Emergence of extended-spectrum beta-lactamases and AmpC-type beta-lactamases in human Salmonella isolated in Spain from 2001 to 2005

Antibiotic Resistance Profiles and Molecular Characteristics of blaCMY-2-Carrying Salmonella enterica Serovar Albany Isolated from Chickens During 2013-2020 in South Korea

The production of β-lactamase by nontyphoidal Salmonella has become a public health issue throughout the world. In this study, we aimed to investigate the antimicrobial resistance profiles and molecular characteristics of β-lactamase-producing Salmonella enterica serovar Albany isolates. A total of 434 Salmonella Albany were obtained from feces and carcasses of healthy and diseased food-producing animals [cattle (n = 2), pigs (n = 3), chickens (n = 391), and ducks (n = 38)] during 2013-2020. Among the 434 Salmonella Albany isolates, 3.7% showed resistance to cefoxitin, and all the cefoxitin-resistant isolates were obtained from chickens. Moreover, Salmonella Albany isolates demonstrated high resistance to nalidixic acid (99.3%), trimethoprim/sulfamethoxazole (97.9%), ampicillin (86.6%), chloramphenicol (86.6%), and tetracycline (85.7%), as well as higher rates of multidrug resistance were detected in cefoxitin-resistant isolates compared to cefoxitin-susceptible isolates. All cefoxitin-resistant isolates harbored CMY-2-type β-lactamase and belonged to seven different pulsotypes, with type IV-b (43.75%) and IV-a (25%) making up the majority. In addition, genes encoding cefoxitin resistant of all blaCMY-2-harboring Salmonella Albany isolates were horizontally transmitted to a recipient Escherichia coli J53 by conjugation. Furthermore, 93.75% (15/16) of conjugative plasmids harboring blaCMY-2 genes belong to ST12/CC12-IncI1. Genetic characteristics of transmitted blaCMY-2 genes were associated with ISEcp1, which can play an essential role in the effective mobilization and expression of these genes. Salmonella Albany containing blaCMY-2 in chickens can potentially be transferred to humans. Therefore, it is necessary to restrict antibiotic use and conduct continuous monitoring and analysis of resistant bacteria in the poultry industry.

Retail chicken giblets contaminated with extended-spectrum cephalosporin- and carbapenem-resistant Salmonella enterica carrying blaCMY-2

Background and Aim:

Chickens are considered as the main source of Salmonella, with infection potentially spreading to the public through outlets. The study aimed to investigate poultry shops for Salmonella enterica resistant to extended-spectrum cephalosporins-resistant (ESCR) and carbapenems-resistant (CR).

Materials and Methods:

Samples were collected from chicken giblets, water tanks, and workers at retail shops. Salmonella was isolated and serotyped; the presence of invA, stn, ompA, and ompF was determined using polymerase chain reaction (PCR). The isolates were tested for ESCR and CR by a disk-diffusion test; a confirmatory extended-spectrum β-lactamase (ESBL) test was performed by combinational disk-diffusion test with clavulanic acid. The resistant isolates were screened for ESBL (blaTEM, blaSHV, blaCTX-M, and blaOXA-1), AmpC blaCMY-2, and carbapenemase (blaKPC, blaNDM, and blaOXA-48) genes using PCR.

Results:

S. enterica was isolated from chicken giblets (13/129) and the 13 isolates were ESCR. Based on the confirmatory ESBL test and CR, the 13 isolates were classified into the following resistance phenotypes: ESBL-producing and CR (n=4), ESBL-producing (n=1), non-ESBL-producing and CR (n=6), and non-ESBL-producing (n=2). All the five isolates with ESBL-producing phenotype carried predominantly blaTEM, blaSHV, and blaCMY-2. Regardless of being phenotypically CR, none of these isolates carried any of the tested carbapenemase genes. Surprisingly, the isolates with non-ESBL phenotype were found to carry blaTEM, blaSHV, and blaCMY-2. The blaKPC was present mainly in the isolates with non-ESBL and CR phenotypes. Interestingly, two isolates of the non-ESBL and CR phenotype showed resistance to cefepime, the fourth generation cephalosporins. Salmonella was also recovered from the water tanks (2/7) and the workers (2/16). The four isolates were ESCR and showed a non-ESBL-producing and CR phenotype; they harbored blaTEM, blaSHV, blaOXA-1, and blaKPC. The blaCMY-2 was found in one isolate from water and one from humans. All Salmonella isolates carried invA, stn, ompA, and ompF.

