 to 7 plasmids ranging from 1 to 103 MDa. Only large plasmids with antibiotic resistance properties were found transferrable via conjugation. Moreover, around 7% (29/384) of E. coli isolates harbored at least one of 10 virulence factors belonging to different E. coli pathotypes.

Conclusions: The findings of this study suggest that the drinking water samples analyzed herein could serve as an important source for exposure and dissemination of MDR, ESBL-producing and pathogenic E. coli lineages, which therewith pose a health risk to the displaced Rohingya people residing in the densely populated camps of Bangladesh.

Phylogenetic Diversity, Antimicrobial Susceptibility and Virulence Characteristics of Escherichia coli Isolates from Pigeon Meat

Monitoring resistance to antibiotics in wild animals may assist in evaluating tendencies in the evolution of this major public health problem. The aims of this research work were to determine the patterns of antibiotic resistance in Escherichia coli isolates from the meat of wild or domestically reared pigeons from Spain, to detect the presence of virulence and antibiotic resistance genes, and to carry out a phylogenetic classification of the isolates. Of the 37 E. coli strains tested, 32.43% of them belonged to the B2 phylogenetic group, which is often implicated in extra-intestinal infections. None of the strains showed extended-spectrum beta-lactamase activity. All the isolates presented resistance or reduced susceptibility to two or more antibiotics, with high levels of resistance to β-lactams, aminoglycosides and tetracycline. Ten resistance genes were detected, the most frequent of which were ampC, conferring resistance to ampicillin and aadA, conferring resistance to streptomycin. In total, 97.30% of the strains carried virulence factors (between one and five). The strains from pigeons reared in captivity harboured higher average numbers of resistance and virulence genes than isolates from wild pigeons. Pigeon meat is an important reservoir of E. coli with genes for antibiotic resistance and virulence having the potential to cause disease in humans.

Microbial Load and Antibiotic Resistance Patterns of Escherichia coli and Enterococcus faecalis Isolates from the Meat of Wild and Domestic Pigeons

An expansion in the consumption of pigeon meat has occurred in recent years. However, little is known about microbial load and antibiotic resistance of this foodstuff. The hygiene status and the antibiotic resistance patterns (disc diffusion; Clinical and Laboratory Standards Institute, CLSI) of Escherichia coli and Enterococcus faecalis isolates from wild and domestic pigeon carcasses were investigated. Average microbial loads (log10 cfu/cm2) ranged from 1.40 ± 1.17 (fecal coliforms) to 3.68 ± 1.40 (psychrotrophs). The highest (p < 0.05) microbial loads were observed in domestic pigeons. No substantial differences were found between isolates from domestic and wild pigeons with regard to the prevalence of antibiotic resistance. Of the E. coli strains, 20.00% were susceptible, 25.00% showed resistance or reduced susceptibility to one antimicrobial and 55.00% were multi-resistant. Among the E. faecalis isolates, 2.22% were susceptible and 97.78% were multi-resistant. The greatest prevalence of resistance or reduced susceptibility among E. coli was observed for amoxicillin-clavulanic acid (20.00% strains), ampicillin (26.67%), streptomycin (55.00%) and tobramycin (20.00%). The prevalence of resistance or reduced susceptibility among E. faecalis ranged from 31.11% (trimethoprim/sulfamethoxazole) to 97.78% (erythromycin). Meat from pigeons is a major reservoir of antibiotic-resistant bacteria. The need for the correct handling of this foodstuff in order to reduce risks to consumers is underlined.

Reduced Susceptibility to Extended-Spectrum β-Lactams in Vibrio cholerae Isolated in Bangladesh

β-lactams are antibiotic molecules able to inhibit cell wall biosynthesis. Among other mechanisms, resistance in Gram-negative bacteria is mostly associated with production of β-lactamase enzymes able to bind and hydrolyze the β-lactam ring. Extended-spectrum β-lactamases extend this ability also to third- and fourth-generation cephalosporins, as well as to carbapenems and monobactams. Vibrio cholerae is the causative agent of epidemic cholera and a public health burden for developing countries like Bangladesh. Although appropriate oral or intravenous rehydration is the therapy of choice for cholera, severe infections and V. cholerae-associated septicemia are treated with antimicrobial drugs, including doxycycline, erythromycin, azithromycin, ciprofloxacin, and/or third-generation cephalosporins. In the years after the introduction of antibiotics in clinical practice, V. cholerae developed resistance to commonly used drugs worldwide mostly through gene acquisition via horizontal gene transfer. Reduced susceptibility of V. cholerae to third-generation cephalosporins has been occasionally documented. However, carbapenemase-producing V. cholerae has been reported at higher rates than resistance to extended-spectrum β-lactams, mainly associated with bla_NDM-1 emergence and successful plasmid dissemination. Recent findings suggest limited β-lactam resistance is present in V. cholerae O1 isolates collected during ecological and epidemiological surveillance in Bangladesh. However, a trend to intermediate-susceptibility insurgence was observed. Horizontal gene transfer of β-lactam resistance from enteric pathogens to environmental microorganisms should not be underrated, given the ability of V. cholerae to acquire new genetic information.

