Antibiotic Resistance of Enterobacteriaceae Isolated from Fresh Fruits and Vegetables and Characterization of their AmpC β-Lactamases

Chronic bee paralysis virus exploits host antimicrobial peptides and alters gut microbiota composition to facilitate viral infection

The significance of gut microbiota in regulating animal immune response to viral infection is increasingly recognized. However, how chronic bee paralysis virus (CBPV) exploits host immune to disturb microbiota for its proliferation remains elusive. Through histopathological examination, we discovered that the hindgut harbored the highest level of CBPV, and displayed visible signs of damages. The metagenomic analysis showed that a notable reduction in the levels of Snodgrassella alvi and Lactobacillus apis, and a significant increase in the abundance of the opportunistic pathogens such as Enterobacter hormaechei and Enterobacter cloacae following CBPV infection. Subsequent co-inoculation experiments showed that these opportunistic pathogens facilitated the CBPV proliferation, leading to accelerated mortality in bees and exacerbation of bloated abdomen symptoms after CBPV infection. The expression level of antimicrobial peptide (AMP) was found to be significantly up-regulated by over 1000 times in response to CBPV infection, as demonstrated by subsequent transcriptome and quantitative real-time PCR investigations. In particular, through correlation analysis and a bacteriostatic test revealed that the AMPs did not exhibit any inhibitory effect against the two opportunistic pathogens. However, they did demonstrate inhibitory activity against S. alvi and L. apis. Our findings provide different evidence that the virus infection may stimulate and utilize the host's AMPs to eradicate probiotic species and facilitate the proliferation of opportunistic bacteria. This process weakens the intestinal barrier and ultimately resulting in the typical bloated abdomen.

Resistance to β-lactams in Enterobacteriaceae isolated from vegetables: a review

Vegetables are crucial for a healthy human diet due to their abundance of essential macronutrients and micronutrients. However, there have been increased reports of antimicrobial-resistant Enterobacteriaceae isolated from vegetables. Enterobacteriaceae is a large group of Gram-negative bacteria that can act as commensals, intestinal pathogens, or opportunistic extraintestinal pathogens. Extraintestinal infections caused by Enterobacteriaceae are a clinical concern due to antimicrobial resistance (AMR). β-lactams have high efficacy against Gram-negative bacteria and low toxicity for eukaryotic cells. These antimicrobials are widely used in the treatment of Enterobacteriaceae extraintestinal infections. This review aimed to conduct a literature survey of the last five years (2018-2023) on the occurrence of β-lactam-resistant Enterobacteriaceae in vegetables. Research was carried out in PubMed, Web of Science, Scopus, ScienceDirect, and LILACS (Latin American and Caribbean Health Sciences Literature) databases. After a careful evaluation, thirty-seven articles were selected. β-lactam-resistant Enterobacteriaceae, including extended-spectrum β-lactamases (ESBLs)-producing, AmpC β-lactamases, and carbapenemases, have been isolated from a wide variety of vegetables. Vegetables are vectors of β-lactam-resistant Enterobacteriaceae, contributing to the dissemination of resistance mechanisms previously observed only in the hospital environment.

Occurrence, Typing, and Resistance Genes of ESBL/AmpC-Producing Enterobacterales in Fresh Vegetables Purchased in Central Israel

Beta-lactam resistance can lead to increased mortality, higher healthcare expenses, and limited therapeutic options. The primary mechanism of beta-lactam resistance is the production of extended-spectrum beta-lactamases (ESBL) and AmpC beta-lactamases. The spread of beta-lactamase-producing Enterobacterales via the food chain may create a resistance reservoir. The aims of this study were to determine the prevalence of ESBL/AmpC-producing Enterobacterales in vegetables, to examine the association between EBSL/AmpC-producing bacteria and types of vegetables, packaging, and markets, and to investigate the genetic features of ESBL-producing isolates. The antibiotic susceptibilities were determined using VITEK. Phenotypic ESBL/AmpC production was confirmed using disk diffusion. ESBL-producing isolates were subjected to Fourier-transform infrared (FT-IR) spectroscopy and to whole genome sequencing using Oxford Nanopore sequencing technology. Of the 301 vegetable samples, 20 (6.6%) were positive for ESBL producers (16 Klebsiella pneumoniae and 4 Escherichia coli), and 63 (20.9%) were positive for AmpC producers (56 Enterobacter cloacae complex, 4 Enterobacter aerogenes/cancerogenus, and 3 Pantoea spp., Aeromonas hydrophila, and Citrobacter braakii). The blaCTX-M and blaSHV genes were most common among ESBL-producing isolates. The beta-lactamase genes of the ESBL producers were mainly carried on plasmids. Multilocus sequence typing and FT-IR typing revealed high diversity among the ESBL producers. AmpC producers were significantly more common in leafy greens and ESBL producers were significantly less common in climbing vegetables. The presence of ESBL/AmpC-producing Enterobacterales in raw vegetables may contribute to the dissemination of resistance genes in the community.