Conclusion:

Virulent ESCR S. enterica were identified in retail shops. The isolates carried blaCMY-2 and ESBL-genes, with a high proportion showing CR. Transmission of such strains to humans through food leads us to recommend regular inspection of retail outlets for antibiotic-resistant bacteria.

Coexistence of virulence and β-lactamase genes in avian pathogenic Escherichia coli

Emergence of multidrug resistance in E. coli and advent of newer strains is becoming serious concern which requires keen observations. This study was designed to find the ciprofloxacin resistant E. coli isolates co-existed with multi-drug resistance along with β-lactamase production from poultry source, and finally the genome sequencing of these strains to explore genetic variations. Study constituted on isolation of n = 225 E. coli from broiler farms of central China which were further subjected to identification of resistance against ciprofloxacin followed by antibiogram of n = 26 antibiotics and identification of β-lactamase production. Whole genome resequencing was performed using Illumina HiSeq 4000 system. PCR results revealed predominant β-lactamase genes i.e.CTX-M, CTX-M-1, CTX-M3, TEM-1 and OXA. Furthermore, the MDR isolates were containing most of the tested virulence genes. The most prevalent virulence genes were pap-C, fim-C, fim-H, iuc-D, irp-2, tra-T, iro-N and iut-A. The single nucleotide polymorphisms (SNPs) loci mentioned in this data give valuable genetic markers to growing high-throughput techniques for fine-determination of genotyping of MDR and virulent isolates. Characterization of SNPs on functional basis shed new bits of knowledge on the evolution, disease transmission and pathogenesis of MDR E. coli isolates. In conclusion, these findings provide evidence that most of poultry E. coli are MDR, β-lactamase producers, and virulent which could be a zoonotic threat to the humans. The whole genome resequencing data provide higher resolution of resistance and virulence characteristics in E. coli which can further be used for the development of prevention and treatment strategies.

Prevalence and Molecular Characterization of Antimicrobial-Resistant Escherichia coli in Pig Farms, Slaughterhouses, and Terminal Markets in Henan Province of China

Escherichia coli is an important foodborne pathogen and also plays key roles in dissemination of antimicrobial resistance genes (ARGs). However, current data on the prevalence of antimicrobial-resistant E. coli at different nodes of the pork supplying chain are still limited. Herein, we investigated drug-resistant phenotypes and molecular characteristics of E. coli strains isolated from different pig farms, slaughterhouses, and terminal markets in the Henan Province of China. A total of 191 (70.74%), 140 (35.09%), and 77 (30.20%) E. coli strains were isolated from 270, 399, and 255 samples collected from pig farms, slaughterhouses, and retailing markets, respectively. Antimicrobial susceptibility testing revealed that these 408 strains showed severe antimicrobial resistance profiles. Approximately 93.19% (178/191), 66.43% (93/140), and 67.53% (52/77) of the isolates from farms, slaughterhouses, and terminal markets were resistant to three of the nine antibiotic classes tested, respectively. Multilocus sequence typing showed that sequence types (STs) 10 and ST101 were commonly identified among the isolates from farms, slaughterhouses, and terminal markets. Isolates belonging to these two STs carried multiple ARGs, conferring resistance to the antibiotics tested. Two important ARGs with great public health concerns (mcr-1 and bla_NDM-1) were found from these two STs. Isolates belonging to these two STs also carried several virulence factor-encoding genes, including astA, tsh, and traT, which might contribute to the pathogenesis of these isolates. The wide prevalence and distribution of these two STs in different nodes of pork supplying chain might represent a big public health threat and should receive more attention.

