Potentially Pathogenic Multidrug-Resistant Escherichia coli in Lamb Meat

Abstract

Extended-spectrum cephalosporin (ESC) resistance remains a threat since ESC are important antimicrobials used to treat infections in humans and animals. Escherichia coli is an important source of ESC-resistance genes, such as those encoding extended-spectrum β-lactamases (ESBLs). E. coli is a common commensal of lambs. Reports that contaminated food can be a source of ESC-resistant bacteria in humans and that ESBL-producing E. coli are found in sheep in Brazil led us to survey their presence in retail lamb meat. Twenty-five samples intended for human consumption were screened for ESC-resistant E. coli, and the isolates were characterized. IncI1-bla_CTX-M-8 and IncHI2-bla_CTX-M-2 were the main plasmids responsible for ESC resistance. The plasmids harbored common ESBL genes in Enterobacteriaceae from food-producing animals in Brazil. IncI1-bla_CTX-M-14 and IncF-bla_CTX-M-55 plasmids, associated with human infections, were also detected. Few CTX-M-producing E. coli have been clustered by typing methods, and some may be genetically pathogenic. The findings indicate the presence of diverse strains of E. coli, harboring important ESBL genes, in lamb meat in Brazil. Surveillance of ESC-resistant bacteria could reduce the spread of antimicrobial resistance through the food chain.

Introduction

Antimicrobial-resistant (AR) pathogens compromise the treatment of bacterial infections, especially, in humans.^1–5 The potential link between the misuse of antimicrobials in food-producing animals and the emergence of resistant pathogens in humans has encouraged surveillance of AR worldwide.⁶ Human exposure to AR Escherichia coli through handling and consumption of contaminated food may contribute to the spread of AR determinants.^2,7,8 During the slaughter of food-producing animals, the carcass may be contaminated by AR commensal bacteria, which might reach humans through the food chain.^7,9–12

Monitoring of commensal bacteria is important because they constitute reservoirs of AR genes, which allows tracking of emerging resistance in livestock and possible spread through animal-derived food.¹³ These microorganisms are a public health concern since they are disseminated globally and cause treatment failure.^14,15

Extended-spectrum cephalosporins (ESCs) are among the few available therapies for serious global Enterobacteriaceae infections in both humans and animals. The use of ESC can cause selection of resistant bacteria in animals. Thus, ESC have the highest priority and are critically important antimicrobials in human and veterinary medicine.^16,17

Treatment with β-lactam antimicrobials select for bacteria that produce extended-spectrum β-lactamase (ESBL) and/or bacteria that are resistant to other antimicrobials due to coselection.^18–22 CTX-M enzymes are the most prevalent ESBL in enterobacterial representatives isolated from clinical samples, food-producing animals, and the environment in Brazil.^23–28 These enzymes, promote an important resistance phenotype to ESC. However, evidence from several studies argues against the role of animals in the dissemination of AR bacteria from food-production chains to humans.^29,30 The resulting ambiguity surrounding the involvement of animals in this dissemination demands further study. Determining whether meat consumed by humans harbors AR bacteria is vital because foodstuff is the final and direct link between food-producing animals and humans.

In general, the majority of studies on ESBL-producing bacteria recovered from meat have been conducted on beef, pork, and chicken meat. Information for other meat, such as lamb meat, is lacking in countries including Brazil, where the consumption of lamb meat is increasing.³¹ To provide clarity, we have been studying AR dissemination through feedlot lambs in the southeastern part of Brazil. We recently reported ESC-resistant E. coli as a commensal of these animals.³² That study and another one³³ led us to continue tracking and comparing resistance to ESC in the lamb meat production chain.

Here, we present data concerning the characterization of CTX-M-producing E. coli isolated from retail lamb meat produced and sold in the State of São Paulo, Brazil, and the emergence of bla_CTX-M variants of human clinical importance.

Materials and Methods

Meat samples and identification of isolates

We investigated the presence of ESC-producing E. coli in 25 lamb meat samples obtained between October 2018 and January 2019 from traditional marketplaces in the State of São Paulo in southeastern Brazil. All meat samples were obtained from Brazilian sheep herds as packed lamb shank and were immediately transported to the laboratory for microbiological analysis. Since this study analyzed meat samples, no Ethic Committee approval as needed.

For bacterial isolation, subsamples of 25 g were dispensed in sterile flasks containing 225 mL Peptone Water (Oxoid, United Kingdom) with ceftiofur (4 mg/L), and incubated at 37°C for 18–20 hr. Serial dilutions made in sterile saline were inoculated onto MacConkey agar (Oxoid) with ceftiofur (4 mg/L), and incubated at 37°C for 18–20 hr. One colony of each morphology suggestive of E. coli from each meat sample was used for by biochemical identification using a commercial kit (NewProv, Brazil).

Antimicrobial susceptibility testing

Antimicrobial susceptibility tests and phenotypic detection of ESBL production were performed using the disc-diffusion method with commercially available discs (Oxoid) according to Clinical and Laboratory Standard Institute guidelines.^34,35 The antimicrobials tested were amoxicillin/clavulanic acid, ceftazidime, cefotaxime, ceftiofur, cefoxitin, ertapenem, amikacin, gentamicin, enrofloxacin, nalidixic acid, tetracycline, trimethoprim/sulfamethoxazole, florfenicol, and fosfomycin. The minimum inhibitory concentration for polymyxin was determined using the Policimbac Commercial Kit (Probac, Brazil). Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 700603, and Pseudomonas aeruginosa ATCC 27853 were used as quality control strains.

ESBL genes and plasmid identification

Genes encoding ESBLs were screened by PCR as previously described (Supplementary Table S1). The detected genes were sequenced using the BigDye Terminator v3.1 Kit (Applied Biosystems) and the 3130 Genetic Analyzer sequencer (Applied Biosystems-HITACHI) using specific primers (Supplementary Table S1). Raw sequences were aligned and analyzed using Accelrys DS Gene 2.0 software. The aligned sequences were compared to those in the GenBank database.