Antimicrobial Resistance and Resistance Genes in Aerobic Bacteria Isolated from Pork at Slaughter

The aim of this study was to investigate the phenotypic and genotypic antimicrobial resistance, integrons, and transferability of resistance markers in 243 aerobic bacteria recovered from pork at slaughter in the People's Republic of China. The organisms belonged to 22 genera of gram-negative bacteria (92.2%) and gram-positive bacteria (7.8%). High levels of resistance were detected to tetracycline, trimethoprim-sulfamethoxazole, and ampicillin (36.2 to 54.3%), and lower levels were detected to nitrofurantoin, cefotaxime, gentamicin, ciprofloxacin, and chloramphenicol (7.8 to 29.2%). Across species, genes conferring antimicrobial resistance were observed with the following frequencies: blaTEM, 40.7%; blaCMY-2, 15.2%; blaCTX-M, 11.5%; sul2, 27.2%; sul1, 14.4%; tet(A), 5.4%; tet(L), 5.4%; tet(M), 5.0%; tet(E), 3.7%; tet(C), 3.3%; tet(S), 2.5%; and tet(K), 0.8%. Various antimicrobial resistance genes were found in new carriers: blaTEM in Lactococcus garvieae, Myroides odoratimimus, Aeromonas hydrophila, Staphylococcus sciuri, Raoultella terrigena, Macrococcus caseolyticus, Acinetobacter ursingii, Sphingobacterium sp., and Oceanobacillus sp.; blaCMY-2 in Lactococcus lactis, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, and Myroides phaeus; tet(L) in M. caseolyticus; sul1 in Vibrio cincinnatiensis; sul2 in Acinetobacter bereziniae, Acinetobacter johnsonii, and V. cincinnatiensis; and the class 1 integron and gene cassette aadA2 in V. cincinnatiensis. Approximately 6.6% of isolates contained class 1 integrons, and one isolate harbored class 2 integrons. Plasmid associated intI1 and androgen receptor- encoding genes were transferred into Escherichia coli J53 and E. coli DH5α by conjugation and transformation experiments, respectively. Our study highlights the importance of aerobic bacteria from pork as reservoirs for antimicrobial resistance genes and mobile genetic elements that can readily be transferred intra- and interspecies.

Fecal Carriage of Extended-Spectrum β-Lactamases in Healthy Humans, Poultry, and Wild Birds in León, Nicaragua-A Shared Pool of blaCTX-M Genes and Possible Interspecies Clonal Spread of Extended-Spectrum β-Lactamases-Producing Escherichia coli

Antibiotic-resistant bacteria are a major concern in the healthcare of today, especially the increasing number of gram-negative bacteria producing β-lactamases such as extended-spectrum β-lactamases (ESBLs). However, little is known about the relationship of ESBL producers in humans and domestic and wild birds, especially in a low-income setting. Therefore, we studied the fecal carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae in healthy humans, poultry, and wild birds in the vicinity of León, Nicaragua. Three hundred fecal samples were collected during December 2012 from humans (n = 100), poultry (n = 100) and wild birds (n = 100). The samples were examined for ESBL-producing E. coli and K. pneumoniae, revealing the prevalence of 27% in humans, 13% in poultry, and 8% in wild birds. Further characterization of the ESBL-producing isolates was performed through polymerase chain reaction (PCR) (NDM, CTX-M), epidemiological typing (ERIC2-PCR), multilocus sequence typing, and sequencing. ESBL producers harbored bla_CTX-M-2, bla_CTX-M-15, bla_CTX-M-22, and bla_CTX-M-3 genotypes. The bla_CTX-M-15 constituted the absolute majority of ESBL genes among all samples. ERIC-PCR demonstrated highly related E. coli clones among humans, poultry, and wild birds. Clinically relevant E. coli clone ST648 was found in humans and poultry. There is a shared pool of bla_CTX-M genes between humans and domesticated and wild birds in Nicaragua, and the results suggest shared clones of ESBL-producing E. coli. The study adds to the notion that wild birds and poultry can pick up antibiotic-resistant bacteria of human origin and function as a melting pot of resistance. Structured surveillance programs of antimicrobial resistance and a more regulated prescription of antibiotics are warranted in Nicaragua.