Are hospital wastewater treatment plants a source of new resistant bacterial strains?

To understand which type of hospital waste may contain the highest amount of antibiotic resistant microorganisms that could be released into the environment, the bacterial strains entering and leaving a hospital wastewater treatment plant (HWTP) were identified and tested for their antibiotic susceptibility. To achieve this goal, samples were collected from three separate sites, inlet and outlet wastewater positions, and sludge generated in a septic tank. After microbiological characterization according to APHA, AWWA, and WEF protocols, the relative susceptibility of the bacterial strains to various antibiotic agents was assessed according to the Clinical and Laboratory Standards Institute guidelines, to determine whether there were higher numbers of resistant bacterial strains in the inlet wastewater sample than in the outlet wastewater and sludge samples. The results showed more antibiotic resistant bacteria in the sludge than in the inlet wastewater, and that the Enterobacteriaceae family was the predominant species in the collected samples. The most antibiotic-resistant families were found to be Streptococcacea and non-Enterobacteriaceae. Some bacterial strains were resistant to all the tested antibiotics. We conclude that the studied HWTP can be considered a source of resistant bacterial strains. It is suggested that outlet water and sludge generated in HWTPs should be monitored, and that efficient treatment to eliminate all bacteria from the different types of hospital waste released into the environment is adopted.

Food risk associated with vegetable consumption, exposure to antimicrobial-resistant strains and pesticide residues

This preliminary study aimed to detect biological and chemical contaminants in vegetables sold in Sicily for human consumption, assess the spread of antimicrobial-resistant (AMR) strains in these foods, and characterize their antimicrobial-resistance genes. A total of 29 fresh and ready-to-eat samples were analyzed. Microbiological analyses were performed for the detection of Salmonella spp. and the enumeration of Enterococci, Enterobacteriaceae, and Escherichia coli. Antimicrobial resistance was assessed by the Kirby-Bauer method, according to the Clinical and Laboratory Standards Institute guidelines. Pesticides were detected by high-performance liquid chromatography and gas chromatography coupled with mass spectrometry. No samples were contaminated by Salmonella spp., E. coli was detected in 1 sample of fresh lettuce at a low bacterial count (2 log cfu/g). 17.24% of vegetables were contaminated by Enterococci and 65.5% by Enterobacteriaceae (bacterial counts between 1.56 log cfu/g and 5.93 log cfu/g and between 1.6 log cfu/g and 5.48 log cfu/g respectively). From 86.2% of vegetables, 53 AMR strains were isolated, and 10/53 isolates were multidrug resistant. Molecular analysis showed that the blaTEM gene was detected in 12/38 β-lactam-resistant/intermediate-resistant isolates. Genes conferring tetracycline resistance (tetA, tetB, tetC, tetD, tetW) were detected in 7/10 isolates. The qnrS gene was detected in 1/5 quinolone-resistant isolates, the sulI gene was detected in 1/4 sulfonamide- resistant/intermediate-resistant isolates and the sulIII gene was never detected. Pesticides were detected in 27.3% of samples, all of which were leafy vegetables. Despite the satisfactory hygienic status of samples, the high percentage of AMR bacteria detected stresses the need for an effective monitoring of these foods as well as adequate strategies to counteract the spread of AMR bacteria along the agricultural chain. Also, the chemical contamination of vegetables should not be underestimated, especially considering that leafy vegetables are commonly consumed raw and that no official guidelines about maximum residue limits of pesticides in ready-to-eat vegetables are available.