Isolation, Antimicrobial Resistance Phenotypes, and Virulence Genes of Bordetella bronchiseptica From Pigs in China, 2018-2020

Bordetella bronchiseptica is a leading cause of respiratory diseases in pigs. However, epidemiological data of B. bronchiseptica in pigs particularly in China, the largest pig rearing country in the world is still limited. We isolated 181 B. bronchiseptica strains from 4259 lung samples of dead pigs with respiratory diseases in 14 provinces in China from 2018 to 2020. The average isolation rate of this 3-year period was 4.25% (181/4259). Antimicrobial susceptibility testing performed by disc diffusion method revealed that most of the B. bronchiseptica isolates in this study were resistant to ampicillin (83.98%), while a proportion of isolates were resistant to cefotaxime (30.39%%), chloramphenicol (12.71%), gentamicin (11.60%), florfenicol (11.60%), tetracycline (8.84%), amoxicillin (8.29%), tobramycin (6.63%), ceftriaxone (4.97%), and cefepime (0.55%). There were no isolates with resistant phenotypes to imipenem, meropenem, polymyxin B, ciprofloxacin, enrofloxacin, and amikacin. In addition, ~13.18% of the isolates showed phenotypes of multidrug resistance. Detection of antimicrobial resistance genes (ARGs) by PCR showed that 16.57% of the B. bronchiseptica isolates in this study was positive to aac(3)-IV, while 3.87%, 2.21%, 1.10%, 0.55%, 0.55%, and 0.55% of the isolates were positive to aac6'-Ib, rmtA, bla_TEM, bla_SHV, oqxB, and tetA, respectively. Detection of virulence factors encoding genes (VFGs) by conventional PCR showed that over 90% of the pig B. bronchiseptica isolates in this study were positive to the five VFGs examined (fhaB, 97.24%; prn, 91.16%; cyaA, 98.34%; dnt, 98.34%; betA, 92.82%). These results demonstrate B. bronchiseptica as an important pathogen associated with pig respiratory disorders in China. The present work contributes to the current understanding of the prevalence, antimicrobial resistance and virulence genes of B. bronchiseptica in pigs.

Resistance to colistin and production of extended-spectrum β-lactamases and/or AmpC enzymes in Salmonella isolates collected from healthy pigs in Northwest Spain in two periods: 2008-2009 and 2018

Salmonellosis is a common subclinical infection in pigs and therefore apparently healthy animals may represent a reservoir of antibiotic-resistant Salmonella for humans. This study estimates and characterizes resistance to two classes of antimicrobials considered of the highest priority within the critically important antimicrobials for humans, i.e. colistin (CR) and 3rd generation cephalosporins (3GC), on a collection of Salmonella isolates from pigs from two periods: between 2008 and 09, when colistin was massively used; and in 2018, after three years under a National Plan against Antibiotic Resistance. Prevalence of CR was low (6 out of 625; 0.96%; 95%CI: 0.44-2.1) in 2008-09 and associated mostly to the mcr-1 gene, which was detected in four S. 4,5,12:i:- isolates. Polymorphisms in the pmrAB genes were detected in a S. 9,12:-:- isolate. No CR was detected in 2018 out of 59 isolates tested. Among 270 Salmonella isolates considered for the assessment of resistance to 3GC in the 2008-2009 sampling, only one Salmonella Bredeney (0.37%; 95%CI: 0.07-2.1) showed resistance to 3GC, which was associated with the bla_CMY-2 gene (AmpC producer). In 2018, six isolates out of 59 (10.2%; 95%CI: 4.7-20.5) showed resistance to 3GC, but only two different strains were identified (S. 4,12:i:- and S. Rissen), both confirmed as extended-spectrum β-lactamases (ESBL) producers. The bla_CTX-M-3 and bla_TEM-1b genes in S. 4,12:i:- and the bla_TEM-1b gene in S. Rissen seemed to be associated with this resistance. Overall, the prevalence of CR in Salmonella appeared to be very low in 2008-2009 despite the considerable use of colistin in pigs at that time, and seemed to remain so in 2018. Resistance to 3GC was even lower in 2008-2009 but somewhat higher in 2018. Resistance was mostly coded by genes associated with mobile genetic elements. Most serotypes involved in these antimicrobial resistances displayed a multidrug resistance pattern and were considered zoonotic.