ESBL-harboring plasmids were transferred by broth-mating conjugation with the Salmonella M1744F^- strain, which naturally lacks AmpC and is susceptible to cephalosporins.³⁶ Plasmid incompatibility groups were detected using the commercially available PBRT 2.0 kit (Diatheva, Italy). Transconjugants were used for plasmid linearization with S1 enzyme (Promega) followed by pulsed-field gel electrophoresis (PFGE) for 20 hr with an initial switch time of 1 sec and a final switch time of 30 sec, and an electric field of 6 V/cm. PFGE resolved that bands were transferred to a nylon membrane (Amersham, England) by capillary Southern blotting followed by hybridization (Roche, Swiss) with specific probes for CTX-M genes or the plasmid incompatibility groups detected.

Phylogenetic grouping and virulence genes

The phylogenetic group of isolates was accessed using a previously described protocol (Supplementary Table S1). Thirty-one genes codifying for virulence factors often related to extraintestinal infections or diarrheagenic E. coli pathovars were screened by PCR according to previously described protocols (Supplementary Table S1).

Typing of isolates

Isolates were typed by total DNA restriction with XbaI endonuclease (Thermo Fisher Scientific) followed by PFGE for 22 hr with an initial switch time of 2.2 sec and a final switch time of 54.2 sec, and an electric field of 6 V/cm. BioNumerics™ 7.6 (Applied Maths, Belgium) was used for dendrogram construction and clustering, based on the band-based Dice's similarity coefficient and the unweighted pair group method using arithmetic averages. Isolates were considered to belong to the same cluster when the similarity coefficient was ≥90%.

Isolates were also typed by multilocus sequence typing according to the Achtman scheme.

Sequence submission

The sequences obtained in this study were deposited in GenBank under the accession numbers MN816267–MN816292.

Results and Discussion

Meat samples and antimicrobial susceptibility

Twenty-six isolates were recovered from 15 lamb meat samples (60.0%). There were some samples from which more than one E. coli isolate was obtained, and there were some samples from which only one E. coli isolate was recovered. The source and date of isolation of each E. coli are shown in Fig. 1. All positive meat samples were inspected by federal service, which indicates that despite inspection for hygiene indicator microorganisms needed for international trade marketing, AR bacteria can be successfully transmitted by this kind of food. Several studies have reported a high percentage of raw meat contamination with ESC-resistant bacteria, especially in retail chicken meat.^25,37–40 To our knowledge, the presence of AR-E. coli in lamb retail meat has not been previously reported.

FIG. 1.

Dendrogram constructed according to XbaI-pulsed-field gel electrophoresis typing of extended-spectrum β-lactamase-producing Escherichia coli isolated from retail lamb meat in southeastern Brazil. Antimicrobial susceptibility profile symbols are as follows: black squares, resistance; dark gray squares, intermediate resistance; and light gray squares, susceptibility to each antimicrobial. The bla genetic localization presents an approximation of the plasmids size in parenthesis. M, meat sample number; AMC, amoxicillin/clavulanic acid; CAZ, ceftazidime; CTX, cefotaxime; EFT, ceftiofur; AK, amikacin; CN, gentamicin; ENR, enrofloxacin; NA, nalidixic acid; TE, tetracycline; SXT, trimethoprim/sulfametoxazol; FFC, florfenicol; PhG, phylogenetic group; ST/CC, sequence type/clonal complex.

Regarding antimicrobial susceptibility (Fig. 1), resistance to at least one of the third-generation cephalosporins tested was detected in 22 (84.6%) isolates. The remaining four isolates presented only intermediate resistance to cefotaxime or ceftiofur. One isolate was resistant to ceftazidime. One isolate was resistant to amoxicillin/clavulanic acid but not to cefoxitin. Concerning the other classes of antimicrobials tested, 21 (80.8%) of the ESC-resistant E. coli isolates were resistant to tetracycline, 18 (69.2%) to trimethoprim/sulfamethoxazole, 15 (57.7%) to nalidixic acid (11 were also resistant to enrofloxacin), 6 (23.1%) to gentamicin and/or amikacin, and 5 (19.2%) to florfenicol. None of the isolates was resistant to cefoxitin, ertapenem, fosfomycin, or polymyxin B (data not shown). This is probably because these antimicrobials are not often used in sheep.

Multidrug-resistant (MDR) Enterobacteriaceae are considered to have resistance to at least one antimicrobial of three different classes.⁴¹ By this criterion, 73.1% of the isolates were considered MDR. This finding is a concern because these bacteria could be a reservoir of such resistance genes and/or transfer them to other bacteria.

Recent studies evaluated AR in E. coli isolated from feces of feedlot lambs in Brazil.^32,33 The reported rates of resistance to the tested antimicrobials differed from the rate found in the present study. This could reflect the different origins of the AR E. coli populations (feces) in the prior studies. A study by our group revealed a significant discrepancy between E. coli isolated from live chickens and chicken meat.³⁷ The finding means that at least some of the AR bacteria were introduced into the food chain through the handling of meat, and only a few representatives could occasionally be transferred from the gut of the animals, contaminate the carcass, and reach humans via the food chain.

Resistance genes and localization

The 26 isolates were ESBL producers. All harbored a variant of the bla_CTX-M gene (Fig. 1). Half of the E. coli isolates carried bla_CTX-M-8 (13/26, 50.0%), followed by bla_CTX-M-2 (10/26, 38.5%). Two isolates (7.7%) harbored bla_CTX-M-55, and one (3.8%) harbored bla_CTX-M-14. All the bla_CTX-M-8 genes were present in IncI1 plasmids ranging from 73 to 97 kb, while bla_CTX-M-2 was harbored by IncHI2 plasmids ranging 242.5 to 290 kb or IncI1 (∼97 kb). The bla_CTX-M-14 gene was also detected in an IncI1 plasmid ∼97 kb. One bla_CTX-M-55 was detected in a small (∼29 kb) IncF plasmid. We could not detect the genetic localization of the second bla_CTX-M-55 (Fig. 1).