Antimicrobial-resistant and ESBL-producing Escherichia coli in different ecological niches in Bangladesh

INTRODUCTION

The rapid and wide-scale environmental spread of multidrug-resistant bacteria in different ecosystems has become a serious issue in recent years.

OBJECTIVES

To investigate the epidemiology of antimicrobial resistance and extended spectrum beta-lactamase (ESBL) in Bangladeshi wild birds and aquatic environments, samples were taken from Open Bill Stork (Anastomus oscitans) (OBS) and the nearby water sources.

METHODS

Water and fresh fecal samples were collected from several locations. All samples were processed and cultured for Escherichia coli and tested for antibiotic susceptibility against commonly used antibiotics. ESBL producers were characterized at genotypic level using polymerase chain reaction (PCR), sequencing, multilocus sequence typing, and rep-PCR.

RESULTS AND DISCUSSION

A total of 76 E. coli isolates from the 170 OBS and 8 E. coli isolates from three river sources were isolated. In total, 29% of E. coli isolated from OBS and all of the E. coli isolated from water sources were resistant to at least one of the tested antimicrobials. Resistant phenotypes were observed with all antimicrobials except tigecycline, gentamicin, imipenem, and chloramphenicol. Multidrug resistance was observed in 2.6% of OBS and 37.5% of the water isolates. Also, 1.2% of the ESBL-producing E. coli were isolated from OBS, whereas 50% of the E. coli isolated from water sources were ESBL producers possessing the CTX-M-15 gene. The most concerning aspect of our findings was the presence of human-associated E. coli sequence types in the water samples, for example, ST156-complex156, ST10-complex10 and ST46.

CONCLUSION

This study reports the presence of multidrug-resistant ESBL-producing E. coli in OBSs and nearby aquatic sources in Bangladesh.

Phenotypic and molecular characterization of extended-spectrum beta-lactamase-producing Escherichia coli in Bangladesh

Background

Resistance to cephalosporins in Enterobacteriaceae is mainly due to the production of extended-spectrum beta-lactamase (ESBL). Little is known about ESBL-producing bacteria in Bangladesh. Therefore, the study presents results of phenotypic and molecular characterization of ESBL-producing Escherichia coli from hospitals in Bangladesh.

Methods

A total of 339 E. coli isolated from patients with urinary tract and wound infections attending three different medical hospitals in urban and rural areas of Bangladesh between 2003–2007 were screened for ESBL-production by the double disk diffusion test. Isolates with ESBL-phenotype were further characterized by antibiotic susceptibility testing, PCR and sequencing of different β-lactamase and virulence genes, serotyping, and XbaI-macrorestriction followed by pulsed-field gel electrophoresis (PFGE).

Results

We identified 40 E. coli with ESBL phenotype. These isolates were resistant to ceftriaxone, ceftazidime, cefotaxime, aztreonam, cefepime, and nalidixic acid but remained susceptible to imipenem. All but one isolate were additionally resistant to ciprofloxacin, and 3 isolates were resistant to cefoxitin. ESBL genes of blaCTX-M-1-group were detected in all isolates; blaTEM-type and blaOXA-1-type genes were detected in 33 (82.5%) and 19 (47.5%) isolates, respectively. Virulence genes that are present in diarrhoeagenic E. coli were not found. Class-1 integron was present in 20 (50%) isolates. All the ESBL-producing E. coli isolates harbored plasmids ranging between 1.1 and 120 MDa. PFGE-typing revealed 26 different pulsotypes, but identical pulsotype showed 6 isolates of serotype O25:H4.

Conclusion

The prevalence of multidrug-resistant ESBL-producing E. coli isolates appears to be high and the majority of the isolates were positive for bla_CTX-M. Although there was genetic heterogeneity among isolates, presence of a cluster of isolates belonging to serotype O25:H4 indicates dissemination of the pandemic uropathogenic E. coli clone in Bangladesh.