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The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2020/2021. EFSA J 2023; 21:e07867. [PMID: 36891283 PMCID: PMC9987209 DOI: 10.2903/j.efsa.2023.7867] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Antimicrobial resistance (AMR) data on zoonotic and indicator bacteria from humans, animals and food are collected annually by the EU Member States (MSs) and reporting countries, jointly analysed by EFSA and ECDC and presented in a yearly EU Summary Report. This report provides an overview of the main findings of the 2020-2021 harmonised AMR monitoring in Salmonella spp., Campylobacter jejuni and C. coli in humans and food-producing animals (broilers, laying hens and turkeys, fattening pigs and bovines under 1 year of age) and relevant meat thereof. For animals and meat thereof, indicator E. coli data on the occurrence of AMR and presumptive Extended spectrum β-lactamases (ESBL)-/AmpC β-lactamases (AmpC)-/carbapenemases (CP)-producers, as well as the occurrence of methicillin-resistant Staphylococcus aureus are also analysed. In 2021, MSs submitted for the first time AMR data on E. coli isolates from meat sampled at border control posts. Where available, monitoring data from humans, food-producing animals and meat thereof were combined and compared at the EU level, with emphasis on multidrug resistance, complete susceptibility and combined resistance patterns to selected and critically important antimicrobials, as well as Salmonella and E. coli isolates exhibiting ESBL-/AmpC-/carbapenemase phenotypes. Resistance was frequently found to commonly used antimicrobials in Salmonella spp. and Campylobacter isolates from humans and animals. Combined resistance to critically important antimicrobials was mainly observed at low levels except in some Salmonella serotypes and in C. coli in some countries. The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, and bla NDM-5 genes) in pigs, bovines and meat thereof by a limited number of MSs (4) in 2021, requests a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC- producers) showed that encouraging progress have been registered in reducing AMR in food-producing animals in several EU MSs over the last years.
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Nakano R, Nakano A, Nishisouzu R, Hikosaka K, Suzuki Y, Kamoshida G, Tansho-Nagakawa S, Endo S, Kasahara K, Ono Y, Yano H. Genetic relatedness of third-generation cephalosporin-resistant Escherichia coli among livestock, farmers, and patients in Japan. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
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Characterization of Escherichia coli and Other Enterobacterales Resistant to Extended-Spectrum Cephalosporins Isolated from Dairy Manure in Ontario, Canada. Appl Environ Microbiol 2023; 89:e0186922. [PMID: 36695602 PMCID: PMC9972979 DOI: 10.1128/aem.01869-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Extended-spectrum cephalosporins (ESCs) resistance genes, such as blaCTX-M, blaCMY, and blaSHV, have been found regularly in bacteria from livestock. However, information on their distribution in dairy cattle in Canada and on the associated genome sequences of ESC-resistant Enterobacterales is sparse. In this study, the diversity and distribution of ESC-resistant Escherichia coli throughout manure treatments in six farms in Southern Ontario were assessed over a one-year period, and their ESC-resistance plasmids were characterized. The manure samples were enriched using selective media. The resulting isolates were screened via polymerase chain reaction for blaCTX-M, blaCMY, and blaSHV. No E. coli carrying blaSHV were detected. Escherichia coli (n = 248) carrying blaCTX-M or blaCMY underwent whole-genome sequencing using an Illumina MiSeq/NextSeq. These isolates were typed using multilocus sequence typing (MLST) and their resistance gene profiles. A subset of E. coli (n = 28) were sequenced using Oxford Nanopore Technologies. Plasmids were assembled using Unicycler and characterized via the resistance genes pattern, replicon type, plasmid MLST, phylogenetic analysis, and Mauve alignments. The recovery of ESC-resistant Enterobacterales (18 species, 8 genera) was drastically reduced in manure outputs. However, multiple treatment stages were needed to attain a significant reduction. 62 sequence types were identified, with ST10, ST46, ST58, ST155, ST190, ST398, ST685, and ST8761 being detected throughout the treatment pipeline. These STs overlapped with those found on multiple farms. The ESC-resistance determinants included CTX-M-1, -14, -15, -17, -24, -32, -55, and CMY-2. The plasmids carrying blaCTX-M were more diverse than were the plasmids carrying blaCMY. Known "epidemic plasmids" were detected for both blaCTX-M and blaCMY. IMPORTANCE The increase in antimicrobial resistance is of concern for human and animal health, especially when resistance is conferred to extended-spectrum cephalosporins, which are used to treat serious infections in both human and veterinary medicine. Bacteria carrying extended-spectrum cephalosporin resistance genes, including blaCTX-M and blaCMY, are frequently found in dairy manure. Manure treatment influences the loads and diversity of bacteria, including those carrying antimicrobial resistance genes, such as Enterobacterales and Escherichia coli. Any bacteria that survive the treatment process are subsequently applied to the environment. Enterobacterales carrying blaCTX-M or blaCMY can contaminate soil and crops consumed by humans and animals, thereby increasing the potential for antimicrobial resistance genes to integrate into the human gut microflora through horizontal gene transfer. This furthers the dissemination of resistance. Therefore, it is imperative to understand the effects manure treatments have on ESC-resistance in environmentally applied manure.
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Jiang Y, Wang ZY, Li QC, Lu MJ, Wu H, Mei CY, Shen PC, Jiao X, Wang J. Characterization of Extensively Drug-Resistant Salmonella enterica Serovar Kentucky Sequence Type 198 Isolates from Chicken Meat Products in Xuancheng, China. Microbiol Spectr 2023; 11:e0321922. [PMID: 36847509 PMCID: PMC10100706 DOI: 10.1128/spectrum.03219-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
The purpose of this study was to characterize extensively drug-resistant Salmonella enterica serovar Kentucky sequence type 198 (ST198) isolates from chicken meat products. Ten S. Kentucky strains obtained from chicken meat products in Xuancheng, China, carried 12 to 17 resistance genes, such as blaCTX-M-55, rmtB, tet(A), floR, and fosA3, combined with mutations within gyrA (S83F and D87N) and parC (S80I), resulting in resistance to numerous antimicrobial agents, including the clinically important antibiotics cephalosporin, ciprofloxacin, tigecycline, and fosfomycin. These S. Kentucky isolates shared a close phylogenetic relationship (21 to 36 single-nucleotide polymorphisms [SNPs]) and showed close genetic relatedness to two human clinical isolates from China. Three S. Kentucky strains were subjected to whole-genome sequencing using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) technology. All antimicrobial resistance genes were located on their chromosomes and clustered in one multiresistance region (MRR) and Salmonella genomic island (SGI) SGI1-K. The MRRs in three S. Kentucky strains were bounded by IS26 at both ends and were inserted downstream of the bcfABCDEFG cluster with 8-bp direct repeats. The MRRs were related to those of IncHI2 plasmids but differed by insertions, deletions, and rearrangements of multiple segments involving resistance genes and plasmid backbones. This finding suggests that the MRR fragment possibly originates from IncHI2 plasmids. Four SGI1-K variants with slight differences were identified in 10 S. Kentucky strains. Mobile elements, particularly IS26, play an essential role in forming distinct MRRs and SGI1-K structures. In conclusion, the emergence of extensively drug-resistant S. Kentucky ST198 strains containing numerous chromosomally located resistance genes is alarming and needs continued surveillance. IMPORTANCE Salmonella spp. are important foodborne pathogens, and multidrug-resistant (MDR) Salmonella strains have become a serious threat to clinical therapy. MDR S. Kentucky ST198 strains have been increasingly reported from various sources and have become a global risk. In this study, we described extensively drug-resistant S. Kentucky ST198 strains from chicken meat products from a city in China. Numerous resistance genes are clustered in the chromosomes of S. Kentucky ST198 strains, possibly acquired with the help of mobile elements. This would facilitate the spread of numerous resistance genes as intrinsic chromosomal genes within this global epidemic clone, with the potential to capture more resistance genes. The emergence and dissemination of extensively drug-resistant S. Kentucky ST198 pose a severe clinical and public health threat; therefore, continuous surveillance is warranted.
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Affiliation(s)
- Yue Jiang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Zhen-Yu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Qiu-Chun Li
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Meng-Jun Lu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Han Wu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Cai-Yue Mei
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Peng-Cheng Shen
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Jing Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
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105
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Impact of NG-Test CTX-M MULTI Immunochromatographic Assay on Antimicrobial Management of Escherichia coli Bloodstream Infections. Antibiotics (Basel) 2023; 12:antibiotics12030473. [PMID: 36978340 PMCID: PMC10044246 DOI: 10.3390/antibiotics12030473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/15/2023] [Accepted: 02/25/2023] [Indexed: 03/02/2023] Open
Abstract
Rapid detection of extended-spectrum-β-lactamase (ESBL) is of paramount importance to accelerate clinical decision-making, optimize antibiotic treatment, and implement adequate infection control measures. This study was aimed at assessing the impact of direct detection of CTX-M ESBL-producers on antimicrobial management of Escherichia coli bloodstream infections over a 2-year period. This study included all E. coli bloodstream infection (BSI) events that were serially processed through a rapid workflow with communication to the clinicians of direct detection of CTX-M ESBL-producers and conventional culture-based workflow. Antimicrobial management was retrospectively analyzed to assess the contribution of the rapid test result. A total of 199 E. coli BSI events with a report of direct detection of CTX-M ESBL production results were included. Of these, 33.7% (n = 67) and 66.3% (n = 132) were reported as positive and negative CTX-M producers, respectively. Detection of CTX-M positive results induced more antibiotic therapy modifications (mainly towards carbapenem-containing regimens, p < 0.01), and antimicrobial susceptibility testing results of CTX-M ESBL-producing E. coli isolates induced more antibiotic escalations towards carbapenem-containing regimens (p < 0.01). Direct detection of CTX-M ESBL-producing E. coli resulted in a remarkable rate of antibiotic optimizations on the same day of blood culture processing. Observing antibiotic management following the availability of antimicrobial susceptibility testing results, additional early optimizations in escalation could probably have been made if the rapid test data had been used. Detection of CTX-M negative results resulted in few therapeutic changes, which could have probably been higher, integrating epidemiological and clinical data.
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106
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Ariyawansa S, Gunawardana KN, Hapudeniya MM, Manelgamage NJ, Karunarathne CR, Madalagama RP, Ubeyratne KH, Wickramasinghe D, Tun HM, Wu P, Lam TTY, Chan OSK. One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka. Antibiotics (Basel) 2023; 12:antibiotics12030446. [PMID: 36978313 PMCID: PMC10044479 DOI: 10.3390/antibiotics12030446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/09/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Sri Lanka is a low-income country, as defined by the World Bank. The country suffered further economic downturn during the COVID-19 pandemic. This situation adversely affected the prioritization of policies and programs around healthcare and public health. In particular, inflation, fuel prices, and shortage of food supplies increased struggles to implement antimicrobial resistance (AMR) programs. However, in the long run, it is crucial to gather data and evidence to plan AMR policies and track interventions. (1) Aim: To establish and reiterate the importance of prioritizing AMR programs in the One Health framework, the Fleming Fellows collected and studied antimicrobial use/consumption (AMU/AMC) and resistance (AMR) in humans, food-producing animals, and the environment. (2) Methods: A systematic and cross-sectional study was conducted between 2019 and 2021. By way of coordinating an AMU/AMC and AMR prevalence study across six agencies from human health and food-producing animal sectors, the authors established a field epidemiology study, laboratory testing, and data processing at their institutions. AMU/AMC patterns were surveyed using questionnaires and interviews, while AMR samples were collected for antibiotic susceptibility tests and genomic tests. Samples were tested for phenotypic and genotypic resistance. (3) Results: In human samples, resistance was highest to beta-lactam antibiotics. In non-human samples, resistance was highest to erythromycin, a highest-priority, critically important antibiotic defined by the World Health Organization. From government records, tylosin was sold the most in the food-producing animal sector. (4) Conclusions: Sri Lanka AMU and AMR trends in human and non-human sectors can be ascertained by a One Health framework. Further coordinated, consistent, and sustainable planning is feasible, and can help implement an AMU/AMR surveillance system in Sri Lanka.