The presence of both bla_CTX-M-8 and bla_CTX-M-2 was expected because these genes are common in bacteria isolated from humans and food-producing animals in Brazil.^{23,26,37,42–46} bla_CTX-M-2 is often detected in the chromosome,^37,43,47,48 but few studies have reported its mobilization by IncHI2 plasmids.^49–52 On the contrary, bla_CTX-M-8 is commonly detected in IncI1 plasmids,^{28,37,53–56} which agrees with our results. The findings corroborate IncI1 as a consistent plasmid in bacteria of animal origin.⁵⁷

The bla_CTX-M-14 gene has not been detected often since its first description in Brazil.⁵⁸ However, some studies have reported this gene in Enterobacteriaceae isolated from humans and food-animals in the country.^32,46,59 The presence of this gene in food-producing animals and subsequently in foodstuffs is a public health concern because it is still a dominant worldwide ESBL-variant in important infections, especially in Asian countries.^60–63 Recent studies support that concern. These studies described bacteria from human infections harboring IncI1-bla_CTX-M-14 or IncHI2-bla_CTX-M-14^64,65 and E. coli from retail meat carrying IncF-bla_CTX-M-14.^63,66 Several reports have identified this gene harbored by different incompatibility groups in Enterobacteriaceae members isolated from food-producing animals or clinical specimens in China, such as the IncF family, IncK, IncI1, IncHI2, and even nontypeable plasmids.^67–70 In our study, bla_CTX-M-14 was carried by an IncI1 plasmid of ∼97 kb, in accordance with Chinese reports.

Finally, the presence of bla_CTX-M-55 was remarkable since it was only recently identified in Brazil in few studies,^37,71,72 a common gene among E. coli isolated from animals in Asian countries.⁷³ To our knowledge, this is the first report of bla_CTX-M-55 in E. coli recovered from food products in Brazil. The aforementioned reports from Brazil associated this gene with 70–100 kb IncF plasmids. However, other plasmids reported globally are also responsible for the mobilization of bla_CTX-M-55.^74,75 In our study, the bla_CTX-M-55 gene was harbored by a small IncF plasmid (Fig. 1). This was different from the others detected in the country. One study reported the insertion of the bla_CTX-M-55 gene into the chromosome of Salmonella recovered from food-animals in China.⁷⁶ This could be the explanation for why we could not determine the genetic localization or conjugate the bla_CTX-M-55.

E. coli phylogroups and virulence genes

E. coli phylogenetic group B1 was the most detected (n = 15, 57.7%), followed by phylogroups D (6/26, 23.1%) and A (5/26, 19.2%) (Fig. 1). Thus, a majority (76.9%) of the isolates were considered as commensal or not potentially pathogenic because they belonged to phylogroups B1 or A.⁷⁷

The results agree with those obtained for virulence genes, in which only 7 of 31 screened genes were detected. Genes codifying for fimbrial adhesins were the most common, with fimH present in 13 isolates (50.0%) and papEF in 6 (23.1%). Genes responsible for siderophores, polysaccharide capsule, and toxin production were also detected. The iutA and iroN genes were present in eight (30.8%) and four (15.4%) isolates, respectively. The kpsMT II gene for capsule serotype K5 was detected in three (11.5%) isolates. The vat gene was detected in one (3.8%) isolate (Fig. 1).

With the exception of vat, the other genes could be considered to function in the adherence and persistence of commensal bacteria in a niche like the gastrointestinal tract of mammals. Thus, they would not confer appreciable pathogenicity. The presence of vat must be considered a concern since the cytotoxin it encodes induces host cell vacuolization.⁷⁸ Isolate LM5, which belongs to the phylogenetic group D, could be classified as a potentially pathogenic ESBL-producing E. coli. In addition, the LT gene, responsible for heat-labile enterotoxin of enterotoxigenic E. coli pathovar,⁷⁹ was detected in 14 (53.8%) isolates (Fig. 1). This is further evidence of the possibility of pathogenicity for the CTX-M-producing isolates recovered from retail lamb meat. Additional studies are required to verify the expression of genes and phenotypic pathogenicity of these isolates.

Typing of isolates

XbaI-PFGE typing revealed an overall dissimilarity among the studied E. coli, with the exception of nine (34.6%) isolates that clustered into four distinct groups (Fig. 1). Interestingly, the clustered E. coli were recovered from different meat samples.

The observation that some were isolated from samples purchased on different days negates the idea of cross-contamination of samples by the laboratory staff during meat processing. Furthermore, some clusters were formed by isolates with important different traits, such as the bla_CTX-M gene or the sequence type (ST) lineage. However, despite the examination of different meat batches, all commercially available packages were prepared from animals slaughtered at the same slaughterhouse. This suggests a focus on CTX-M-producing E. coli dissemination. In addition, this could indicate the use of insufficient hygiene methods that allowed contamination of different meat products with bacteria.

Mistakes in carcass preparation can make the product a potential carrier for AR bacteria, since bacteria in the gastrointestinal tract of sheep or in the abattoir environment could contaminate the meat during handling.^80–85 Considering that the analyzed meats were inspected by federal services, we suggest that inspection of AR bacteria should also be performed in addition to coliforms as determinants of health safe food at the establishments.