Antimicrobial Susceptibility of Fresh Produce-Associated Enterobacteriaceae and Enterococci in Oman

Fresh produce bacteria may have phenotypic and/or genotypic antimicrobial resistance traits that may lead to various consequences on the environment and human health. This study evaluated the susceptibility of fresh produce bacteria (banana, cabbage, capsicum, carrots, cucumber, dates, lettuce, mango, papaya, pomegranate, radish, tomato and watermelon) to chlorhexidine and the antibiotic resistance of enterococci. Eighty-eight Enterobacteriaceae bacteria and 31 enterococci were screened for their susceptibility to chlorhexidine using the broth microdilution method. Susceptibility of enterococci to various antibiotics was determined using agar dilution, colorimetric, and Kirby-Bauer disc diffusion methods. Enterococci were more susceptible to chlorhexidine than Enterobacteriaceae indicated by chlorhexidine minimum inhibitory concentration (MIC) of 1 to 8 µg/mL for the former and 1 to 64 µg/mL for the latter. The IntI 1, qacEΔ1, qacE and qacG genes were distributed weakly in three, two, two, and three Enterobacteriaceae isolates, respectively. Enterococci had resistance to chloramphenicol (3%), tetracycline (19%), erythromycin (68%), ciprofloxacin (55%), and vancomycin (10%) while 19% of them were multi-drug resistant. In conclusion, this research detected a low to moderate level of antibiotic resistance in enterococci. Some Enterobacteriaceae bacteria had reduced chlorhexidine MICs that were not 10x less than the recommended concentration (100–200 µg/mL) in food production areas which might challenge the success of the disinfection processes or have clinical implications if the involved bacteria are pathogens. The prevalence of antimicrobial-resistant bacteria in fresh produce should be monitored in the future.

Antimicrobial-resistant foodborne pathogens in the Middle East: a systematic review

Foodborne pathogens are known as significant public health hazards worldwide, particularly in the Middle East region. Antimicrobial resistance (AMR) among foodborne pathogens becomes one of the top challenges for the environment, public health, and food safety sectors. However, less is known about antimicrobial-resistant foodborne pathogens in the Middle East region. Possibly because of the lack of surveillance, documentation, and reporting. This review focuses on the current status of antimicrobial resistance profiling among foodborne pathogens in the Middle East. Therefore, PubMed and other relevant databases were searched following PRISMA guidelines. Subject heading and texts were searched for "antimicrobial resistances," "foodborne," and "Middle East" to identify observational studies on AMR foodborne pathogens published during the last 10 years (2011 to 2020). Article retrieval and screening were done using a structured search string and strict inclusion/exclusion criteria. Median and interquartile ranges of percent resistance were calculated for each antibiotic-bacterium combination. A total of 249 articles were included in the final analysis from ten countries, where only five countries had more than 85% of the included articles. The most commonly reported pathogens were Escherichia coli, Salmonella spp. Staphylococcus aureus, and Listeria spp. An apparent rise in drug resistance among foodborne pathogens was recorded particularly against amoxicillin-clavulanic acid, ampicillin, nalidixic acid, streptomycin, and tetracycline that are commonly prescribed in most countries in the Middle East. Besides, there is a lack of standardization and quality control for microbiological identification and susceptibility testing methods in many of the Middle East countries.

Emerging Status of Multidrug-Resistant Bacteria and Fungi in the Arabian Peninsula

Simple Summary

The incidence and developing status of multidrug-resistant bacteria and fungi, as well as their related mortality, is reviewed by a systematic published literature search from nine countries in the Arabian Peninsula. In order to analyse the emerging status and mortality, a total of 382 research articles were selected from a comprehensive screening of 1705 papers. More than 850 deaths reported since 2010 in the Arabian Peninsula due to the infection of multidrug-resistant bacteria and fungi. Multidrug-resistant bacteria Acinetobacter baumannii, Mycobacterium tuberculosis, Staphylococcus aureus, and fungi Candida auris are the most prevalent and causing high deaths. To control these infections and associated deaths in the Arabian Peninsula, continuous preventive measures, accurate methods for early diagnosis of infection, active surveillance, constant monitoring, developing vaccines, eradicating multidrug resistance modulators, and data sharing among countries are required.