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Affiliation(s)
- Sujeewa Ariyawansa
- National Aquatic Resources Research and Development Agency, Crow Island, Colombo 01500, Sri Lanka
| | | | | | - Nimal J. Manelgamage
- Department of Animal Production and Health, No. 13, Getambe, Peradeniya, Kandy 20400, Sri Lanka
| | - Chinthana R. Karunarathne
- Department of Animal Production and Health, Veterinary Investigation Centre, Court Road, Wariyapola 60400, Sri Lanka
| | | | | | | | - Hein M. Tun
- The Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peng Wu
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Tommy T. Y. Lam
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | - Olivia S. K. Chan
- The School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 7 Sassoon Road, Pokfulam, Hong Kong SAR, China
- Correspondence: or
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107
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Edwards T, Williams CT, Olwala M, Andang'o P, Otieno W, Nalwa GN, Akindolire A, Cubas-Atienzar AI, Ross T, Tongo OO, Adams ER, Nabwera H, Allen S. Molecular surveillance reveals widespread colonisation by carbapenemase and extended spectrum beta-lactamase producing organisms in neonatal units in Kenya and Nigeria. Antimicrob Resist Infect Control 2023; 12:14. [PMID: 36814315 PMCID: PMC9945588 DOI: 10.1186/s13756-023-01216-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/13/2023] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVES Neonatal sepsis, a major cause of death amongst infants in sub-Saharan Africa, is often gut derived. Gut colonisation by Enterobacteriaceae producing extended spectrum beta-lactamase (ESBL) or carbapenemase enzymes can lead to antimicrobial-resistant (AMR) or untreatable infections. We sought to explore the rates of colonisation by ESBL or carbapenemase producers in two neonatal units (NNUs) in West and East Africa. METHODS Stool and rectal swab samples were taken at multiple timepoints from newborns admitted to the NNUs at the University College Hospital, Ibadan, Nigeria and the Jaramogi Oginga Odinga Teaching and Referral Hospital, Kisumu, western Kenya. Samples were tested for ESBL and carbapenemase genes using a previously validated qPCR assay. Kaplan-Meier survival analysis was used to examine colonisation rates at both sites. RESULTS In total 119 stool and rectal swab samples were taken from 42 infants admitted to the two NNUs. Colonisation with ESBL (37 infants, 89%) was more common than with carbapenemase producers (26, 62.4%; P = 0.093). Median survival time before colonisation with ESBL organisms was 7 days and with carbapenemase producers 16 days (P = 0.035). The majority of ESBL genes detected belonged to the CTX-M-1 (36/38; 95%), and CTX-M-9 (2/36; 5%) groups, and the most prevalent carbapenemase was blaNDM (27/29, 93%). CONCLUSIONS Gut colonisation of neonates by AMR organisms was common and occurred rapidly in NNUs in Kenya and Nigeria. Active surveillance of colonisation will improve the understanding of AMR in these settings and guide infection control and antibiotic prescribing practice to improve clinical outcomes.
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Affiliation(s)
- Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK.
| | | | - Macrine Olwala
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | - Pauline Andang'o
- Department of Public Health, School of Public Health and Community Development, Maseno University, Maseno, Kenya
| | - Walter Otieno
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | - Grace N Nalwa
- Jaramogi Oginga Odinga Teaching and Referral Hospital, Jomo Kenyatta Highway Kaloleni Kisumu KE Central, Maseno, Kenya
| | | | - Ana I Cubas-Atienzar
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Toby Ross
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Emily R Adams
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Helen Nabwera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Stephen Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
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108
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Akunda IK, Kariuki DW, Matulis G, Mwaura P, Maina B, Mohammed H, Paul A, Onyambu FG, Ole Kwallah A, Martins DJ, von Fricken ME, Kamau JM. Antimicrobial resistance patterns and characterisation of emerging beta-lactamase-producing Escherichia coli in camels sampled from Northern Kenya. Vet Med Sci 2023; 9:1407-1416. [PMID: 36795022 DOI: 10.1002/vms3.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Animal husbandry practices in different livestock production systems and increased livestock-wildlife interactions are thought to be primary drivers of antimicrobial resistance (AMR) in Arid and Semi-Arid Lands (ASALs). Despite a tenfold increase in the camel population within the last decade, paired with widespread use of camel products, there is a lack of comprehensive information concerning beta-lactamase-producing Escherichia coli (E. coli) within these production systems. OBJECTIVES Our study sought to establish an AMR profile and to identify and characterise emerging beta-lactamase-producing E. coli isolated from faecal samples obtained from camel herds in Northern Kenya. METHODS The antimicrobial susceptibility profiles of E. coli isolates were established using the disk diffusion method, with beta-lactamase (bla) gene PCR product sequencing performed for phylogenetic grouping and genetic diversity assessments. RESULTS Here we show, among the recovered E. coli isolates (n = 123), the highest level of resistance was observed for cefaclor at 28.5% of isolates, followed by cefotaxime at 16.3% and ampicillin at 9.7%. Moreover, extended-spectrum beta-lactamase (ESBL)-producing E. coli harbouring the blaCTX-M-15 or blaCTX-M-27 genes were detected in 3.3% of total samples, and are associated with phylogenetic groups B1, B2 and D. Multiple variants of non-ESBL blaTEM genes were detected, the majority of which were the blaTEM-1 and blaTEM-116 genes. CONCLUSIONS Findings from this study shed light on the increased occurrence of ESBL- and non-ESBL-encoding gene variants in E. coli isolates with demonstrated multidrug resistant phenotypes. This study highlights the need for an expanded One Health approach to understanding AMR transmission dynamics, drivers of AMR development, and appropriate practices for antimicrobial stewardship in camel production systems within ASALs.
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Affiliation(s)
- Irene Karegi Akunda
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.,One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Daniel W Kariuki
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Graham Matulis
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Patrick Mwaura
- One Health Center, Institute of Primate Research, Nairobi, Kenya
| | - Brian Maina
- Centre of Microbiology, Washington State University, Nairobi, Kenya
| | - Halima Mohammed
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya
| | - Ayieko Paul
- Regional Veterinary Investigation Laboratory, Nakuru, Kenya
| | - Frank G Onyambu
- Centre for Molecular Biosciences and Genomics, Nairobi, Kenya.,School of Health Sciences, Meru University of Science and Technology, Meru, Kenya
| | - Allan Ole Kwallah
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Dino J Martins
- Mpala Research Centre, Nanyuki, Kenya.,Turkana Basin Institute, Stony Brook University, Stony Brook, NY, USA
| | - Michael E von Fricken
- Department of Global and Community Health, George Mason University, Fairfax County, Virginia
| | - Joseph M Kamau
- One Health Center, Institute of Primate Research, Nairobi, Kenya
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109
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Henriot CP, Celle H, Klaba V, Biguenet A, Miège C, Daval A, Amiotte-Suchet P, Beugnot JC, Karbowiak T, Bertrand X. Effect of a karst system (France) on extended spectrum beta-lactamase (ESBL)-producing Escherichia coli. WATER RESEARCH 2023; 230:119582. [PMID: 36642030 DOI: 10.1016/j.watres.2023.119582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Karst aquifers are an important water resource worldwide particularly exposed to anthropogenic pollution, including antibiotic-resistance. The release of antibiotic-resistant bacterial pathogens in the environment is a major public health challenge worldwide. In this One Health study, we aimed to determine the effect of karst on antibiotic-resistant bacteria. For this purpose, we determined the concentrations of extended-spectrum β-lactamases-producing Escherichia coli (ESBL-Ec) for 92 weeks in a rural karst hydrosystem providing drinking water. ESBL-Ec isolates (n = 130) were sequenced by whole genome sequencing. We analysed the isolates at different levels of granularity, i.e., phylogroup, sequence type, presence of antibiotic-resistance genes, mutations conferring antibiotic-resistance, and virulence genes. The ESBL-Ec concentrations were spatially and temporally heterogeneous in the studied karst hydrosystem. ESBL-Ec isolates survived in the karst and their concentrations were mostly explained by the hydrodynamic of the hydrosystem. We demonstrate that the studied karst has no filtration effect on ESBL-Ec, either quantitatively (i.e., in the ESBL-Ec concentrations) or qualitatively (i.e., in the genetic characteristics of ESBL-Ec isolates).
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Affiliation(s)
- Charles P Henriot
- Chrono-Environnement UMR 6249, CNRS, Université de Franche-Comté, Besançon 25000, France.
| | - Hélène Celle
- Chrono-Environnement UMR 6249, CNRS, Université de Franche-Comté, Besançon 25000, France
| | - Victor Klaba
- Chrono-Environnement UMR 6249, CNRS, Université de Franche-Comté, Besançon 25000, France
| | - Adrien Biguenet
- Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 Boulevard Fleming, Besançon 25030, France
| | - Cécile Miège
- INRAE, RiverLy, 5 rue de la Doua, CS20244, Villeurbanne 69625, France
| | - Amandine Daval
- INRAE, RiverLy, 5 rue de la Doua, CS20244, Villeurbanne 69625, France
| | - Philippe Amiotte-Suchet
- UMR CNRS 6282 Biogéosciences, Université de Bourgogne Franche-Comté, 6 Boulevard Gabriel, Dijon 21000, France
| | - Jean-Charles Beugnot
- UMR CNRS 6174 FEMTO-ST, Université de Bourgogne Franche-Comté, 15B Avenue des Montboucons, Besançon 25030, France
| | - Thomas Karbowiak
- Institut Agro Dijon, University Bourgogne Franche-Comté, UMR PAM 02 102, 1 Esplanade Erasme, Dijon 21000, France
| | - Xavier Bertrand
- Chrono-Environnement UMR 6249, CNRS, Université de Franche-Comté, Besançon 25000, France; Hygiène Hospitalière, Centre Hospitalier Universitaire de Besançon, 3 Boulevard Fleming, Besançon 25030, France
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110
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Higgins O, Chueiri A, O'Connor L, Lahiff S, Burke L, Morris D, Pfeifer NM, Santamarina BG, Berens C, Menge C, Caniça M, Manageiro V, Kisand V, Hassan MM, Gardner B, van Vliet AHM, La Ragione RM, Gonzalez-Zorn B, Smith TJ. Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification. Microbiol Spectr 2023; 11:e0331622. [PMID: 36511696 PMCID: PMC9927312 DOI: 10.1128/spectrum.03316-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022] Open
Abstract
Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.
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Affiliation(s)
- Owen Higgins
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Alexandra Chueiri
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Sinéad Lahiff
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Liam Burke
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Dearbhaile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
| | - Nicola Maria Pfeifer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Belén González Santamarina
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Berens
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, Jena, Germany
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Marwa M. Hassan
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Brian Gardner
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Roberto M. La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Bruno Gonzalez-Zorn
- Antimicrobial Resistance Unit, Veterinary School and VISAVET, Complutense University of Madrid, Spain
| | - Terry J. Smith
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
- Centre for One Health, Ryan Institute, University of Galway, Galway, Ireland
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Hirano T, Ohge H, Ikawa K, Uegami S, Watadani Y, Shigemoto N, Yoshimura K, Kitagawa H, Kaiki Y, Morikawa N, Takahashi S. Pharmacokinetics of flomoxef in plasma, peritoneal fluid, peritoneum, and subcutaneous adipose tissue of patients undergoing lower gastrointestinal surgery: Dosing considerations based on site-specific pharmacodynamic target attainment. J Infect Chemother 2023; 29:186-192. [PMID: 36341996 DOI: 10.1016/j.jiac.2022.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/08/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Flomoxef is generally used to treat abdominal infections and as antibiotic prophylaxis during lower gastrointestinal surgery. It is reportedly effective against extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae and an increasingly valuable alternative to carbapenems. However, its abdominal pharmacokinetics remain unclear. Herein, pharmacokinetic analysis of flomoxef in the abdominal tissue was conducted to simulate dosing regimens for pharmacodynamic target attainment in abdominal sites. METHODS Flomoxef (1 g) was administered intravenously to a patient 30 min before commencing elective lower gastrointestinal surgery. Samples of plasma, peritoneal fluid, peritoneum, and subcutaneous adipose tissue were collected during surgery. The flomoxef tissue concentrations were measured. Accordingly, non-compartmental and compartmental pharmacokinetic parameters were calculated, and simulations were conducted to evaluate site-specific pharmacodynamic target values. RESULTS Overall, 41 plasma samples, 34 peritoneal fluid samples, 38 peritoneum samples, and 41 subcutaneous adipose samples from 10 patients were collected. The mean peritoneal fluid-to-plasma ratio in the areas under the drug concentration-time curve was 0.68, the mean peritoneum-to-plasma ratio was 0.40, and the mean subcutaneous adipose tissue-to-plasma was 0.16. The simulation based on these results showed the dosing regimens (q8h [3 g/day] and q6h [4 g/day]) achieved the bactericidal effect (% T > minimum inhibitory concentration [MIC] = 40%) in all tissues at an MIC of 1 mg/L. CONCLUSIONS We elucidated the pharmacokinetics of flomoxef and simulated pharmacodynamics target attainment in the abdominal tissue. This study provides evidence concerning the use of optimal dosing regimens for treating abdominal infection caused by strains like ESBL-producing bacteria.