Concerning MLST, the following STs/clonal complexes (CC) were identified: ST 23/CC 23, ST 58/CC 155, ST 106/CC 69, ST 117, ST/CC 155/155, ST 205/CC 205, ST 349/CC 349, ST 398/CC 398, ST/CC 448/448, ST/CC 761/10, ST 1169, ST 1204, ST 1290, ST/CC 1308/86, ST 1653, ST 2612, ST 4680, and ST 6228, with up to three isolates per ST/CC (Fig. 1). These data agree with the XbaI-PFGE results. The considerable distinction among the AR isolates supports the idea that the bla_CTX-M genes detected are spread by plasmids instead of specific strains or clones. This idea is also corroborated by the common plasmids detected in this study that can mobilize the bla_CTX-M-2 and bla_CTX-M-8 genes.

The lineage E. coli ST 58/CC 155 was previously reported as a commensal in feedlot lambs by our group.³² The lineage is also present in humans and poultry in Brazil, according to the EnteroBase website. It is interesting to note that most of the STs detected are already described as pathogenic and nonpathogenic to humans and animals in several countries.

Thus, instead of presenting a general low pathogenic level, several lineages found in lamb meat in Brazil have already been associated with hard-to-treat human infections. This is particularly possible for the LM5 phylogroup D-ST 117 isolate, which harbors the vat and LT genes. In addition, isolates LM9 and LM16 were positive for the LT gene. They belong to phylogenetic group D and ST/CC 349/349 and have been reported as the cause of infections associated with extraintestinal pathogenic E. coli, according to the EnteroBase website.

Other isolates belonging to phylogenetic group D, such as LM11, LM25, and LM34, are also representatives of important ST lineages, such as ST/CC 349/349, ST 2612, and ST/CC 106/69, respectively. The isolates from this study were a clear source and reservoir of ESC-resistance genes. The presence of genes frequently detected in bacteria isolated from humans and animals in other regions, such as bla_CTX-M-14 and bla_CTX-M-55, corroborates the significance of this spread.

In conclusion, despite the small amount of lamb meat that was sampled, it is a source of potentially pathogenic MDR-E. coli. These bacteria carry the same bla_CTX-M genes in plasmids that are present in food-producing animals or humans. The data indicate the emergence of bla_CTX-M-55 in bacteria present in food in Brazil. The findings bring up issues concerning the global spread of antimicrobial resistance from the One Health perspective.

Footnotes

Acknowledgments

We are very grateful to Juliana Rodrigues Froes, Luciana Moran Conceição, and Valéria D'Artibale Fraga for technical support. We thank Editage for English language editing.

Disclosure Statement

No competing financial interests exist.

Funding Information

This work was supported by the São Paulo Research Foundation (FAPESP) (grant numbers #2018/02691-4, #2018/16147-4, #2018/16343-8, #2019/16003-5) and the Brazilian Coordenação de Aperfeiçoamento de Pessoal de Nível Superior.

Supplementary Material

References

Kaesbohrer

, Schroeter

, Tenhagen

B.A

, Alt

, Guerra

, and Appel

. 2012. Emerging antimicrobial resistance in commensal Escherichia coli with public health relevance. Zoonoses Public Health, 59:158–165.

Hammerum

A.M.

, and Heuer

O.E.

. 2009. Human health hazards from antimicrobial-resistant Escherichia coli of animal origin. Clin. Infect. Dis. 48:916–921.

Pitout

J.D.D

. 2010. Infections with extended-spectrum β-lactamase-producing Enterobacteriaceae. Drugs, 70:313–333.

Jean

S.S.

, Coombs

, Ling

, Balaji

, Rodrigues

, Mikamo

, Kim

M.J

, Rajasekaram

D.G

, Mendoza

, Tan

T.Y

, Kiratisin

, Ni

, Weinman

, Xu

, and Hsueh

P.R.

. 2016. Epidemiology and antimicrobial susceptibility profiles of pathogens causing urinary tract infections in the Asia-Pacific region: results from the Study for Monitoring Antimicrobial Resistance Trends (SMART), 2010–2013. Int. J. Antimicrob. Agents, 47:328–334.

Thorpe

K.E.

, Joski

, and Johnston

K.J.

. 2018. Antibiotic-resistant infection treatment costs have doubled since 2002, now exceeding $2 billion annually. Health Aff. 37:662–669.

WHO. 2017. Integrated Surveillance of Antimicrobial Resistance in Foodborne Bacteria: Application of a One Health Approach. World Health Organization,, Geneva, Switzerland.

Projahn

, von Tippelskirch

, Semmler

, Guenther

, Alter

, and Roesler

. 2019. Contamination of chicken meat with extended-spectrum beta-lactamase producing-Klebsiella pneumoniae and Escherichia coli during scalding and defeathering of broiler carcasses. Food Microbiol. 77:185–191.

Rozwandowicz

, Brouwer

M.S.M

, Fischer

, Wagenaar

J.A

, Gonzalez-Zorn

, Guerra

, Mevius

D.J

, and Hordijk

. 2018. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J. Antimicrob. Chemother. 73:1121–1137.

Stella

, Beloeil

P.A

, Guerra

, Hugas

, and Liebana

. 2018. The role of the European Food Safety Authority (EFSA) in the fight against antimicrobial resistance (AMR). Food Prot. Trends, 38:72–80.

10.

Founou

L.L.

, Founou

R.C

, and Essack

S.Y.

. 2016. Antibiotic resistance in the food chain: a developing country-perspective. Front. Microbiol. 7:1881.

11.

Florez-Cuadrado

, Moreno

M.A

, Ugarte-Ruíz

, and Domínguez

. 2018. Antimicrobial resistance in the food chain in the European Union. Adv. Food Nutr. Res. 86:115–136.

12.

Economou

, and Gousia

. 2015. Agriculture and food animals as a source of antimicrobial-resistant bacteria. Infect. Drug Resist. 8:49–61.

13.

Madec

J.-Y.

, and Haenni

. 2018. Antimicrobial resistance plasmid reservoir in food and food-producing animals. Plasmid, 99:72–81.

14.

Patel

H.B.

, Lusk

K.A

, and Cota

J.M.

. 2019. The role of cefepime in the treatment of extended-spectrum beta-lactamase infections. J. Pharm. Pract. 32:458–463.