Abstract

We aimed to identify the prevalence and emerging status of multidrug-resistant bacteria and fungi and their associated mortality in nine countries in the Arabian Peninsula. Original research articles and case studies regarding multidrug-resistant bacteria and fungi in the Arabian Peninsula, published during the last 10 years, were retrieved from PubMed and Scopus. A total of 382 studies were included as per the inclusion and exclusion criteria, as well as the PRISMA guidelines, from a thorough screening of 1705 articles, in order to analyse the emerging status and mortality. The emerging nature of >120 multidrug-resistant (MDR) bacteria and fungi in the Arabian Peninsula is a serious concern that requires continuous monitoring and immediate preventive measures. More than 50% (n = 453) of multidrug-resistant, microbe-associated mortality (n = 871) in the Arabian Peninsula was due to MDR Acinetobacter baumannii, Mycobacterium tuberculosis and Staphylococcus aureus infection. Overall, a 16.51% mortality was reported among MDR-infected patients in the Arabian Peninsula from the 382 articles of this registered systematic review. MDR A. baumannii (5600 isolates) prevailed in all the nine countries of the Arabian Peninsula and was one of the fastest emerging MDR bacteria with the highest mortality (n = 210). A total of 13,087 Mycobacterium tuberculosis isolates were reported in the region. Candida auris (580 strains) is the most prevalent among the MDR fungal pathogen in the Arabian Peninsula, having caused 54 mortalities. Active surveillance, constant monitoring, the development of a candidate vaccine, an early diagnosis of MDR infection, the elimination of multidrug resistance modulators and uninterrupted preventive measures with enhanced data sharing are mandatory to control MDR infection and associated diseases of the Arabian Peninsula. Accurate and rapid detection methods are needed to differentiate MDR strain from other strains of the species. This review summarises the logical relation, prevalence, emerging status and associated mortality of MDR microbes in the Arabian Peninsula.

Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador

In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The bla_CTX–M–55, bla_{CTX–M 65}, and bla_{CTX–M 15} genes were the most frequently found gene associated with the ESBL phenotype and coincided with the bla_CTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.

Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa

The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.

A review of antimicrobial resistance in imported foods

Antimicrobial resistance is one of the most serious threats to medical science. Food supply is recognized as a potential source of resistant bacteria, leading to the development of surveillance programs targeting primarily poultry, pork, and beef. These programs are limited in scope, not only in the commodities tested, but also in the organisms targeted (Escherichia coli, Salmonella, and Campylobacter); consequently, neither the breadth of food products available nor the organisms that may harbour clinically relevant and (or) mobile resistance genes are identified. Furthermore, there is an inadequate understanding of how international trade in food products contributes to the global dissemination of resistance. This is despite the recognized role of international travel in disseminating antimicrobial-resistant organisms, notably New Delhi metallo-beta-lactamase. An increasing number of studies describing antimicrobial-resistant organisms in a variety of imported foods are summarized in this review.

Tracing Antibiotic Resistance Genes along the Irrigation Water Chain to Chive: Does Tap or Surface Water Make a Difference?

Irrigation water is well known as potential source of pathogens in fresh produce. However, its role in transferring antibiotic resistance determinants is less well investigated. Therefore, we analyzed the contribution of surface and tap water to the resistome of overhead-irrigated chive plants. Field-grown chive was irrigated with either surface water (R-system) or tap water (D-system), from planting to harvest. Water along the two irrigation chains as well as the respective plants were repeatedly sampled and screened for 264 antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), using high-capacity qPCR. Differentially abundant (DA) ARGs were determined by comparing the two systems. On R-chive, β-lactam ARGs, multidrug-resistance (MDR) determinants, and MGEs were most abundant, while D-chive featured DA ARGs from the vancomycin class. Diversity and number of DA ARGs was the highest on young chives, strongly diminished at harvest, and increased again at the end of shelf life. Most ARGs highly enriched on R- compared to D-chive were also enriched in R- compared to D-sprinkler water, indicating that water played a major role in ARG enrichment. Of note, blaKPC was detected at high levels in surface water and chive. We conclude that water quality significantly affects the resistome of the irrigated produce.

Agricultural land-use change and rotation system exert considerable influences on the soil antibiotic resistome in Lake Tai Basin

In this study, we use high-throughput quantitative polymerase chain reaction approaches to comprehensively assess the effects of agricultural land-use change on the antibiotic resistome of agricultural runoffs after rainfalls in Lake Tai Basin. For the first time in this region, our findings show that orchard runoffs harbored more diverse and abundant antibiotic resistance genes (ARGs) than traditional cropland runoffs. Network analysis demonstrated that orchard runoffs possessed a strong ability for ARG dissemination via horizontal gene transfer. These results suggest that residents might be exposed to a higher public health threat than before. Moreover, the present study confirmed that the rice-wheat rotation system plays a key role in regulating the soil antibiotic resistome profile. Using 16S rRNA high-throughput sequencing technology, this study clarified the relationships between the antibiotic resistome and soil microbiome composition. Finally, we discuss the key environmental factors driving changes in the soil antibiotic resistome. In summary, this study gives insight into the dissemination of environmental ARGs to the people living in the Lake Tai Basin.