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Affiliation(s)
- Toshinori Hirano
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Kazuro Ikawa
- Department of Clinical Pharmacotherapy, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Shinnosuke Uegami
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Yusuke Watadani
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Norifumi Shigemoto
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Kosuke Yoshimura
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Yuki Kaiki
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Norifumi Morikawa
- Department of Clinical Pharmacotherapy, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
| | - Shinya Takahashi
- Department of Surgery, Graduate School of Biomedical & Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture, 734-8551, Japan.
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Bhowmick S, Pal S, Sunder J, Sujatha T, De AK, Mondal T, Singh AD, Joardar SN, Batabyal K, Dutta TK, Bandyopadhyay S, Tiwari A, Samanta I. Exploring broilers and native fowls of Andaman and Nicobar Islands as a source of β-lactamase-producing Enterobacteriaceae even with limited anthropogenic activities and docking-based identification of catalytic domains in novel β-lactamase variants. Front Vet Sci 2023; 9:1075133. [PMID: 36686169 PMCID: PMC9849777 DOI: 10.3389/fvets.2022.1075133] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Objectives The present study was conducted to detect the occurrence of β-lactamase and biofilm-producing Escherichia coli, Salmonella, and Klebsiella in broilers and native fowl reared in the Andaman and Nicobar Islands, India. The study also included molecular docking experiments to confirm the nature of the catalytic domains found in the β-lactamase variants obtained and to reveal the clonal relationship of the isolates with human clinical strains from the database. Materials and methods A total of 199 cloacal swabs were collected from five poultry breeds/varieties (broiler, Vanraja, Desi, Nicobari, and layer) in three districts of the Andaman and Nicobar Islands. E. coli, Salmonella enterica, and Klebsiella pneumoniae were isolated by standard techniques and confirmed by PCR. Phenotypical β-lactamase producers were identified by a double-disc test. The genes (bla CTX, bla SHV, bla TEM , and bla AmpC) were screened, and selected sequences of β-lactamase variants were submitted to DDBJ. Homology modeling, model validation, and active site identification of different β-lactamase variants were done by the SWISS-MODEL. Molecular docking was performed to identify the catalytic domains of the β-lactamase variants. The selected β-lactamase sequences were compared with the Indian ESBL sequences from human clinical strains in NCBI-GenBank. Results In total, 425 Enterobacteriaceae strains were isolated from the collected samples. Klebsiella pneumoniae (42.58%) was found to be the most prevalent, followed by Salmonella enterica (30.82%) and E. coli (26.58%). The phenotypical antibiogram of all 425 isolates showed the highest resistance against oxytetracycline (61-76%) and the lowest against gentamicin (15-20%). Phenotypical production of β-lactamase enzymes was observed in 141 (33.38%) isolates. The isolation rate of β-lactamase producing E. coli, Salmonella enterica, and Klebsiella pneumoniae was significantly higher (p < 0.05) in the birds reared in the South Andaman district (25.6, 17.5, and 18.7%, respectively) than in Nicobar (11.5, 7.6, 7.1%, respectively). Genotyping of the β-lactamase-producing isolates revealed the maximum possession of bla TEM, followed by bla SHV and bla CTX - M. The nucleotide sequences were found to be similar with bla CTX - M-15, bla SHV - 11, bla SHV - 27, bla SHV - 228, bla TEM - 1, and bla AmpC in BLAST search. Distribution of studied biofilm-associated genes in Enterobacteriaceae strains from different varieties of the birds revealed that the layer birds had the maximum possession, followed by Vanraja, Desi, broilers, and Nicobari fowls. The phylogenetic analysis of selected sequences revealed a partial clonal relationship with human clinical strains of the Indian subcontinent. Molecular docking depicted the Gibbs free energy release for 10 different macromolecules (proteins) and ligand (antibiotic) complexes, ranging from -8.1 (SHV-27 + cefotaxime) to -7 (TEM-1 + cefotaxime) kcal/mol. Conclusion and relevance The study revealed β-lactamase variants circulating in the fowl population of the Andaman and Nicobar Islands (India), even in remote places with low anthropogenic activity. Most of the strains possessed bla TEM - 1, followed by bla CTX - M-15. Possession of bla SHV - 11, bla SHV - 27, and bla SHV - 228 in poultry Enterobacteriaceae strains was not reported earlier from any part of the world. The phylogenetic analysis revealed a partial clonal relationship of β-lactamase sequences with the human clinical strains isolated from the Indian subcontinent.
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Affiliation(s)
- Sneha Bhowmick
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India,Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Surajit Pal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Jai Sunder
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - T. Sujatha
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Tousif Mondal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Abhishek D. Singh
- Department of Veterinary Public Health, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Siddhartha Narayan Joardar
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Kunal Batabyal
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India
| | - Tapan Kumar Dutta
- Department of Veterinary Microbiology, Central Agricultural University, Aizawl, Mizoram, India
| | - Samiran Bandyopadhyay
- ICAR-Indian Veterinary Research Institute, Eastern Regional Station, Kolkata, West Bengal, India
| | - Ananda Tiwari
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland,Ananda Tiwari ✉
| | - Indranil Samanta
- Department of Veterinary Microbiology, West Bengal University of Animal and Fishery Sciences, Kolkata, West Bengal, India,*Correspondence: Indranil Samanta ✉; ✉
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Fang H, Lee CH, Cao H, Jiang S, So SYC, Tse CWS, Cheng VCC, Ho PL. Evaluation of a Lateral Flow Immunoassay for Rapid Detection of CTX-M Producers from Blood Cultures. Microorganisms 2023; 11:microorganisms11010128. [PMID: 36677420 PMCID: PMC9860775 DOI: 10.3390/microorganisms11010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/30/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Bacteremia caused by extended-spectrum β-lactamases-producing Enterobacterales has increased rapidly and is mainly attributed to CTX-M enzymes. This study aimed to evaluate the NG-Test® CTX-M MULTI lateral flow assay (CTX-M LFA) for rapid detection of CTX-M producers in blood cultures (BCs) positive for Gram-negative bacilli in spiked and clinical BCs. Retrospective testing was performed on BC bottles spiked with a collection of well-characterized Enterobacterales isolates producing CTX-M (n = 15) and CTX-M-like (n = 27) β-lactamases. Prospective testing of clinical, non-duplicate BCs (n = 350) was performed in two hospital microbiology laboratories from April 2021 to March 2022 following detection of Gram-negative bacilli by microscopic examination. Results were compared against molecular testing as the reference. In the spiked BCs, the CTX-M LFA correctly detected all CTX-M producers including 5 isolates with hybrid CTX-M variants. However, false-positive results were observed for several CTX-M-like β-lactamases, including OXY-1-3, OXY-2-8, OXY-5-3, FONA-8, -9, -10, 11, 13 and SFO-1. In clinical BCs, the CTX-M LFA showed 100% (95% CI, 96.0-100%) sensitivity and 99.6% (97.9-100%) specificity. In conclusion, this study showed that rapid detection of CTX-M producers in BC broths can be reliably achieved using the CTX-M LFA, thus providing an opportunity for early optimization of antibiotics.
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Affiliation(s)
- Hanshu Fang
- Department of Microbiology, Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
| | - Chung-Ho Lee
- Department of Clinical Pathology, Kwong Wah Hospital, Hospital Authority, Hong Kong, China
| | - Huiluo Cao
- Department of Microbiology, Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
| | - Shuo Jiang
- Department of Microbiology, Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
| | - Simon Yung-Chun So
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
| | - Cindy Wing-Sze Tse
- Department of Clinical Pathology, Kwong Wah Hospital, Hospital Authority, Hong Kong, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
| | - Pak-Leung Ho
- Department of Microbiology, Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Department of Microbiology, Queen Mary Hospital, Hospital Authority, Hong Kong, China
- Correspondence: ; Tel.: +852-2255-2579
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Song HJ, Moon DC, Kim SJ, Mechesso AF, Choi JH, Boby N, Kang HY, Na SH, Yoon SS, Lim SK. Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Cattle and Pigs in Korea. Foodborne Pathog Dis 2023; 20:7-16. [PMID: 36577050 DOI: 10.1089/fpd.2022.0051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Antimicrobial-resistant bacteria isolated from food animals pose a major health threat to the public on this planet. This study aimed to determine the susceptibility profiles of Escherichia coli isolated from cattle and pig fecal samples and investigate the molecular characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli using gene identification, conjugation, and Southern blot approach. Overall 293 E. coli were recovered from cattle (120 isolates) and pigs (173 isolates) in 7 provinces of Korea during 2017-2018. Ampicillin, chloramphenicol, streptomycin, and sulfisoxazole resistance rates were the highest in pigs' isolates (>60%, p ≤ 0.001) compared to that in cattle (3-39%). Multidrug resistance (MDR) was higher in pig isolates (73%) than in cattle (31%), and the MDR profile usually includes streptomycin, sulfisoxazole, and tetracycline. Resistance to critically important antimicrobials such as ceftiofur, colistin, and ciprofloxacin was higher in weaners than those from finishers in pigs. The qnrS gene was detected in 13% of the pig isolates. Eight isolates from pigs and one isolate from cattle were identified as ESBL-producers and ESBL genes belonged to blaCTX-M-55 (n = 4), blaCTX-M-14 (n = 3), and blaCTX-M-65 (n = 2). Notably, the blaCTX-M-65 and qnrS1 genes were found to be carried together in an identical plasmid (IncHI2) in two isolates from finisher pigs. The blaCTX-M-carrying isolates belonged to phylogenetic groups B1 (n = 4), B2 (n = 2), A (n = 2), and D (n = 1). The blaCTX-M genes and non-β-lactam resistance traits were transferred to the E. coli J53 recipient from seven blaCTX-M-positive strains isolated from pigs. The blaCTX-M genes belonged to the IncI1α, IncFII, and IncHI2 plasmids and are also associated with the ISEcp1, IS26, IS903, and orf477 elements. These findings suggested the possibility of blaCTX-M-carrying E. coli transmission to humans through direct contact with cattle and pigs or contamination of food products.
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Affiliation(s)
- Hyun-Ju Song
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Dong Chan Moon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea.,Division of Antimicrobial Resistance, Centre for Infectious Diseases Research, Korea Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Su-Jeong Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Abraham Fikru Mechesso
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea.,Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ji-Hyun Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Naila Boby
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Hee Young Kang
- Division of Antimicrobial Resistance, Centre for Infectious Diseases Research, Korea Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Seok-Hyeon Na
- Division of Antimicrobial Resistance, Centre for Infectious Diseases Research, Korea Centers for Disease Control and Prevention, Cheongju, South Korea
| | - Soon-Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
| | - Suk-Kyung Lim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon-si, Republic of Korea
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Karami-Zarandi M, Rahdar HA, Esmaeili H, Ranjbar R. Klebsiella pneumoniae: an update on antibiotic resistance mechanisms. Future Microbiol 2023; 18:65-81. [PMID: 36632990 DOI: 10.2217/fmb-2022-0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Klebsiella pneumoniae colonizes mucosal surfaces of healthy humans and is responsible for one third of all Gram-negative infections in hospitalized patients. K. pneumoniae is compatible with acquiring antibiotic resistance elements such as plasmids and transposons encoding various β-lactamases and efflux pumps. Mutations in different proteins such as β-lactamases, efflux proteins, outer membrane proteins, gene replication enzymes, protein synthesis complexes and transcription enzymes also generate resistance to antibiotics. Biofilm formation is another strategy that facilitates antibiotic resistance. Resistant strains can be treated by combination therapy using available antibiotics, though proper management of antibiotic consumption in hospitals is important to reduce the emergence and proliferation of resistance to current antibiotics.