15.

McCollister

, Kotter

C.V

, Frank

D.N

, Washburn

, and Jobling

M.G.

. 2016. Whole genome sequencing identifies in vivo acquisition of a bla_CTX-M-27-encoding IncFII transmissible plasmid as the cause of ceftriaxone treatment failure for an invasive Salmonella enterica serovar Typhimurium infection. Antimicrob. Agents Chemother. 61:AAC.01649-16.

16.

WHO. 2019. Critically Important Antimicrobials for Human Medicine-6th Revision. World Health Organization,, Geneva, Switzerland.

17.

OIE. 2019. OIE List of Antimicrobials of Veterinary Importance. World Organisation for Animal Health,, Geneva, Switzerland.

18.

Tacão

, Moura

, Correia

, and Henriques

. 2014. Co-resistance to different classes of antibiotics among ESBL-producers from aquatic systems. Water Res. 48:100–107.

19.

Jiang

H.X.

, Song

, Liu

, Zhang

X.H

, Ren

Y.N

, Zhang

W.H

, Zhang

J.Y

, Liu

Y.H

, Webber

M.A

, Ogbolu

D.O

, Zeng

Z.L

, and Piddock

L.J.V

. 2014. Multiple transmissible genes encoding fluoroquinolone and third-generation cephalosporin resistance co-located in non-typhoidal Salmonella isolated from food-producing animals in China. Int. J. Antimicrob. Agents, 43:242–247.

20.

Rao

, Lv

, Zeng

, Chen

, He

, Chen

, Wu

, Wang

, Yang

, Wu

, Liu

, and Liu

J.H.

. 2014. Increasing prevalence of extended-spectrum cephalosporin-resistant Escherichia coli in food animals and the diversity of CTX-M genotypes during 2003–2012. Vet. Microbiol. 172:534–541.

21.

Pouwels

K.B.

, Muller-Pebody

, Smieszek

, Hopkins

, and Robotham

J. V.

. 2019. Selection and co-selection of antibiotic resistances among Escherichia coli by antibiotic use in primary care: an ecological analysis. PLoS One, 14:1–17.

22.

Bush

2018. Past and present perspectives on β-lactamases. Antimicrob. Agents Chemother. 62:1–20.

23.

Rocha

F.R.

, Pinto

V.P.T

, and Barbosa

F.C.B

. 2016. The spread of CTX-M-Type extended-spectrum β-lactamases in Brazil: a systematic review. Microb. Drug Resist. 22:301–311.

24.

Gonçalves

L.F.

, Martins-Junior

P.D.O

, de Melo

A.B.F

, R. da Silva

C.R.M

, V.d. Martins

, Pitondo-Silva

, and de Campos

T.A.

. 2016. Multidrug resistance dissemination by extended-spectrum β-lactamase-producing Escherichia coli causing community-acquired urinary tract infection in the Central-Western Region, Brazil. J. Glob. Antimicrob. Resist. 6:1–4.

25.

Casella

, Nogueira

M.C.L

, Saras

, Haenni

, and Madec

J.Y.

. 2017. High prevalence of ESBLs in retail chicken meat despite reduced use of antimicrobials in chicken production, France. Int. J. Food Microbiol. 257:271–275.

26.

Hoepers

P.G.

, Silva

P.L

, Rossi

D.A

, Valadares Júnior

E.C

, Ferreira

B.C

, Zuffo

J.P

, Koerich

P.K

, and Fonseca

B.B.

. 2018. The association between extended spectrum beta-lactamase (ESBL) and ampicillin C (AmpC) beta-lactamase genes with multidrug resistance in Escherichia coli isolates recovered from turkeys in Brazil. Br. Poult. Sci. 59:396–401.

27.

Batalha de Jesus

A.A.

, Freitas

A.A.R

, De Souza

J.C

, Martins

, Botelho

L.A.B

, Girão

V.B.C

, Teixeira

L.M

, Riley

L.W

, and Moreira

B.M.

. 2019. High-level multidrug-resistant Escherichia coli isolates from wild birds in a large urban environment. Microb. Drug Resist. 25:167–172.

28.

Dropa

, Lincopan

, Balsalobre

L.C

, Oliveira

D.E

, Moura

R.A

, Fernandes

M.R

, da Silva

Q.M

, Matté

G.R

, Sato

M.I.Z

, and Matté

M.H

. 2016. Genetic background of novel sequence types of CTX-M-8- and CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae from public wastewater treatment plants in São Paulo, Brazil. Environ. Sci. Pollut. Res. Int. 23:4953–4958.

29.

Ludden

, Raven

K.E

, Jamrozy

, Gouliouris

, Blane

, Coll

, de Goffau

, Naydenova

, Horner

, Hernandez-Garcia

, Wood

, Hadjirin

, Radakovic

, Brown

N.M

, Holmes

, Parkhill

, and Peacock

S.J.

. 2019. One Health genomic surveillance of Escherichia coli demonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock. mBio, 10:1–12.

30.

Ojer-Usoz

, González

, and Vitas

A.I.

. 2017. Clonal diversity of ESBL-producing Escherichia coli isolated from environmental, human and food samples. Int. J. Environ. Res. Public Health, 14:10–12.

31.

FAO. 2018. FAOSTAT. Available at http://fao.org/faostat/en/#data/QL (accessed September 1, 2020).

32.

Gozi

K.S.

, Froes

J.R

, Deus Ajude

L.P.T

, da Silva

C.R

, Baptista

R.S

, Peiró

J.R

, Marinho

, Mendes

L.C.N

, Nogueira

M.C.L

, and Casella

. 2019. Dissemination of multidrug-resistant commensal Escherichia coli in feedlot lambs in Southeastern Brazil. Front. Microbiol. 10:1394.

33.

Furlan

J.P.R.