First Clinical Case of In Vivo Acquisition of DHA-1 Plasmid-Mediated AmpC in a Salmonella enterica subsp. enterica Isolate

A pan-susceptible Salmonella enterica serovar Worthington isolate was detected in the stool of a man returning from Sri Lanka. Under ceftriaxone treatment, a third-generation cephalosporin (3GC)-resistant Salmonella Worthington was isolated after 8 days. Molecular analyses indicated that the two isolates were identical. However, the latter strain acquired a blaDHA-1-carrying IncFII plasmid probably from a Citrobacter amalonaticus isolate colonizing the gut. This is the first report of in vivo acquisition of plasmid-mediated resistance to 3GCs in S. enterica.

Metal impacts on the persistence and proliferation of β-lactam resistance genes in Xiangjiang River, China

Currently, the emergence of clinically relevant multi-resistant bacteria and the associated β-lactamases resistance genes which threaten the last frontier for antibiotics presents a major challenge for medical treatment. Xiangjiang River is typically contaminated with heavy metals due to the intensive metal mining activities within this watershed. The occurrence and distribution of several β-lactam antibiotics and ten β-lactam resistance genes (bla_TEM, bla_VIM, bla_SHV, bla_GES, bla_DHA, bla_OXA-1, bla_OXA-2, bla_OXA-10, bla_CMY-2, and bla_ampC) were investigated in the Xiangjiang River, China. The absolute abundance of bla genes was as high as (7.0 ± 0.6) × 10⁶ copies/mL for surface water and (2.3 ± 0.7) × 10⁸ copies/g for sediment. In contrast, all the detected β-lactam antibiotic compounds were below the detection limit. The distribution of individual bla gene subtypes was correlated with speciation of heavy metals which might affect the bacterial community structure. The principal coordinate analysis (PCoA) and Mantal test reconfirmed that the heavy metals had a correlation with the bla genes and the bla genes were correlated with bacterial community structure, suggesting that heavy metals impacted on the distribution of the bla genes by shifting bacterial community structure under the long-term selective pressure. The microcosm experiments indicated metal-induced persistence of bla genes in the resistant bacteria (Bacillus megaterium, Staphylococcus epidermidis). The persistence of β-lactam resistance under metal selective pressure is beneficial to the survival of resistant bacteria, thereby contributing to the shift of the bacterial community structure, consequently impacts on the distribution of bla genes.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017

The data on antimicrobial resistance in zoonotic and indicator bacteria in 2017, submitted by 28 EU Member States (MSs), were jointly analysed by EFSA and ECDC. Resistance in zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as meticillin‐resistant Staphylococcus aureus in animals and food were addressed, and temporal trends assessed. ‘Microbiological’ resistance was assessed using epidemiological cut‐off (ECOFF) values; for some countries, qualitative data on human isolates were interpreted in a way which corresponds closely to the ECOFF‐defined ‘microbiological’ resistance. In Salmonella from humans, as well as in Salmonella and E. coli isolates from fattening pigs and calves of less than 1 year of age, high proportions of isolates were resistant to ampicillin, sulfonamides and tetracyclines, whereas resistance to third‐generation cephalosporins was uncommon. Varying occurrence/prevalence rates of presumptive extended‐spectrum beta‐lactamase (ESBL)/AmpC producers in Salmonella and E. coli monitored in meat (pork and beef), fattening pigs and calves, and Salmonella monitored in humans, were observed between countries. Carbapenemase‐producing E. coli were detected in one single sample from fattening pigs in one MS. Resistance to colistin was observed at low levels in Salmonella and E. coli from fattening pigs and calves and meat thereof and in Salmonella from humans. In Campylobacter from humans, high to extremely high proportions of isolates were resistant to ciprofloxacin and tetracyclines, particularly in Campylobacter coli. In five countries, high to very high proportions of C. coli from humans were resistant also to erythromycin, leaving few options for treatment of severe Campylobacter infections. High resistance to ciprofloxacin and tetracyclines was observed in C. coli isolates from fattening pigs, whereas much lower levels were recorded for erythromycin. Combined resistance to critically important antimicrobials in both human and animal isolates was generally uncommon but very high to extremely high multidrug resistance levels were observed in S. Typhimurium and its monophasic variant in both humans and animals. S. Kentucky from humans exhibited high‐level resistance to ciprofloxacin, in addition to a high prevalence of ESBL.