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Affiliation(s)
- Morteza Karami-Zarandi
- Department of Microbiology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, 4513956111, Iran
| | - Hossein Ali Rahdar
- Department of Microbiology, School of Medicine, Iranshahr University of Medical Sciences, Iranshahr, 7618815676, Iran
| | - Hadi Esmaeili
- Applied Virology Research Center, Baqiyatallah University of Medical Sciences, Tehran, 1435916471, Iran
| | - Reza Ranjbar
- Molecular Biology Research Center, Systems Biology & Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, 1435916471, Iran
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Yoshimura K, Ohge H, Ikawa K, Uegami S, Watadani Y, Shigemoto N, Hirano T, Kitagawa H, Kaiki Y, Morikawa N, Takahashi S. Ceftolozane-Tazobactam Pharmacokinetics in the Abdominal Tissue of Patients Undergoing Lower Gastrointestinal Surgery: Dosing Considerations Based on Site-Specific Pharmacodynamic Target Attainment. Infect Dis Ther 2023; 12:193-207. [PMID: 36418742 PMCID: PMC9868209 DOI: 10.1007/s40121-022-00720-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/21/2022] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Recently, complicated intra-abdominal infections (cIAI) have been caused not only by Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, and Pseudomonas aeruginosa, but also by extended-spectrum β-lactamase-producing Enterobacterales members. Ceftolozane-tazobactam (CTLZ-TAZ) is considered to exhibit therapeutic effects against cIAI. Studies on the concentrations of antibiotics in abdominal tissues directly affected by cIAI are limited. Therefore, in this study, we investigated the pharmacokinetics of CTLZ-TAZ in abdominal tissue and simulated the administration regimen required to achieve the pharmacodynamic target for cIAI-causing bacteria. METHODS Patients scheduled for elective lower gastrointestinal surgery were intravenously administered preoperative CTLZ-TAZ (1 g CTLZ and 0.5 g TAZ). Plasma, peritoneal fluid, peritoneum, and subcutaneous adipose tissue samples were collected during the surgery, and CTLZ as well as TAZ concentrations were measured. The noncompartmental and compartmental pharmacokinetic parameters were then estimated. Site-specific pharmacodynamic target attainment analysis using 1.5 g of CTLZ-TAZ was performed. RESULTS CTLZ-TAZ was administered to nine patients (once to five patients and twice to four patients). The mean peritoneal fluid-to-plasma ratio (one dose/two doses) for CTLZ was 0.74/1.15, which was slightly higher than the mean peritoneal fluid-to-plasma ratio for TAZ (0.95/1.13). The ratio for subcutaneous adipose was lower than those for peritoneal fluid and peritoneum tissues. We also discovered that the average ratio of CTLZ and TAZ concentrations in all tissues was maintained at or above 2:1. In our investigation of pharmacodynamic target attainment in each tissue, the desired bactericidal effect was attained with all CTLZ-TAZ (1.5 g) administration regimens [q12h (3 g/day), q8h (4.5 g/day), and q6h (6 g/day)]. CONCLUSION To the best of our knowledge, this is the first study investigating the optimal pharmacodynamic level of CTLZ-TAZ in the abdominal tissue against cIAI-causing bacteria. This study also serves as a guideline for designing an optimal administration regimen based on pharmacodynamic target attainment for cIAI-causing bacteria. DETAILS OF THE TRIAL REGISTRATION The institutional review board of Hiroshima University Hospital, CRB6180006. The Japan Registry of Clinical Trials, jRCTs061190025.
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Affiliation(s)
- Kosuke Yoshimura
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Kazuro Ikawa
- Department of Clinical Pharmacotherapy, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Shinnosuke Uegami
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Yusuke Watadani
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Norifumi Shigemoto
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Toshinori Hirano
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Yuki Kaiki
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Norifumi Morikawa
- Department of Clinical Pharmacotherapy, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
| | - Shinya Takahashi
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-Ku, Hiroshima City, Hiroshima Prefecture 734-8551 Japan
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Mills EG, Martin MJ, Luo TL, Ong AC, Maybank R, Corey BW, Harless C, Preston LN, Rosado-Mendez JA, Preston SB, Kwak YI, Backlund MG, Bennett JW, Mc Gann PT, Lebreton F. A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network. Genome Med 2022; 14:147. [PMID: 36585742 PMCID: PMC9801656 DOI: 10.1186/s13073-022-01150-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Extra-intestinal pathogenic Escherichia coli (ExPEC) are a leading cause of bloodstream and urinary tract infections worldwide. Over the last two decades, increased rates of antibiotic resistance in E. coli have been reported, further complicating treatment. Worryingly, specific lineages expressing extended-spectrum β-lactamases (ESBLs) and fluoroquinolone resistance have proliferated and are now considered a serious threat. Obtaining contemporary information on the epidemiology and prevalence of these circulating lineages is critical for containing their spread globally and within the clinic. METHODS Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. RESULTS The isolates represented two main phylogenetic groups, B2 and D, with six lineages accounting for 53% of strains: ST-69, ST-73, ST-95, ST-131, ST-127, and ST-1193. Twenty-seven percent of the primary isolates were multidrug resistant (MDR) and 5% carried an ESBL gene. Importantly, 74% of the ESBL-E.coli were co-resistant to fluoroquinolones and mostly belonged to pandemic ST-131 and emerging ST-1193. SNP-based detection of possible outbreaks identified 95 potential transmission clusters totaling 258 isolates (12% of the whole population) from ≥ 2 patients. While the proportion of MDR isolates was enriched in the set of putative transmission isolates compared to sporadic infections (35 vs 27%, p = 0.007), a large fraction (61%) of the predicted outbreaks (including the largest cluster grouping isolates from 12 patients) were caused by the transmission of non-MDR clones. CONCLUSION By coupling in-depth genomic characterization with a complete sampling of clinical isolates for a full year, this study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins. This increased awareness is key for implementing effective WGS-based surveillance as a routine technology for infection control.
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Affiliation(s)
- Emma G. Mills
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Melissa J. Martin
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ting L. Luo
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Ana C. Ong
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Rosslyn Maybank
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Brendan W. Corey
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Casey Harless
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Lan N. Preston
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Joshua A. Rosado-Mendez
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Scott B. Preston
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Yoon I. Kwak
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Michael G. Backlund
- grid.414467.40000 0001 0560 6544Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD USA
| | - Jason W. Bennett
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Patrick T. Mc Gann
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Francois Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, MD USA
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Sun L, Meng N, Wang Z, Hong J, Dai Y, Wang Z, Wang J, Jiao X. Genomic Characterization of ESBL/AmpC-Producing Escherichia coli in Stray Dogs Sheltered in Yangzhou, China. Infect Drug Resist 2022; 15:7741-7750. [PMID: 36597449 PMCID: PMC9805715 DOI: 10.2147/idr.s397872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Purpose Limited data are available on the prevalence and antimicrobial resistance of extended spectrum β-lactamase- (ESBL) and AmpC β-lactamase-producing Escherichia coli in stray dogs. We aimed to investigate the genomic characteristics of ESBL/AmpC-producing E. coli isolated from stray dogs sheltered in Yangzhou, China. Methods We collected 156 samples including 115 fecal swabs, 35 kennel floor swabs, two breeder hand and shoe sole swabs, and four feed samples. The isolates were tested for resistance by antimicrobial susceptibility testing and further analyzed for cefotaxime-resistant E. coli isolates by whole genome sequencing. Results We identified 80 cefotaxime-resistant E. coli isolates (51.3%), 59 isolates (73.8%) from feces and 21 (26.2%) from the environment. Whole-genome sequencing analysis showed that bla CTX-M-15 (n=30) and bla CTX-M-55 (n=29) were the most prevalent genotypes. Two isolates only carried the AmpC β-lactamase gene bla CMY-2; one isolate had a combination of AmpC β-lactamase gene bla DHA-1 and ESBL β-lactamase gene bla CTX-M-14. Other important resistance genes such as bla OXA-10, bla TEM-1B, bla TEM-135, bla TEM-106, tet(A), qnrS1, qnrB4, and oqxAB were also detected. The serotype combination was highly abundant, with O10:H25 predominating (n=12). Most cefotaxime-resistant E. coli isolates belonged to phylogroup A (62.5%, n=50), followed by phylogroup B1 (26.3%, n=21). Thirty different sequence types (STs) and 27 distinct plasmid replicons were identified, among which ST2325 (n=12) and IncFII (n=38) was the most frequent ST and plasmid, respectively. ESBL/AmpC-producing isolates were divided into four major clades; clade IV was the primary lineage containing 37 isolates from feces and 13 from the environment. Three high-risk E. coli clone ST23 strains and one ST10 strain belonged to clades III and IV, respectively. Conclusion Our study provides a comprehensive overview of resistance profiles and genomic characteristics in ESBL/AmpC-producing E. coli and highlights the possible role of stray dogs as an antibiotic resistance gene reservoir.
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Affiliation(s)
- Lin Sun
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
| | - Nan Meng
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Zecheng Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Jiaxin Hong
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yuqi Dai
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Zhenyu Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China
| | - Jing Wang
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China,Correspondence: Jing Wang; Xinan Jiao, Email ;
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People’s Republic of China,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, People’s Republic of China
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Liao M, Wu J, Li Y, Lu X, Tan H, Chen S, Huang W, Lian X, Sun J, Liao X, Liu Y, Feng S, Zhang R. Prevalence and Persistence of Ceftiofur-Resistant Escherichia coli in A Chicken Layer Breeding Program. Animals (Basel) 2022; 13:ani13010090. [PMID: 36611699 PMCID: PMC9817529 DOI: 10.3390/ani13010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were blaCTX-M-55, blaCMY and blaNDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms.
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Affiliation(s)
- Meina Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jiaen Wu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Yafei Li
- Institute of Quality Standard and Monitoring Technology for Agro-Products, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xiaoqing Lu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Huizhen Tan
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Shanshan Chen
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Wenqing Huang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Xinlei Lian
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Jian Sun
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoping Liao
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Yahong Liu
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
| | - Saixiang Feng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (S.F.); (R.Z.)
| | - Rongmin Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (S.F.); (R.Z.)
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Genetic Predictive Factors for Nonsusceptible Phenotypes and Multidrug Resistance in Expanded-Spectrum Cephalosporin-Resistant Uropathogenic Escherichia coli from a Multicenter Cohort: Insights into the Phenotypic and Genetic Basis of Coresistance. mSphere 2022; 7:e0047122. [PMID: 36377882 PMCID: PMC9769571 DOI: 10.1128/msphere.00471-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance in urinary tract infections (UTIs) is a major public health concern. This study aims to characterize the phenotypic and genetic basis of multidrug resistance (MDR) among expanded-spectrum cephalosporin-resistant (ESCR) uropathogenic Escherichia coli (UPEC) causing UTIs in California patient populations. Between February and October 2019, 577 ESCR UPEC isolates were collected from patients at 6 clinical laboratory sites across California. Lineage and antibiotic resistance genes were determined by analysis of whole-genome sequence data. The lineages ST131, ST1193, ST648, and ST69 were predominant, representing 46%, 5.5%, 4.5%, and 4.5% of the collection, respectively. Overall, 527 (91%) isolates had an expanded-spectrum β-lactamase (ESBL) phenotype, with blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-M-14 being the most prevalent ESBL genes. In the 50 non-ESBL phenotype isolates, 40 (62%) contained blaCMY-2, which was the predominant plasmid-mediated AmpC (pAmpC) gene. Narrow-spectrum β-lactamases, blaTEM-1B and blaOXA-1, were also found in 44.9% and 32.1% of isolates, respectively. Among ESCR UPEC isolates, isolates with an ESBL phenotype had a 1.7-times-greater likelihood of being MDR than non-ESBL phenotype isolates (P < 0.001). The cooccurrence of blaCTX-M-15, blaOXA-1, and aac(6')-Ib-cr within ESCR UPEC isolates was strongly correlated. Cooccurrence of blaCTX-M-15, blaOXA-1, and aac(6')-Ib-cr was associated with an increased risk of nonsusceptibility to piperacillin-tazobactam, cefepime, fluoroquinolones, and amikacin as well as MDR. Multivariate regression revealed the presence of blaCTX-M-55, blaTEM-1B, and the ST131 genotype as predictors of MDR. IMPORTANCE The rising incidence of resistance to expanded-spectrum cephalosporins among Escherichia coli strains, the most common cause of UTIs, is threatening our ability to successfully empirically treat these infections. ESCR E. coli strains are often MDR; therefore, UTI caused by these organisms often leads to treatment failure, increased length of hospital stay, and severe complications (D. G. Mark, Y.-Y. Hung, Z. Salim, N. J. Tarlton, et al., Ann Emerg Med 78:357-369, 2021, https://doi.org/10.1016/j.annemergmed.2021.01.003). Here, we performed an in-depth analysis of genetic factors of ESCR E. coli associated with coresistance and MDR. Such knowledge is critical to advance UTI diagnosis, treatment, and antibiotic stewardship.
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Fonseca EL, Morgado SM, Caldart RV, Vicente AC. Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections. Microorganisms 2022; 10:microorganisms10122482. [PMID: 36557735 PMCID: PMC9787326 DOI: 10.3390/microorganisms10122482] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes. METHODS A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses. RESULTS In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020). CONCLUSIONS This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections.