, Gallo

I.F.L

, A. de Campos

C.L.P

, Navarro

, Kobayashi

R.K.T

, Nakazato

, and Stehling

E.G.

. 2019. Characterization of non-O157 Shiga toxin-producing Escherichia coli (STEC) obtained from feces of sheep in Brazil. World J. Microbiol. Biotechnol. 35:1–8.

34.

CLSI. 2018. M100 Performance Standards for Antimicrobial Susceptibility Testing. CLSI, Wayne, PA.

35.

CLSI. 2008. Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals; Approved Standard. 3rd ed. Informational Supplement M31-A33. CLSI, Wayne, PA.

36.

Pasteran

F.G.

, Otaegui

, Guerriero

, Radice

, Maggiora

, Rapoport

, Faccone

, Di Martino

, and Galas

. 2008. Klebsiella pneumoniae carbapenemase-2, Buenos Aires, Argentina. Emerg. Infect. Dis. 14:1178–1180.

37.

Casella

, Haenni

, Madela

N.K

, de Andrade

L.K

, Pradela

L.K

, de Andrade

L.N

, A.L.d. Darini

, Madec

J.Y

, and Nogueira

M.C.L

. 2018. Extended-spectrum cephalosporin-resistant Escherichia coli isolated from chickens and chicken meat in Brazil is associated with rare and complex resistance plasmids and pandemic ST lineages. J. Antimicrob. Chemother. 73:3293–3297.

38.

Leverstein-Van Hall

M.A.

, Dierikx

C.M

, Stuart

J.C

, Voets

G.M

, van den Munckhof

M.P

, van Essen-Zandbergen

, Platteel

, Fluit

A.C

, van de Sande-Bruinsma

, Scharinga

, Bonten

M.J.M

, and Mevius

D.J.

. 2011. Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains. Clin. Microbiol. Infect. 17:873–880.

39.

Randall

L.P.

, Lodge

M.P

, Elviss

N.C

, Lemma

F.L

, Hopkins

K.L

, Teale

C.J

, and Woodford

. 2017. Evaluation of meat, fruit and vegetables from retail stores in five United Kingdom regions as sources of extended-spectrum beta-lactamase (ESBL)-producing and carbapenem-resistant Escherichia coli. Int. J. Food Microbiol. 241:283–290.

40.

Kim

Y.J.

, Moon

J.S

, Oh

D.H

, Chon

J.W

, Song

B.R

, Lim

J.S

, Heo

E.J

, Park

H.J

, Wee

S.H

, and Sung

. 2018. Genotypic characterization of ESBL-producing E. coli from imported meat in South Korea. Food Res. Int. 107:158–164.

41.

Magiorakos

A.-P.

, Srinivasan

, Carey

R.B

, Carmeli

, Falagas

M.E

, Giske

C.G

, Harbarth

, Hindler

J.F

, Kahlmeter

, Olsson-Liljequist

, Paterson

D.L

, Rice

L.B

, Stelling

, Struelens

M.J

, Vatopoulos

, Weber

J.T

, and Monnet

D.L.

. 2012. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 18:268–281.

42.

Ferreira

J.C.

, Penha Filho

R.A.C

, Andrade

L.N

, Berchieri

Jr. , and A.L.d. Darini

. 2014. IncI1/ST113 and IncI1/ST114 conjugative plasmids carrying bla_CTX-M-8 in Escherichia coli isolated from poultry in Brazil. Diagn. Microbiol. Infect. Dis. 80:304–306.

43.

Ferreira

J.C.

, Penha Filho

R.A.C

, Andrade

L.N

, Berchieri

Jr. , and A.L.d. Darini

. 2014. Detection of chromosomal bla_CTX-M-2 in diverse Escherichia coli isolates from healthy broiler chickens. Clin. Microbiol. Infect. 20:O623–O626.

44.

Chagas

T.P.G.

, Alves

R.M

, Vallim

D.C

, Seki

L.M

, Campos

L.C

, and Asensi

M.D.

. 2011. Diversity of genotypes in CTX-M-producing Klebsiella pneumoniae isolated in different hospitals in Brazil. Braz. J. Infect. Dis. 15:420–425.

45.

Minarini

L.A.

, Poirel

, Trevisani

N.A

, A.L.d. Darini

, and Nordmann

. 2009. Predominance of CTX-M-type extended-spectrum beta-lactamase genes among enterobacterial isolates from outpatients in Brazil. Diagn. Microbiol. Infect. Dis. 65:202–206.

46.

Berman

, Barberino

M.G

, Moreira

E.D

Jr. , Riley

, and Reis

J.N

. 2014. Distribution of strain type and antimicrobial susceptibility of Escherichia coli isolates causing meningitis in a large urban setting in Brazil. J. Clin. Microbiol. 52:1418–1422.

47.

Harada

, Ishii

, Saga

, Kouyama

, Tateda

, and Yamaguchi

. 2012. Chromosomal integration and location on IncT plasmids of the bla_CTX-M-2 gene in Proteus mirabilis clinical isolates. Antimicrob. Agents Chemother. 56:1093–1096.

48.

Song

, Kim

, Bae

I.K

, Jeong

S.H

, Seo

Y.H

, Shin

J.H

, Jang

S.J

, Uh

, Shin

J.H

, Lee

M.-K

, and Lee

. 2011. Chromosome-encoded AmpC and CTX-M extended-spectrum beta-lactamases in clinical isolates of Proteus mirabilis from Korea. Antimicrob. Agents Chemother. 55:1414–1419.

49.

Dierikx

, van Essen-Zandbergen

, Veldman

, Smith

, and Mevius

. 2010. Increased detection of extended spectrum beta-lactamase producing Salmonella enterica and Escherichia coli isolates from poultry. Vet. Microbiol. 145:273–278.

50.