Characterization and Phylodiversity of Implicated Enteric Bacteria Strains in Retailed Tomato (Lycopersicon esculentum Mill.) Fruits in Southwest Nigeria

BACKGROUND: Tomatoes (Lycopersicon esculentum Mill.) have very huge health-promoting benefits due to high nutritional composition; however, these fruits are potential reservoir of enteric food-borne pathogens causing major public health concerns. AIM: Characterization and phylo-analysis of implicated enteric bacteria strains in retailed Tomato fruits in southwest Nigeria were studied. METHODS: Ready to be retailed fresh tomato fruits were purchased from common food markets in southwest, Nigeria, which lies between latitudes 6° 21′ to 8° 30′ N and longitudes 2° 30′ to 5° 30′ E. Observation of sample storage potentials at different conditions and bio-typing of associated bacterial strains were carried out for consecutive 14 days. Enteric bacteria strains were genotyped with 16S rRNA assay and further profiled for antibiotic susceptibility to common antibiotics. High population rate frequently consume tomatoes. RESULTS: Early spoilage characterized with yellow fluid, fungal growth and visible lesions were observed at 25°C storage compare to few patches of lesion at 4°C after 14 days. Higher bacterial count of 4.0–7.18 Log CFU/g was recorded at ambient storage compare to refrigerated samples with more than 10% occurrence rate of Citrobacter spp., Klebsiella spp. and Enterobacter spp. Identified Citrobacter spp. and Klebsiella spp. showed 100% resistant to beta-lactam antibiotics (ceftazidime, cefuroxime, cefixime, ciprofloxacin, and amoxicillin-clavulanic acid). Two-resistant enteric bacteria strains, Klebsiella aerogenes B18 and Citrobacter freundii B27 obtained from Nigerian tomato clustered with Citrobacter strains in food (China), water strains (India, Poland, Malaysia), milk (Germany), and human fecal (China). CONCLUSION: Implicated multidrug-resistant enteric bacilli in retailed tomatoes can cause severe food-borne diseases which public oriented awareness, strategic farm to market surveillance are needed to be intensified.

Phylogenetic characterization and multidrug resistance of bacteria isolated from seafood cocktails

The continual increase in resistance to antibacterial drugs has become a major public health problem, and their indiscriminate use in agriculture, aquaculture, and the treatment of human and animal diseases has severely contributed to the occurrence and spread of multidrug resistance genes. This study phylogenetically characterized multidrug-resistant bacteria isolated from seafood cocktails. Seafood cocktail dishes from 20 establishments on public roads were sampled. Samples were grown on TCBS agar and blood agar. Forty colonies with different macro- and microscopic characteristics were isolated. The 16S rRNA gene V4 and V6 hypervariable regions were amplified, sequenced and phylogenetically analyzed. Antibacterial drug resistance was determined by disk diffusion assay. Isolated bacteria were identical to species of the genera Enterococcus, Proteus, Vibrio, Staphylococcus, Lactococcus, Vagococcus, Micrococcus, Acinetobacter, Enterobacter, and Brevibacterium, with 75-100% presenting resistance or intermediate resistance to dicloxacillin, ampicillin, and penicillin; 50-70% to cephalosporins; 30-67.5% to amikacin, netilmicin and gentamicin; 40% to nitrofurantoin and other antibacterial drugs; 25% to chloramphenicol; and 2.5% to trimethoprim with sulfamethoxazole. In general, 80% of the bacteria showed resistance to multiple antibiotics. The high degree of bacterial resistance to antibacterial drugs indicates that their use in producing raw material for marine foods requires established guidelines and the implementation of good practices.

Draft Genome Sequence of Enterobacter asburiae UFMG-H9, Isolated from Urine from a Healthy Bovine Heifer (Gyr Breed)

Enterobacter asburiae is part of the Enterobacter cloacae complex, related to nosocomial opportunistic infections in humans. Here, we report the draft genome of E. asburiae strain UFMG-H9, an isolate from urine from a healthy Gyr heifer.

Enterobacter asburiae is part of the Enterobacter cloacae complex, related to nosocomial opportunistic infections in humans. Here, we report the draft genome of E. asburiae strain UFMG-H9, an isolate from urine from a healthy Gyr heifer.