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Affiliation(s)
- Erica L. Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil
- Correspondence: ; Tel.: +55-21-3865-8176
| | - Sergio M. Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil
| | - Raquel V. Caldart
- Centro de Ciências da Saúde, Universidade Federal de Roraima, Boa Vista 69300-000, RR, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz—FIOCRUZ, Rio de Janeiro 21040-360, RJ, Brazil
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Current and Emerging Treatment Options for Multidrug Resistant Escherichia coli Urosepsis: A Review. Antibiotics (Basel) 2022; 11:antibiotics11121821. [PMID: 36551478 PMCID: PMC9774639 DOI: 10.3390/antibiotics11121821] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Escherichia coli is a versatile commensal and pathogenic member of the human microflora. As the primary causative pathogen in urosepsis, E. coli places an immense burden on healthcare systems worldwide. To further exacerbate the issue, multi drug resistance (MDR) has spread rapidly through E. coli populations, making infections more troublesome and costlier to treat. This paper aimed to review the literature concerning the development of MDR in uropathogenic E. coli (UPEC) and explore the existing evidence of current and emerging treatment strategies. While some MDR strains maybe treated with β-lactam-β-lactamase inhibitor combinations as well as cephalosporins, cephamycin, temocillin and fosfomycin, current treatment strategies for many MDR UPEC strains are reliant on carbapenems. Carbapenem overreliance may contribute to the alarming dissemination of carbapenem-resistance amongst some UPEC communities, which has ushered in a new age of difficult to treat infections. Alternative treatment options for carbapenem resistant UPEC may include novel β-lactam-β-lactamase or carbapenemase inhibitor combinations, cefiderocol, polymyxins, tigecycline, aminoglycosides or fosfomycin. For metallo-β-lactamase producing strains (e.g., NDM, IMP-4), combinations of cefazidime-avibacam with aztreonam have been used. Additionally, the emergence of new antimicrobials brings new hope to the treatment of such infections. However, continued research is required to successfully bring these into the clinic for the treatment of MDR E. coli urosepsis.
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Zamudio R, Boerlin P, Beyrouthy R, Madec JY, Schwarz S, Mulvey MR, Zhanel GG, Cormier A, Chalmers G, Bonnet R, Haenni M, Eichhorn I, Kaspar H, Garcia-Fierro R, Wood JLN, Mather AE. Dynamics of extended-spectrum cephalosporin resistance genes in Escherichia coli from Europe and North America. Nat Commun 2022; 13:7490. [PMID: 36509735 PMCID: PMC9744880 DOI: 10.1038/s41467-022-34970-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Extended-spectrum cephalosporins (ESCs) are critically important antimicrobial agents for human and veterinary medicine. ESC resistance (ESC-R) genes have spread worldwide through plasmids and clonal expansion, yet the distribution and dynamics of ESC-R genes in different ecological compartments are poorly understood. Here we use whole genome sequence data of Enterobacterales isolates of human and animal origin from Europe and North America and identify contrasting temporal dynamics. AmpC β-lactamases were initially more dominant in North America in humans and farm animals, only later emerging in Europe. In contrast, specific extended-spectrum β-lactamases (ESBLs) were initially common in animals from Europe and later emerged in North America. This study identifies differences in the relative importance of plasmids and clonal expansion across different compartments for the spread of different ESC-R genes. Understanding the mechanisms of transmission will be critical in the design of interventions to reduce the spread of antimicrobial resistance.
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Affiliation(s)
- Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Patrick Boerlin
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Racha Beyrouthy
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, R3E 3R2, Canada
| | - George G Zhanel
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Ashley Cormier
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Gabhan Chalmers
- Department of Pathobiology, University of Guelph, Guelph, N1G 2W1, Canada
| | - Richard Bonnet
- Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2ISH), Faculté de Médecine, Université Clermont Auvergne, Clermont-Ferrand, 63001, France.,Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Clermont-Ferrand, Clermont-Ferrand, 63000, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany.,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, Berlin, 14163, Germany
| | - Heike Kaspar
- Department Method Standardisation, Resistance to Antibiotics Unit Monitoring of Resistance to Antibiotics, Federal Office of Consumer Protection and Food Safety, Berlin, 12277, Germany
| | - Raquel Garcia-Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Anses Laboratoire de Lyon, Université de Lyon, Lyon, 69007, France
| | - James L N Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK. .,University of East Anglia, Norwich, NR4 7TJ, UK.
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Clonal Lineages and Virulence Factors of Carbapenem Resistant E. coli in Alameda County, California, 2017-2019. Antibiotics (Basel) 2022; 11:antibiotics11121794. [PMID: 36551451 PMCID: PMC9774732 DOI: 10.3390/antibiotics11121794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The prevalence of carbapenem-resistant Enterobacterales (CRE) has been increasing since the year 2000 and is considered a serious public health threat according to the Centers for Disease Control and Prevention. Limited studies have genotyped Carbapenem-resistant Escherichia coli using whole genome sequencing to characterize the most common lineages and resistance and virulence genes. The aim of this study was to characterize sequence data from carbapenem-resistant E. coli isolates (n = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. E. coli genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic E. coli virulence factor genes (VFGs). The carbapenem-resistant E. coli lineages were diverse, with 24 distinct sequence types (STs) represented, including clinically important STs: ST131, ST69, ST95, and ST73. All Ambler classes of Carbapenemases were present, with NDM-5 being most the frequently detected. Nearly all isolates (90%) contained genes encoding resistance to third-generation cephalosporins; blaCTX-M genes were most common. The number of virulence genes present within pandemic STs was significantly higher than the number in non-pandemic lineages (p = 0.035). Virulence genes fimA (92%), trat (71%), kpsM (54%), and iutA (46%) were the most prevalent within the isolates. Considering the public health risk associated with CRE, these data enhance our understanding of the diversity of clinically important E. coli that are circulating in Alameda County, California.
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125
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Impact of a Primary Care Antimicrobial Stewardship Program on Bacterial Resistance Control and Ecological Imprint in Urinary Tract Infections. Antibiotics (Basel) 2022; 11:antibiotics11121776. [PMID: 36551433 PMCID: PMC9774161 DOI: 10.3390/antibiotics11121776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial stewardship programs (ASPs) are a central component in reducing the overprescription of unnecessary antibiotics, with multiple studies showing benefits in the reduction of bacterial resistance. Less commonly, ASPs have been performed in outpatient settings, but there is a lack of available data in these settings. We implemented an ASP in a large regional outpatient setting to assess its feasibility and effectiveness. Over a 5-year post-implementation period, compared to the pre-intervention period, a significant reduction in antibiotic prescription occurred, with a reduction in resistance in E. coli urinary isolates. ASP activities also were found to be cost-effective, with a reduction in medication prescription.
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126
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Tilevik D, Pernestig AK, Fagerlind M, Tilevik A, Ljungström L, Johansson M, Enroth H. Sequence-based genotyping of extra-intestinal pathogenic Escherichia coli isolates from patients with suspected community-onset sepsis, Sweden. Microb Pathog 2022; 173:105836. [DOI: 10.1016/j.micpath.2022.105836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/30/2022]
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127
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A three-year evolution and comparison of the bla genes in pathogenic and non-pathogenic Escherichia coli isolated from young diarrheic and septicaemic calves in Belgium. Res Vet Sci 2022; 152:647-650. [DOI: 10.1016/j.rvsc.2022.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
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128
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Ma K, Zong Z. Resistance to aztreonam-avibactam due to CTX-M-15 in the presence of penicillin-binding protein 3 with extra amino acids in Escherichia coli. Front Microbiol 2022; 13:1047109. [PMID: 36406430 PMCID: PMC9674307 DOI: 10.3389/fmicb.2022.1047109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Aztreonam-avibactam is a promising combination to treat carbapenem-resistant Enterobacterales including coverage for metallo-β-lactamases. Escherichia coli strains resistant to aztreonam-avibactam have emerged but resistance mechanisms remain to be elucidated. We performed a study to investigate the mechanism for aztreonam-avibactam in a carbapenem-resistant Escherichia coli clinical strain. This strain was resistant to aztreonam-avibactam (aztreonam MIC, 16 mg/L in the presence of 4 mg/L avibactam). Whole genome sequencing revealed that the strain carried metallo-β-lactamase gene blaNDM-4 and the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-15 and had a YRIK four amino acid insertion in penicillin-binding protein 3 (PBP3). blaCTX-M-15 was cloned into pET-28a(+), followed by the transformation, with the gene, of E. coli strain 035125∆pCMY42 possessing the YRIK insertion in PBP3 and strain BL21 with the wildtype PBP3. blaCTX-M-14, another common ESBL gene, and blaCTX-M-199, a hybrid of blaCTX-M-14 and blaCTX-M-15 were also individually cloned into both E. coli strains for comparison. Aztreonam-avibactam resistance was only observed in the E. coli strains with the YRIK insertion in PBP3 that produced CTX-M-15 or its hybrid enzyme CTX-M-199. Checkerboard titration assays were performed to determine the synergistic effects between aztreonam-avibactam and ceftazidime or meropenem. Doubling avibactam concentration in vitro reversed aztreonam-avibactam resistance, while the combination of aztreonam-avibactam and ceftazidime or meropenem did not. In conclusion, CTX-M enzymes with activity against aztreonam, (e.g., CTX-M-15 and CTX-M-199), can confer resistance in the combination of PBP3 with YRIK insertions in metallo-β-lactamase-producing carbapenem-resistant E. coli. Doubling the concentration of avibactam may overcome such resistance.
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Affiliation(s)
- Ke Ma
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- *Correspondence: Zhiyong Zong,
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129
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Epidemiology of Plasmid Lineages Mediating the Spread of Extended-Spectrum Beta-Lactamases among Clinical Escherichia coli. mSystems 2022; 7:e0051922. [PMID: 35993734 PMCID: PMC9601178 DOI: 10.1128/msystems.00519-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The prevalence of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Escherichia coli has been increasing, with this spread driven by ESBL-encoding plasmids. However, the epidemiology of ESBL-disseminating plasmids remains understudied, obscuring the roles of individual plasmid lineages in ESBL spread. To address this, we performed an in-depth genomic investigation of 149 clinical ESBL-like E. coli isolates from a tertiary care hospital. We obtained high-quality assemblies for 446 plasmids, revealing an extensive map of plasmid sharing that crosses time, space, and bacterial sequence type boundaries. Through a sequence-based network, we identified specific plasmid lineages that are responsible for the dissemination of major ESBLs. Notably, we demonstrate that IncF plasmids separate into 2 distinct lineages that are enriched for different ESBLs and occupy distinct host ranges. Our work provides a detailed picture of plasmid-mediated spread of ESBLs, demonstrating the extensive sequence diversity within identified lineages, while highlighting the genetic elements that underlie the persistence of these plasmids within the clinical E. coli population. IMPORTANCE The increasing incidence of nosocomial infections with extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli represents a significant threat to public health, given the limited treatment options available for such infections. The rapid ESBL spread is suggested to be driven by localization of the resistance genes on conjugative plasmids. Here, we identify the contributions of different plasmid lineages in the nosocomial spread of ESBLs. We provide further support for plasmid-mediated spread of ESBLs but demonstrate that some ESBL genes rely on dissemination through plasmids more than the others. We identify key plasmid lineages that are enriched in major ESBL genes and highlight the encoded genetic elements that facilitate the transmission and stable maintenance of these plasmid groups within the clinical E. coli population. Overall, our work provides valuable insight into the dissemination of ESBLs through plasmids, furthering our understating of factors underlying the increased prevalence of these genes in nosocomial settings.
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130
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Sewunet T, K. K. S, Nguyen HH, Sithivong N, Hoang NTB, Sychareun V, Nengmongvang K, Larsson M, Olson L, Westerlund F, Giske CG. Fecal carriage and clonal dissemination of blaNDM-1 carrying Klebsiella pneumoniae sequence type 147 at an intensive care unit in Lao PDR. PLoS One 2022; 17:e0274419. [PMID: 36194564 PMCID: PMC9531820 DOI: 10.1371/journal.pone.0274419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/29/2022] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVES Carbapenemase-producing Enterobacterales (CPE) are high priority targets of global antimicrobial surveillance. Herein, we determined the colonization rate of CPE on admission to intensive care units in Vientiane, Lao PDR in August-September 2019. METHODS Data regarding clinical conditions, infection control, and antibiotic usage were collected during admission. Rectal swab samples (n = 137) collected during admission were inoculated to selective chromogenic agars, followed by confirmatory tests for extended-spectrum beta-lactamases and carbapenemases. All CPE isolates were sequenced on Illumina (HiSeq2500), reads assembled using SPAdes 3.13, and the draft genomes used to query a database (https://www.genomicepidemiology.org) for resistome, plasmid replicons, and sequence types (ST). Optical DNA mapping (ODM) was used to characterize plasmids and to determine location of resistance genes. Minimum spanning tree was generated using the Bacterial Isolate Genome Sequence database (BIGSdb) and annotated using iTOL. RESULT From 47 Enterobacterales isolated on selective agars, K. pneumoniae (25/47) and E. coli (12/47) were the most prevalent species, followed by K aerogenes (2/47), K. variicola (1/47), and K. oxytoca (1/47). The overall prevalence of ESBLs was 51.0%; E. coli 83.3% (10/12) and Klebsiella spp. 41.3% (12/29). Twenty percent of the K. pneumoniae (5/25) isolates were carbapenem-resistant, and 4/5 contained the blaNDM-1 gene. All blaNDM-1 isolates belonged to ST147 and were indistinguishable with cgMLST. ODM showed that the blaNDM-1 gene was located on identical plasmids in all isolates. CONCLUSION The prevalence of ESBL-producing Enterobacterales was high, while carbapenemases were less common. However, the detection of clonal dissemination of blaNDM-1-producing K. pneumoniae isolates in one of the intensive care units calls for vigilance. Stringent infection prevention and antimicrobial stewardship strategies are highly important measures.