Doublet

, Praud

, Nguyen-Ho-Bao

, Argudin

M.A

, Bertrand

, Butaye

, and Cloeckaert

. 2014. Extended-spectrum beta-lactamase- and AmpC beta-lactamase-producing d-tartrate-positive Salmonella enterica serovar Paratyphi B from broilers and human patients in Belgium, 2008–2010. J. Antimicrob. Chemother. 69:1257–1264.

51.

García Fernández

, Cloeckaert

, Bertini

, Praud

, Doublet

, Weill

F.X

, and Carattoli

. 2007. Comparative analysis of IncHI2 plasmids carrying bla_CTX-M-2 or bla_CTX-M-9 from Escherichia coli and Salmonella enterica strains isolated from poultry and humans. Antimicrob. Agents Chemother. 51:4177–4180.

52.

Guo

, Ding

, Jové

, Stoesser

, Cooper

V.S

, Wang

, and Doi

. 2016. Characterization of a novel IncHI2 plasmid carrying tandem copies of bla_CTX-M-2 in a fosA6-harboring Escherichia coli sequence type 410 strain. Antimicrob. Agents Chemother. 60:6742–6747.

53.

Eller

, Leistner

, Guerra

, Fischer

, Wendt

, Rabsch

, Werner

, and Pfeifer

. 2014. Emergence of extended-spectrum β-lactamase (ESBL) CTX-M-8 in Germany. J. Antimicrob. Chemother. 69:562–564.

54.

Melo

L.C.

, Oresco

, Leigue

, Netto

H.M

, Melville

P.A

, Benites

N.R

, Saras

, Haenni

, Lincopan

, and Madec

J.Y.

. 2018. Prevalence and molecular features of ESBL/pAmpC-producing Enterobacteriaceae in healthy and diseased companion animals in Brazil. Vet. Microbiol. 221:59–66.

55.

Norizuki

, Wachino

, Suzuki

, Kawamura

, Nagano

, Kimura

, and Arakawa

. 2017. Specific bla_CTX-M-8/IncI1 plasmid transfer among genetically diverse Escherichia coli isolates between humans and chickens. Antimicrob. Agents Chemother. 61:e00663-17.

56.

Sacramento

A.G.

, Fernandes

M.R

, Sellera

F.P

, Muñoz

M.E

, Vivas

, Dolabella

S.S

, and Lincopan

. 2018. Genomic analysis of MCR-1 and CTX-M-8 co-producing Escherichia coli ST58 isolated from a polluted mangrove ecosystem in Brazil. J. Glob. Antimicrob. Resist. 15:288–289.

57.

Carattoli

, Villa

, Fortini

, and García-Fernández

. 2018. Contemporary IncI1 plasmids involved in the transmission and spread of antimicrobial resistance in Enterobacteriaceae. Plasmid [Epub ahead of print]; DOI: 10.1016/j.plasmid.2018.12.001.

58.

Cergole-Novella

M.C.

, Guth

B.E

, Castanheira

, Carmo

M.S

, and Pignatari

A.C.

. 2010. First description of bla_CTX-M-14- and bla_CTX-M-15-producing Escherichia coli isolates in Brazil. Microb. Drug Resist. 16:177–184.

59.

Fitch

F.M.

, Carmo-Rodrigues

M.S

, Oliveira

V.G.S

, Gaspari

M.V

, dos Santos

, de Freitas

J.B

, and Pignatari

A.C.C

. 2016. β-Lactam resistance genes: characterization, epidemiology, and first detection of bla_CTX-M-1 and bla_CTX-M-14 in Salmonella spp. isolated from poultry in Brazil—Brazil Ministry of Agriculture's pathogen reduction. Microb. Drug Resist. 22:164–171.

60.

Logan

L.K.

, Medernach

R.L

, Domitrovic

T.N

, Rispens

J.R

, Hujer

A.M

, Qureshi

N.K

, Marshall

S.H

, Nguyen

D.C

, Rudin

S.D

, Zheng

, Konda

, Weinstein

R.A

, and Bonomo

R.A.

. 2019. The clinical and molecular epidemiology of CTX-M-9 group producing Enterobacteriaceae infections in children. Infect. Dis. Ther. 8:243–254.

61.

Peirano

, and Pitout

J.D.D

. 2019. Extended-spectrum β-lactamase-producing Enterobacteriaceae: update on molecular epidemiology and treatment options. Drugs, 79:1529–1541.

62.

Zhao

W.-H.

, and Hu

Z.-Q.

. 2013. Epidemiology and genetics of CTX-M extended-spectrum β-lactamases in Gram-negative bacteria. Crit. Rev. Microbiol. 39:79–101.

63.

Hayashi

, Ohsaki

, Taniguchi

, Koide

, Kawamura

, Suzuki

, Kimura

, Ichi Wachino

, Nagano

, Arakawa

, and Nagano

. 2018. High prevalence of bla_CTX-M-14 among genetically diverse Escherichia coli recovered from retail raw chicken meat portions in Japan. Int. J. Food Microbiol. 284:98–104.

64.

Chen

C.Y.

, Hsieh

P.H

, Chang

C.Y

, Yang

S.T

, Chen

Y.H

, Chang

, and Lu

P.L.

. 2019. Molecular epidemiology of the emerging ceftriaxone resistant non-typhoidal Salmonella in southern Taiwan. J. Microbiol. Immunol. Infect. 52:289–296.

65.

Di Pilato

, Papa-Ezdra

, Chiarelli

, García-Fulgueiras

, Pallecchi

, and Vignoli

. 2019. Characterization of the first bla_CTX-M-14/ermB-carrying IncI1 plasmid from Latin America. Plasmid, 102:1–5.

66.

Rebbah

, Messai

, Châtre

, Haenni

, Madec

J.Y

, and Bakour

. 2018. Diversity of CTX-M extended-spectrum β-lactamases in Escherichia coli isolates from retail raw ground beef: first report of CTX-M-24 and CTX-M-32 in Algeria. Microb. Drug Resist. 24:896–908.

67.

Liao

X.P.

, Xia

, Yang

, Li

, Sun

, Liu

Y.H

, and Jiang

H.X

. 2015. Characterization of CTX-M-14-producing Escherichia coli from food-producing animals. Front. Microbiol. 6:1136.

68.

Zhang

, Yin

, Zhao

, Feng

, Jiang

, Zhan

, Wu

, Chen

, Wang

, Li

, and Zhou

. 2017. p1220-CTXM, a pKP048-related IncFII K plasmid carrying bla_CTX-M-14 and qnrB4. Future Microbiol. 12:1035–1043.

69.

Ruan

, Sun

, Jia

, Huang

, Zhou

, Xie

, and Zhang

. 2019. Emergence of a ST2570 Klebsiella pneumoniae isolate carrying mcr-1 and bla_CTX-M-14 recovered from a bloodstream infection in China. Clin. Microbiol. Infect. 25:916–918.

70.

Yuan

, Wu

, and Zheng

. 2019. Complete genome sequence of an IMP-8, CTX-M-14, CTX-M-3 and QnrS1 co-producing Enterobacter asburiae isolate from a patient with wound infection. J. Glob. Antimicrob. Resist. 18:52–54.

71.

Cunha

M.P. V

, Lincopan

, Cerdeira

, Esposito

, Dropa

, Franco

L.S

, Moreno

A.M

, and Knöbl

. 2017. Coexistence of CTX-M-2, CTX-M-55, CMY-2, FosA3, and QnrB19 in extraintestinal pathogenic Escherichia coli from poultry in Brazil. Antimicrob. Agents Chemother. 61:e02474-16.

72.

Fernandes

M.R.

, Sellera

F.P

, Moura

, Souza

T.A

, and Lincopan

. 2018. Draft genome sequence of a CTX-M-8, CTX-M-55 and FosA3 co-producing Escherichia coli ST117/B2 isolated from an asymptomatic carrier. J. Glob. Antimicrob. Resist. 12:183–184.

73.

Zheng

, Zeng

, Chen

, Liu

, Yao

, Deng

, Chen

, Lv

, Zhuo

, Chen

, and Liu

J.H.

. 2012. Prevalence and characterisation of CTX-M β-lactamases amongst Escherichia coli isolates from healthy food animals in China. Int. J. Antimicrob. Agents, 39:305–310.

74.

Xia

, Liu

, Xia

, Kudinha

, Xiao

S.N

, Zhong

N.S

, Ren

G.S

, and Zhuo

. 2017. Prevalence of ST1193 clone and IncI1/ST16 plasmid in E. coli isolates carrying bla_CTX-M-55 gene from urinary tract infections patients in China. Sci. Rep. 7:1–8.

75.

Nadimpalli

, Fabre

, Yith

, Sem

, Gouali

, Delarocque-Astagneau

, Sreng

, and Le Hello

. 2019. CTX-M-55-type ESBL-producing Salmonella enterica are emerging among retail meats in Phnom Penh, Cambodia. J. Antimicrob. Chemother. 74:342–348.

76.

Zhang

C.-Z.

, Ding

X.-M

, Lin

X.-L

, Sun

R.-Y

, Lu

Y.-W

, Cai

R.-M

, Webber

M.A

, Ding

H.-Z

, and Jiang

H.-X.

. 2019. The emergence of chromosomally located bla_CTX-M-55 in Salmonella from foodborne animals in China. Front. Microbiol. 10:1–8.

77.

Clermont

, Bonacorsi

, and Bingen

. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66:4.

78.

Sarowska

, Futoma-Koloch

, Jama-Kmiecik

, Frej-Madrzak

, Ksiazczyk

, Bugla-Ploskonska

, and Choroszy-Krol

. 2019. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports. Gut Pathog. 11:1–16.

79.

Aranda

K.R.S.

, Fagundes-Neto

, and Scaletsky

I.C.A

. 2004. Evaluation of multiplex PCRs for diagnosis of infection with diarrheagenic Escherichia coli and Shigella spp. J. Clin. Microbiol. 42:5849–5853.

80.

Sancheza

H.M.

, Echeverria

, Thulsiraj

, Zimmer-Faust

, Flores

, Laitz

, Healy

, Mahendra

, Paulson

S.E

, Zhu

, and Jay

J.A.

. 2016. Antibiotic resistance in airborne bacteria near conventional and organic beef cattle farms in California, USA. Water Air Soil Pollut. 227:280.

81.

Biasino

, De Zutter

, Woollard

, Mattheus

, Bertrand

, Uyttendaele

, and Van Damme

. 2018. Reduced contamination of pig carcasses using an alternative pluck set removal procedure during slaughter. Meat Sci. 145:23–30.

82.

Chuah

L.-O.

, Shamila Syuhada

A.-K

, Mohamad Suhaimi

, Farah Hanim

, and Rusul

. 2018. Genetic relatedness, antimicrobial resistance and biofilm formation of Salmonella isolated from naturally contaminated poultry and their processing environment in northern Malaysia. Food Res. Int. 105:743–751.

83.

Thanner

, Drissner

, and Walsh

. 2016. Antimicrobial resistance in agriculture. mBio, 7:1–7.

84.

Pesciaroli

, Cucco

, De Luca

, Massacci

F.R

, Maresca

, Medici

, Paniccià

, Scoccia

, Staffolani

, Pezzotti

, and Magistrali

C.F.

. 2017. Association between pigs with high caecal Salmonella loads and carcass contamination. Int. J. Food Microbiol. 242:82–86.

85.

Bolton

D.J.

, Ivory

, and McDowell

. 2013. A study of Salmonella in pigs from birth to carcass: serotypes, genotypes, antibiotic resistance and virulence profiles. Int. J. Food Microbiol. 160:298–303.

Supplementary Material

Please find the following supplemental material available below.

For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.

For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.

0.00 MB

0.05 MB