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Affiliation(s)
- Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Sriram K. K.
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ha Hoang Nguyen
- Hanoi Medical University, Hanoi, Vietnam
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
| | - Noikaseumsy Sithivong
- National Center for Laboratory and Epidemiology, Ministry of Health, Vientiane, Lao PDR
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Vanphanom Sychareun
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Kokasia Nengmongvang
- Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Mattias Larsson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Linus Olson
- Training and Research Academic Collaboration (TRAC) Sweden, Vietnam
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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Triponney P, Bour M, Beyrouthy R, Bonnet R, Plésiat P, Jeannot K. Role of megaplasmids and chromosomal integration in acquisition of CTX-M-encoding genes by Pseudomonas aeruginosa. J Antimicrob Chemother 2022; 77:3194-3198. [PMID: 36177785 DOI: 10.1093/jac/dkac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Pauline Triponney
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Maxime Bour
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | - Racha Beyrouthy
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France.,CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Richard Bonnet
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France.,CHU Clermont-Ferrand, Laboratoire de Bactériologie Clinique, Clermont-Ferrand, France.,Centre National de Référence de la Résistance aux Antibiotiques, laboratoire associé, Clermont-Ferrand, France
| | - Patrick Plésiat
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France
| | - Katy Jeannot
- Centre National de Référence de la résistance aux antibiotiques, Centre Hospitalier Universitaire de Besançon, Besançon, France.,UMR6249 CNRS Chrono-Environnement, Université de Franche-Comté, Besançon, France.,CHU Jean Minjoz, Laboratoire de Bactériologie, Besançon, France
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Yoshida H, Motohashi T, De Bus L, De Waele J, Takaba A, Kuriyama A, Kobayashi A, Tanaka C, Hashi H, Hashimoto H, Nashiki H, Shibata M, Kanamoto M, Inoue M, Hashimoto S, Katayama S, Fujiwara S, Kameda S, Shindo S, Suzuki T, Komuro T, Kawagishi T, Kawano Y, Fujita Y, Kida Y, Hara Y, Fujitani S. Use of broad-spectrum antimicrobials for more than 72 h and the detection of multidrug-resistant bacteria in Japanese intensive care units: a multicenter retrospective cohort study. Antimicrob Resist Infect Control 2022; 11:119. [PMID: 36175948 PMCID: PMC9520832 DOI: 10.1186/s13756-022-01146-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Large multicenter studies reporting on the association between the duration of broad-spectrum antimicrobial administration and the detection of multidrug-resistant (MDR) bacteria in the intensive care unit (ICU) are scarce. We evaluated the impact of broad-spectrum antimicrobial therapy for more than 72 h on the detection of MDR bacteria using the data from Japanese patients enrolled in the DIANA study.
Methods
We analyzed the data of ICU patients in the DIANA study (a multicenter international observational cohort study from Japan). Patients who received empirical antimicrobials were divided into a broad-spectrum antimicrobial group and a narrow-spectrum antimicrobial group, based on whether they received broad-spectrum antimicrobials for more or less than 72 h, respectively. Differences in patient characteristics, background of infectious diseases and empirical antimicrobial administration, and outcomes between the two groups were compared using the chi-square tests (Monte Carlo method) for categorical variables and the Mann–Whitney U-test for continuous variables. We also conducted a logistic regression analysis to investigate the factors associated with the detection of new MDR bacteria.
Results
A total of 254 patients from 31 Japanese ICUs were included in the analysis, of whom 159 (62.6%) were included in the broad-spectrum antimicrobial group and 95 (37.4%) were included in the narrow-spectrum antimicrobial group. The detection of new MDR bacteria was significantly higher in the broad-spectrum antimicrobial group (11.9% vs. 4.2%, p = 0.042). Logistic regression showed that broad-spectrum antimicrobial continuation for more than 72 h (OR [odds ratio] 3.09, p = 0.047) and cerebrovascular comorbidity on ICU admission (OR 2.91, p = 0.041) were associated with the detection of new MDR bacteria.
Conclusions
Among Japanese ICU patients treated with empirical antimicrobials, broad-spectrum antimicrobial usage for more than 72 h was associated with the increased detection of new MDR bacteria. Antimicrobial stewardship programs in ICUs should discourage the prolonged use of empirical broad-spectrum antimicrobial therapy.
Trial registration ClinicalTrials.gov, NCT02920463, Registered 30 September 2016, https://clinicaltrials.gov/ct2/show/NCT02920463
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Mhaya A, Trabelsi R, Aillerie S, M’Zali F, Bégu D, Tounsi S, Gdoura R, Arpin C. Detection of Clones B2-ST131-C2 and A-ST617 in Escherichia coli Producing Both CTX-M-15 and CTX-M-27 from Tunisian Community Patients. Antibiotics (Basel) 2022; 11:antibiotics11101329. [PMID: 36289987 PMCID: PMC9598323 DOI: 10.3390/antibiotics11101329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/18/2023] Open
Abstract
During a two-month period (2017–2018), 336 urine samples positive for Escherichia coli were collected from Tunisian patients. Of the 336 samples, 266 were collected from community patients and 70 from hospital settings. In all, 15 ESBL producers were identified (8 and 7, respectively) and assigned to 13 pulsotypes, including four ESBL-producing E. coli (ESBL-E) with E1 and E2 profiles (2 isolates each) from community patients. The two strains E1 were identified as B2-ST131 subclade C2 and the two isolates E2, A-ST617. The four strains carrying both CTX-M-15 and CTX-M-27, exhibited the multireplicon IncFII/F1A/F1B with the same formula F31:A4:B1. Two isolates with patterns E3 and E4 (Dice coefficient, 78.7%) isolated from community and hospital settings of two geographic areas were assigned to the emerging ST131 C1-M27 subclade and contained the replicon F1:A-:B20. The remaining ESBL-E divided into different sequence types/associated CTX-M: 2 ST131-C2/CTX-M-15 and ST744/CTX-M-55, ST617/CTM-15, ST2973/CTX-M-55, ST6448/CTX-M-15, ST224/CTX-M-15, ST1431/CTX-M-15, and ST38/CTX-M-27, one isolate each. Our study reports for the first time the presence in the Tunisian community of two clones of E. coli, including the virulent clone ST131-C2 harboring both CTX-M-15 and CTX-M-27, and confirms the spread of the emergent clone ST131-C1-M-27, notably in community urinary tract infections.
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Affiliation(s)
- Amel Mhaya
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Rahma Trabelsi
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Sabine Aillerie
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Fatima M’Zali
- University of Bordeaux, Aquitaine Microbiologie, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Dominique Bégu
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Slim Tounsi
- Centre of Biotechnology of Sfax, Laboratory of Biopesticides, Road of Sidi Mansour Km 6, 3018 Sfax, Tunisia
| | - Radhouane Gdoura
- University of Sfax, Department of Life Science, Research Laboratory of Environmental Toxicology-Microbiology and Health, Road of Soukra Km 3.5, 3000 Sfax, Tunisia
| | - Corinne Arpin
- University of Bordeaux, Department of Biological and Medical Sciences, UMR CNRS 5234, 146 Rue Léo Saignat, 33076 Bordeaux, France
- Correspondence:
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134
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Gelalcha BD, Kerro Dego O. Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health. Antibiotics (Basel) 2022; 11:1313. [PMID: 36289970 PMCID: PMC9598938 DOI: 10.3390/antibiotics11101313] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.
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Affiliation(s)
| | - Oudessa Kerro Dego
- Department of Animal Science, University of Tennessee, Knoxville, TN 37996, USA
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Samtiya M, Matthews KR, Dhewa T, Puniya AK. Antimicrobial Resistance in the Food Chain: Trends, Mechanisms, Pathways, and Possible Regulation Strategies. Foods 2022; 11:2966. [PMID: 36230040 PMCID: PMC9614604 DOI: 10.3390/foods11192966] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/09/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) remains of major interest for different types of food stakeholders since it can negatively impact human health on a global scale. Antimicrobial-resistant bacteria and/or antimicrobial resistance genes (transfer in pathogenic bacteria) may contaminate food at any stage, from the field to retail. Research demonstrates that antimicrobial-resistant bacterial infection(s) occur more frequently in low- and middle-income countries (LMICs) than in developed countries. Worldwide, foodborne pathogens are a primary cause of morbidity and mortality. The spread of pathogenic bacteria from food to consumers may occur by direct or indirect routes. Therefore, an array of approaches both at the national and international level to control the spread of foodborne pathogens and promote food safety and security are essential. Zoonotic microbes can spread through the environment, animals, humans, and the food chain. Antimicrobial drugs are used globally to treat infections in humans and animals and prophylactically in production agriculture. Research highlights that foods may become contaminated with AMR bacteria (AMRB) during the continuum from the farm to processing to retail to the consumer. To mitigate the risk of AMRB in humans, it is crucial to control antibiotic use throughout food production, both for animal and crop agriculture. The main inferences of this review are (1) routes by which AMRB enters the food chain during crop and animal production and other modes, (2) prevention and control steps for AMRB, and (3) impact on human health if AMR is not addressed globally. A thorough perspective is presented on the gaps in current systems for surveillance of antimicrobial use in food production and/ or AMR in the food chain.
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Affiliation(s)
- Mrinal Samtiya
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh 123029, India
| | - Karl R. Matthews
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Tejpal Dhewa
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh 123029, India
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal 132001, India
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136
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Sekizuka T, Tanaka R, Hashino M, Yatsu K, Kuroda M. Comprehensive Genome and Plasmidome Analysis of Antimicrobial Resistant Bacteria in Wastewater Treatment Plant Effluent of Tokyo. Antibiotics (Basel) 2022; 11:antibiotics11101283. [PMID: 36289941 PMCID: PMC9598598 DOI: 10.3390/antibiotics11101283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 01/01/2023] Open
Abstract
To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring blaCTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring blaCTX-M, blaKPC, and blaGES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited blaCTX-M, blaKPC, and blaNDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities.
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137
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Tacão M, Laço J, Teixeira P, Henriques I. CTX-M-Producing Bacteria Isolated from a Highly Polluted River System in Portugal. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191911858. [PMID: 36231185 PMCID: PMC9565674 DOI: 10.3390/ijerph191911858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 06/13/2023]
Abstract
Enterobacteriaceae resistant to third-generation cephalosporins are a great concern for public health, as these are first-line drugs to treat infections. The production of carbapenemases and extended spectrum beta-lactamases (ESBLs) and/or the overexpression of AmpC β-lactamases are the main mechanisms of resistance to these antibiotics. Among the ESBLs, CTX-M β-lactamases are the most prevalent worldwide. Our aims were to determine the prevalence of cefotaxime-resistant Enterobacteriaceae along a heavily polluted river and characterize blaCTX-M carriers. River water was collected in 11 sites along the main course and tributaries, in two sampling moments. Water quality was evaluated and a collection of cefotaxime-resistant isolates was obtained. blaCTX-M carriers were characterized regarding phylogenetic affiliation, clonality, antibiotic susceptibility, gene diversity, and context. Water presented very low quality in all sites. From 147 cefotaxime-resistant isolates, 46% carried blaCTX-M and were affiliated with Escherichia, Klebsiella, Enterobacter, and Citrobacter. Molecular typing revealed clonal isolates in different sites and over the two years, suggesting survival of the strains in the river or continuous pollution inputs from the same sources. Eight variants of blaCTX-M were found, with blaCTX-M-15 being the most prevalent (52.5%). Sites with a lower water quality showed the highest resistance rates and prevalence of blaCTX-M, suggesting that river water may embody human health risks.
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Affiliation(s)
- Marta Tacão
- CESAM and Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - José Laço
- Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Pedro Teixeira
- CESAM and Biology Department, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Isabel Henriques
- Department of Life Sciences and CFE, University of Coimbra, 3000-456 Coimbra, Portugal
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Choonara FE, Haldorsen BC, Janice J, Mbanga J, Ndhlovu I, Saulosi O, Maida T, Lampiao F, Simonsen GS, Essack SY, Sundsfjord A. Molecular Epidemiological Characterisation of ESBL- and Plasmid-Mediated AmpC-Producing Escherichia coli and Klebsiella pneumoniae at Kamuzu Central Hospital, Lilongwe, Malawi. Trop Med Infect Dis 2022; 7:245. [PMID: 36136656 PMCID: PMC9501462 DOI: 10.3390/tropicalmed7090245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The global rise in infections caused by multidrug resistant (MDR) Enterobacterales poses a public health problem. We have performed a molecular epidemiological characterisation of representative plasmid-mediated AmpC (pAmpC) and ESBL-positive clinical isolates of Escherichia coli (n = 38) and Klebsiella pneumoniae (n = 17) from a tertiary hospital in Malawi collected in 2017. BlaCTX-M-15 was the most prevalent ESBL-determinant in E. coli (n = 30/38) and K. pneumoniae (n = 17/17), whereas blaCMY-2 was detected in nearly all AmpC-phenotype E. coli (n = 15/17). Whole genome sequencing revealed dominant globally disseminated E. coli sequence types (STs); ST410 (n = 16), ST131 (n = 7), and ST617 (n = 6). The ST distribution in K. pneumoniae was more diverse but included ST101 (n = 2), ST14 (n = 2), and ST340 (n = 2), all considered high-risk MDR clones. The isolates expressed an MDR profile, including resistance against commonly used antibiotics, such as fluoroquinolones, aminoglycosides, and/or trimethoprim-sulfamethoxazole, and harboured corresponding resistance determinants. Clonal analyses of the major STs of E. coli revealed closely related genetic clusters within ST410, ST131, and ST617 supporting within-hospital transmission between patients and/or via a common reservoir. The overall findings add to the limited knowledge on the molecular epidemiology of MDR E. coli and K. pneumoniae in Malawi and may help health policy makers to identify areas to target when addressing this major threat of antibiotic resistance.
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Affiliation(s)
- Faheema Ebrahim Choonara
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4041, South Africa
- Microbiology Laboratory, Kamuzu Central Hospital, Lilongwe P.O. Box 149, Malawi
- Africa Centre of Excellence in Public Health and Herbal Medicine, College of Medicine, University of Malawi, Private Bag 360, Blantyre 3, Malawi
| | - Bjørg Christina Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Joshua Mbanga
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4041, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Corner Cecil & Gwanda Road, Private Bag 939, Bulwayo P.O. Box AC939, Zimbabwe
| | - Isaac Ndhlovu
- Microbiology Laboratory, Kamuzu Central Hospital, Lilongwe P.O. Box 149, Malawi
| | - Osborne Saulosi
- Microbiology Laboratory, Kamuzu Central Hospital, Lilongwe P.O. Box 149, Malawi
| | - Tarsizio Maida
- Microbiology Laboratory, Kamuzu Central Hospital, Lilongwe P.O. Box 149, Malawi
| | - Fanuel Lampiao
- Africa Centre of Excellence in Public Health and Herbal Medicine, College of Medicine, University of Malawi, Private Bag 360, Blantyre 3, Malawi
| | - Gunnar Skov Simonsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Sabiha Yusuf Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4041, South Africa
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance (K-res), Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
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139
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Cardoso M, Prata I, Rebelo I, Nunes T, Pires A, Carneiro C, Bexiga R. Antimicrobial (ESBL) resistance genes in faecal E. coli of calves fed waste milk with antimicrobial residues. J DAIRY RES 2022; 89:1-6. [PMID: 36039956 DOI: 10.1017/s0022029922000486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This research paper aimed to evaluate the association between feeding waste milk to calves and the occurrence of antimicrobial multi-resistance by extended spectrum β-lactamase (ESBL) enzymes through determining their production by E. coli isolates from 32 dairy farms. Among β-lactamase enzymes, ESBL provide resistance to a wide variety of β-lactam antimicrobials including penicillin and 2nd, 3rd and 4th generation cephalosporins. Feeding waste milk to calves has been observed to lead to increased antimicrobial resistance in faecal isolates of calves. In each farm included in this study, faecal samples were collected from the rectum of five healthy calves in the first month of life and pooled into a single container. Five isolates from each pool were selected and confirmed to be E. coli by amplification of the 16S rRNA gene. ESBL production was confirmed phenotypically on 148 isolates from 31 farms by use of the double-disk synergy test. Genotypic confirmation of ESBL production was performed by PCR for the genes blaCTX-M-1, -2, -8, -9 and blaCMY-2. A questionnaire was also performed and a mixed logistic regression model was used to identify risk factors for the occurrence of antimicrobial resistance. A negative binomial regression model was also used, in order to assess whether there was any association between certain farm management practices and the number of ESBL-producing E. coli isolates from each farm. Phenotypic confirmation of ESBL production was obtained on 40 E. coli isolates from 15 farms (48.4%), whereas genotypic confirmation was obtained on 55 isolates from 20 farms (64.5%). The use of three or more different intramammary antimicrobials to treat mastitis within the previous year significantly impacted the number of ESBL-producing E. coli isolates; on farms that did so, there were more isolates in which ESBL-producing E. coli was present, when compared to farms that had used less formulations within the same time span.
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Affiliation(s)
- Manuel Cardoso
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
| | - Inês Prata
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
- HVME - Hospital Veterinário Muralha de Évora, Évora, Portugal
| | - Inês Rebelo
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
| | - Telmo Nunes
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
| | - Ana Pires
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
| | - Carla Carneiro
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
| | - Ricardo Bexiga
- Faculty of Veterinary Medicine, CIISA - Centre for Interdisciplinary Research in Animal Health, University of Lisbon, Lisbon, Portugal
- Faculty of Veterinary Medicine, Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Lisbon, Lisbon, Portugal
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140
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Jouini A, Klibi A, Kmiha S, Hamrouni S, Ghram A, Maaroufi A. Lineages, Virulence Gene Associated and Integrons among Extended Spectrum β-Lactamase (ESBL) and CMY-2 Producing Enterobacteriaceae from Bovine Mastitis, in Tunisia. Pathogens 2022; 11:pathogens11080948. [PMID: 36015067 PMCID: PMC9416333 DOI: 10.3390/pathogens11080948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/24/2022] Open
Abstract
Extended Spectrum Beta-Lactamase (ESBL) Enterobacteriaceae are becoming widespread enzymes in food-producing animals worldwide. Escherichia coli and Klebseilla pneumoniae are two of the most significant pathogens causing mastitis. Our study focused on the characterization of the genetic support of ESBL/pAmpC and antibiotic resistance mechanisms in cefotaxime-resistant (CTXR) and susceptible (CTXS) Enterobacteriaceae isolates, recovered from bovine mastitis in Tunisia, as well as the analyses of their clonal lineage and virulence-associated genes. The study was carried out on 17 ESBL/pAmpC E. coli and K. pneumoniae and 50 CTXS E. coli. Detection of resistance genes and clonal diversity was performed by PCR amplification and sequencing. The following β-lactamase genes were detected: blaCTX-M-15 (n = 6), blaCTX-M-15 + blaOXA-1 (2), bla CTX-M-15 + blaOXA-1 + blaTEM-1b (2), blaCTX-M-15 + blaTEM-1b (4), blaCMY-2 (3). The MLST showed the following STs: ST405 (n = 4 strains); ST58 (n = 3); ST155 (n = 3); ST471 (n = 2); and ST101 (n = 2). ST399 (n = 1) and ST617 (n = 1) were identified in p(AmpC) E. coli producer strains. The phylogroups A and B1 were the most detected ones, followed by the pathogenic phylogroup B2 that harbored the shigatoxin genes stx1/stx2, associated with the cnf, fimA, and aer virulence factors. The qnrA/qnrB, aac(6′)-Ib-cr genes and integrons class 1 with different gene cassettes were detected amongst these CTXR/S isolated strains. The presence of different genetic lineages, associated with resistance and virulence genes in pathogenic bacteria in dairy farms, may complicate antibiotic therapies and pose a potential risk to public health.
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141
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Harbaoui S, Ferjani S, Abbassi M, Saidani M, Gargueh T, Ferjani M, Hammi Y, Boutiba‐Ben Boubaker I. Genetic heterogeneity and predominance of
bla
CTX‐M
‐15
in cefotaxime‐resistant
Enterobacteriaceae
isolates colonizing hospitalized children in Tunisia. Lett Appl Microbiol 2022; 75:1460-1474. [DOI: 10.1111/lam.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- S. Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - S. Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - M.S. Abbassi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie Tunis Tunisie
| | - M. Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
| | - T. Gargueh
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - M. Ferjani
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - Y. Hammi
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - I. Boutiba‐Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
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Tian T, Dai S, Liu D, Wang Y, Qiao W, Yang M, Zhang Y. Occurrence and transfer characteristics of bla CTX-M genes among Escherichia coli in anaerobic digestion systems treating swine waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155321. [PMID: 35452730 DOI: 10.1016/j.scitotenv.2022.155321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Livestock waste is a known reservoir of Escherichia coli (E. coli) carrying clinically important CTX-M-type extended-spectrum β-lactamase genes (blaCTX-M), however, the occurrence and transfer characteristics of blaCTX-M genes during anaerobic digestion (AD) remain unclear. Herein, four full-scale and two parallel lab-scale AD systems treating swine waste under ambient and mesophilic conditions were investigated by both molecular- and culture-based methods to reveal the occurrence and transfer behaviors of blaCTX-M genes during AD. Real-time TaqMan polymerase chain reaction revealed 1.3 × 104-6.8 × 105 and 3.0 × 104-7.0 × 105 copies/mL of blaCTX-M groups 1 and 9 in all feeding substrates. While AD reduced the absolute abundance of groups 1 and 9 by 0.63-2.24 and 0.08-1.30 log (P < 0.05), 5.0 × 102-4.1 × 103 and 1.1 × 104-3.5 × 104 copies/mL of groups 1 and 9 remained in the anaerobic effluent, respectively. In total, 141 blaCTX-M-carrying E. coli isolates resistant to cefotaxime were obtained from the AD reactors. Whole-genome sequencing showed that blaCTX-M-65 mainly carried by E. coli ST155 was the most frequently detected group 9 subtype in the feeding substrate; whereas blaCTX-M-14 associated with the dominant clones E. coli ST6802 and ST155 became the major subtype in AD effluent. Furthermore, blaCTX-M-14 was flanked by ΔIS26 upstream and ΔIS903B downstream. The ΔIS26-blaCTX-M-14-ΔIS903B element was mainly located on the IncHI2 plasmid in E. coli ST48 and ST6802 and also the IncFIB plasmid in ST155 in anaerobic effluent. Conjugation assays showed that the plasmids harboring blaCTX-M-14 could be successfully transferred at a frequency of 10-3-10-2 cells per recipient cell. This study revealed that blaCTX-M genes remained in both the full-scale and lab-scale AD effluents of swine waste. Thus, additional efforts should be implemented to block the discharge and spread of antibiotic resistance genes to the environment.
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Affiliation(s)
- Tiantian Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiting Dai
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Collis RM, Biggs PJ, Burgess SA, Midwinter AC, Brightwell G, Cookson AL. Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments. Front Microbiol 2022; 13:960748. [PMID: 36033848 PMCID: PMC9403332 DOI: 10.3389/fmicb.2022.960748] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.
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Affiliation(s)
- Rose M. Collis
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- Rose M. Collis,
| | - Patrick J. Biggs
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Sara A. Burgess
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Anne C. Midwinter
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Gale Brightwell
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- New Zealand Food Safety Science and Research Centre, Massey University, Palmerston North, New Zealand
| | - Adrian L. Cookson
- The Hopkirk Research Institute, AgResearch Ltd., Massey University, Palmerston North, New Zealand
- EpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
- *Correspondence: Adrian L. Cookson,
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Wang ZY, Jiang Y, Shao YQ, Lu HF, Lu MJ, Jiao X, Li QC, Wang J. Nasal carriage of CTX-M-55-producing Escherichia coli ST8369 in a healthy cohort in the city of Yangzhou, China. Front Cell Infect Microbiol 2022; 12:970940. [PMID: 35992163 PMCID: PMC9382594 DOI: 10.3389/fcimb.2022.970940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/15/2022] [Indexed: 11/21/2022] Open
Abstract
This study aimed to investigate the prevalence and diversity of extended-spectrum β-lactamases (ESBL)-producing Escherichia coli isolates from healthy individuals in a community and to elucidate their dissemination mechanism. Cefotaxime-resistant E. coli were isolated from 95 samples of healthy persons from one community in Yangzhou, China, and were tested for minimal inhibitory concentrations of 14 antimicrobial agents. The isolates were subjected to whole genome sequencing by Illumina Hiseq or PacBio single-molecule real-time sequencing. A total of 30 cefotaxime-resistant E. coli isolates were obtained, carrying blaCTX-M (n=29) or blaDHA (n=1), of which the blaCTX-M-55 (n=19) was the most predominant genotype. One novel blaCTX-M variant blaCTX-M-252 was identified. Thirteen CTX-M-55-producing E. coli isolates belonged to ST8369 from nasal (n=12) or faecal (n=1) samples shared the identical cgMLST type, resistance profiles, resistance genes, plasmid replicons, and a 5,053-bp blaCTX-M-55 structure ΔIS26-ΔISEcp1-blaCTX-M-55-Δorf477-ΔTn2. The blaCTX-M-55 gene was located on IncHI2/ST3 plasmid in E. coli ST8369. The lengths of blaCTX-M/blaDHA-carrying contigs in the remaining 17 E. coli strains ranged from 1,663 to 382,836 bp, located on chromosome (n=4) or plasmids (n=5); the location of the other eight contigs could not be determined due to incomplete assembly. The blaCTX-M was associated with ISEcp1 as previously reported. Nasal colonization of CTX-M-55-producing ST8369 E. coli strains has occurred among healthy individuals in one community. There is a potential risk of antimicrobial resistance dissemination between humans within one community through close contact or environment via aerosols or dust. Therefore, surveillance of nasal carriage of blaCTX-M in communities is warranted to further monitor the spread of the antimicrobial resistance genes in China.
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Affiliation(s)
- Zhen-Yu Wang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Yue Jiang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Yi-Qiao Shao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Heng-Fan Lu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Meng-Jun Lu
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
| | - Qiu-Chun Li
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- *Correspondence: Qiu-Chun Li, ; Jing Wang,
| | - Jing Wang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou, China
- *Correspondence: Qiu-Chun Li, ; Jing Wang,
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145
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Comparison of the Treatment Outcome of Piperacillin-Tazobactam versus Carbapenems for Patients with Bacteremia Caused by Extended-Spectrum β-Lactamase-Producing Escherichia coli in Areas with Low Frequency of Coproduction of OXA-1: a Preliminary Analysis. Microbiol Spectr 2022; 10:e0220622. [PMID: 35916524 PMCID: PMC9430612 DOI: 10.1128/spectrum.02206-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although piperacillin-tazobactam (TZP) was shown to be less effective than carbapenems in treating bacteremia due to extended-spectrum β-lactamase-producing (ESBL)-producing organisms in a randomized controlled trial, the fact that many of the causative organisms co-produced inhibitor-resistant OXA-1 along with ESBLs may have influenced the results. In this study, we compared the therapeutic effectiveness of TZP and carbapenem in treating ESBL-producing Escherichia coli bacteremia in areas with low frequency of OXA-1 co-production. Forty patients, 14 in the TZP treatment group and 26 in the carbapenem treatment group, were included in the analysis. There were no significant differences in patient background between the two groups. Urinary tract infection or cholangitis was the source of bacteremia in 26 patients (65%), and the Pitt bacteremia score was zero or one in 35 patients (87.5%). Only four (11.4%) of the 35 causative isolates available for microbiological analysis harbored blaOXA-1, and only three (8.6%) were non-susceptible to TZP. Seventeen (48.6%) isolates carried blaCTX-M-27, none of which carried other β-lactamase genes. No significant difference in the frequency of treatment failure on day 14 of bacteremia was documented between the TZP and carbapenem treatment groups in both the crude analysis and the inverse probability of treatment weighting-adjusted analysis. This study demonstrates that TZP may be a treatment option for non-severe cases of ESBL-producing E. coli bacteremia in areas with low frequency of OXA-1 co-production. IMPORTANCE Although carbapenems are considered the drug of choice for severe infections caused by extended-spectrum β-lactamase-producing (ESBL)-producing organisms, other therapeutic options are being explored to avoid increasing the selective pressure for carbapenem-resistant organisms. In this study, it was suggested that piperacillin-tazobactam may be as effective as carbapenems for the treatment of mild bacteremia caused by ESBL-producing Escherichia coli in areas where OXA-1 co-production by ESBL-producing E. coli is rare. The genetic background of each regional epidemic clone differs even among multidrug-resistant bacteria classified under the same name (e.g., ESBL-producing organisms), resulting in possible differences in the efficacy of therapeutic agents. Exploration of treatment options for multidrug-resistant organisms according to local epidemiology is worthwhile from the perspective of antimicrobial stewardship.
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146
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Yeh TK, Lin HJ, Liu PY, Wang JH, Hsueh PR. Antibiotic resistance in Enterobacter hormaechei. Int J Antimicrob Agents 2022; 60:106650. [DOI: 10.1016/j.ijantimicag.2022.106650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/25/2022] [Accepted: 07/31/2022] [Indexed: 11/28/2022]
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147
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Torres RT, Cunha MV, Araujo D, Ferreira H, Fonseca C, Palmeira JD. A walk on the wild side: Wild ungulates as potential reservoirs of multi-drug resistant bacteria and genes, including Escherichia coli harbouring CTX-M beta-lactamases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119367. [PMID: 35489528 DOI: 10.1016/j.envpol.2022.119367] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/15/2022] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales have been classified as critical priority pathogens by the World Health Organization (WHO). ESBL are universally distributed and, in 2006, were firstly reported on a wild animal. Understanding the relative contributions of wild animals to ESBL circulation in the environment is urgently needed. In this work, we have conducted a nationwide study in Portugal to investigate the occurrence of bacteria carrying clinically significant antimicrobial resistance genes (ARG), using widely distributed wild ungulates as model species. A total of 151 antimicrobial resistant-Enterobacterales isolates were detected from 181 wild ungulates: 50% (44/88) of isolates from wild boar (Sus scrofa), 40.3% (25/62) from red deer (Cervus elaphus), 41.4% (12/29) from fallow deer (Dama dama) and 100% (2/2) from mouflon (Ovis aries subsp. musimon). Selected isolates showed a diversified resistance profile, with particularly high values corresponding to ampicillin (71.5%) and tetracycline (63.6%). Enterobacterales strains carried blaTEM, tetA, tetB, sul2, sul1 or dfrA1 ARG genes. They also carried blaCTX-M-type genes, which are prevalent in human infections, namely CTX-M-14, CTX-M-15 and CTX-M-98. Strikingly, this is the first report of CTX-M-98 in wildlife. Almost 40% (n = 59) of Enterobacterales were multi-drug resistant. The diversity of plasmids carried by ESBL isolates was remarkable, including IncF, K and P. This study highlights the potential role of wild ungulates as environmental reservoirs of CTX-M ESBL-producing E. coli and in the spill-over of AMR bacteria and their determinants. Our findings suggest that wild ungulates are useful as strategic sentinel species of AMR in terrestrial environments, especially in response to potential sources of anthropogenic pollution, providing early warning of potential risks to human, animal and environmental health.
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Affiliation(s)
- Rita Tinoco Torres
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal.
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Débora Araujo
- Faculty of Engineering of University of Porto, Porto, Portugal
| | - Helena Ferreira
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE - University of Porto, Porto, Portugal; Microbiology, Biological Sciences Department, Faculty of Pharmacy of University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801, Vila Real, Portugal
| | - Josman Dantas Palmeira
- Departament of Biology & CESAM, University of Aveiro, Campus de Santiago, 3810-193, Aveiro, Portugal
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148
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Mohamed NM, Zakaria AS, Edward EA. Genomic Characterization of International High-Risk Clone ST410 Escherichia coli Co-Harboring ESBL-Encoding Genes and blaNDM-5 on IncFIA/IncFIB/IncFII/IncQ1 Multireplicon Plasmid and Carrying a Chromosome-Borne blaCMY-2 from Egypt. Antibiotics (Basel) 2022; 11:antibiotics11081031. [PMID: 36009900 PMCID: PMC9405272 DOI: 10.3390/antibiotics11081031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 02/01/2023] Open
Abstract
The accelerated dispersion of multidrug-resistant (MDR) Escherichia coli due to the production of extended-spectrum β-lactamases (ESBLs) or AmpC enzymes has been noted in Egypt, presenting a serious treatment challenge. In this study, we investigate the prevalence of ESBLs and AmpC enzymes among 48 E. coli isolates collected from patients with urinary tract infections admitted to a teaching hospital in Alexandria. Phenotypic and genotypic methods of detection are conducted. Isolates producing both enzymes are tested for the mobilization of their genes by a broth mating experiment. Whole genome sequencing (WGS) is performed for isolate EC13655. The results indicate that 80% of the isolates are MDR, among which 52% and 13% were ESBL and AmpC producers, respectively. Conjugation experiments fail to show the mobilization of blaCMY-2 in EC13655, which was chosen for WGS. In silico analysis reveals that the isolate belongs to a ST410-H24Rx high-risk clone. It coharbors the ESBL-encoding genes blaCTX-M-15, blaTEM-1, and blaOXA-1 on an IncFIA/IncFIB/IncFII/IncQ1 multireplicon plasmid. The chromosomal location of blaCMY-2 is detected with a flanking upstream copy of ISEcp1. This chromosomal integration of blaCMY-2 establishes the stable maintenance of the gene and thus, necessitates an imperative local surveillance to reduce further spread of such strains in different clinical settings.
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149
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Prevalence and Molecular Characterization of Extended-Spectrum β-Lactamases and AmpC β-lactamase-Producing Enterobacteriaceae among Human, Cattle, and Poultry. Pathogens 2022; 11:pathogens11080852. [PMID: 36014973 PMCID: PMC9414889 DOI: 10.3390/pathogens11080852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are a universal public health alarm frequently identified among humans, animals, and poultry. Livestock and poultry production are a possible source of multidrug-resistant microorganisms, including ESBL-producing Enterobacteriaceae, which confer antimicrobial resistance to different β-lactam antimicrobial agents. From January to May 2020, a cross-sectional study was carried out in three dairy cattle farms and four poultry farms in different districts of northern Egypt to assess the prevalence of ESBLs, AmpC beta-lactamase-producing E. coli and Klebsiella in livestock, poultry, and human contacts, and to investigate the genetic relatedness of the recovered isolates. In total, 140 samples were collected, including human fecal samples (n = 20) of workers with intimate livestock contact, cattle rectal swabs (n = 34), milk (n = 14), milking machine swabs (n = 8), rations (n = 2), and water (n = 2) from different cattle farms, as well as cloacal swabs (n = 45), rations (n = 5), water (n = 5) and litter (n = 5) from poultry farms. The specimens were investigated for ESBL-producing E. coli and Klebsiella using HiCrome ESBL media agar. The agar disk diffusion method characterized the isolated strains for their phenotypic antimicrobial susceptibility. The prevalence of ESBL-producing Enterobacteriaceae was 30.0%, 20.0%, and 25.0% in humans, cattle, and poultry, respectively. Further genotypic characterization was performed using conventional and multiplex PCR assays for the molecular identification of ESBL and AmpC genes. The majority of the ESBL-producing Enterobacteriaceae showed a multi-drug resistant phenotype. Additionally, blaSHV was the predominant ESBL genotype (n = 31; 93.94%), and was mainly identified in humans (n = 6), cattle (n = 11), and poultry (14); its existence in various reservoirs is a concern, and highlights the necessity of the development of definite control strategies to limit the abuse of antimicrobial agents.
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150
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Genomic analysis of Escherichia coli circulating in the Brazilian poultry sector. Braz J Microbiol 2022; 53:2121-2131. [PMID: 35864380 PMCID: PMC9679118 DOI: 10.1007/s42770-022-00799-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/12/2022] [Indexed: 01/13/2023] Open
Abstract
Escherichia coli are gut commensal bacteria and opportunistic pathogens, and the emergence of antimicrobial resistance threatens the safety of the food chain. To know the E. coli strains circulating in the Brazilian poultry sector is important since the country corresponds to a significant chicken meat production. Thus, we analyzed 90 publicly genomes available in a database using web-based tools. Genomic analysis revealed that sul alleles were the most detected resistance genes, followed by aadA, blaCTX-M, and dfrA. Plasmids of the IncF family were important, followed by IncI1-Iα, Col-like, and p0111. Genes of specific metabolic pathways that contribute to virulence (terC and gad) were predominant, followed by sitA, traT, and iss. Additionally, pap, usp, vat, sfa/foc, ibeA, cnf1, eae, and sat were also predicted. In this regard, 11 E. coli were characterized as avian pathogenic E. coli and one as atypical enteropathogenic E. coli. Phylogenetic analysis confirmed the predominant occurrence of B1 but also A, D, B2, F, E, G, C, and Clade I phylogroups, whereas international clones ST38, ST73, ST117, ST155, and ST224 were predicted among 53 different sequence types identified. Serotypes O6:H1 and:H25 were prevalent, and fimH31 and fimH32 were the most representatives among the 36 FimH types detected. Finally, single nucleotide polymorphisms-based phylogenetic analysis confirmed high genomic diversity among E. coli strains. While international E. coli clones have adapted to the Brazilian poultry sector, the virulome background of these strains support a pathogenic potential to humans and animals, with lineages carrying resistance genes that can lead to hard-to-treat infections.
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