Distribution and Antimicrobial Resistance of Salmonella Isolated from Pigs with Diarrhea in China

Salmonella can cause enteric diseases in humans and a wide range of animals, and even outbreaks of foodborne illness. The aim of this study was to investigate the frequency and distribution of serovars, and antimicrobial resistance in Salmonella isolates from pigs with diarrhea in 26 provinces in China from 2014 to 2016. A total of 104 Salmonella isolates were identified and the dominant serovar was S. 4,[5],12:i:- (53.9%). All Salmonella isolates were resistant to trimethoprim-sulfamethoxazole, and many were resistant to ampicillin (80.8%) and tetracycline (76.9%). Among 104 Salmonella isolates, aac(6')-Ib-cr was the dominant plasmid-mediated quinolone resistance gene (80.8%), followed by qnrS (47.1%). The pulsed-field gel electrophoresis results suggest that the Salmonella isolates from different regions were genetically diverse, and ST34 was the most prevalent. S. 4,[5],12:i:- isolates is the widespread presence of heavy metal tolerance genes. The fact that the same sequence types were found in different regions and the high similarity coefficient of S. 4,[5],12:i:- isolates from different regions indicate the clonal expansion of the isolates, and the isolates carried various antimicrobial resistance genes. The multidrug resistant Salmonella can be widely detected in pigs, which will present a challenge for farm husbandry.

Emergence of CMY-2-Producing Salmonella Heidelberg Associated with IncI1 Plasmids Isolated from Poultry in Brazil

In this study we report the characterization of plasmid-mediated CMY-2-producing Salmonella Heidelberg recovered from food, poultry, and poultry environment in Brazil, between 2014 and 2016. The bla_CMY-2 resistance gene was allocated in large (90-148 kb) IncI1 type transferable plasmids. Salmonella Heidelberg isolates were genetically related, indicating the dissemination of closely related isolates among food, poultry, and its environment. This is the first report of IncI1 replicon-types of plasmids encoding the bla_CMY-2 resistance gene in Salmonella Heidelberg isolates in Brazil, the world's biggest exporter of chickens.

Extended-Spectrum Cephalosporin-Resistant Salmonella enterica serovar Heidelberg Strains, the Netherlands(1)

Extended-spectrum cephalosporin-resistant Salmonella enterica serovar Heidelberg strains (JF6X01.0022/XbaI.0251, JF6X01.0326/XbaI.1966, JF6X01.0258/XbaI.1968, and JF6X01.0045/XbaI.1970) have been identified in the United States with pulsed-field gel electrophoresis. Our examination of isolates showed introduction of these strains in the Netherlands and highlight the need for active surveillance and intervention strategies by public health organizations.

Prevalence and Antibiotic Resistance of Non-typhoidal Salmonella Isolated from Raw Chicken Carcasses of Commercial Broilers and Spent Hens in Tai'an, China

The present study was aimed to determine the prevalence and characteristics of Salmonella isolated from meat samples of commercial broilers (CB) and spent hens (SH). Between March and June 2016, 200 retail raw chicken carcasses (100 from CB and 100 from SH) were obtained from local supermarkets in Tai’an city of China, and Salmonella isolates were then analyzed for antibiotic resistance, serotype, β-lactamase genes, and the presence of class 1 integron. Forty Salmonella strains were obtained in this study (CB: 21/100, 21%; SH: 19/100, 19%). Three serotypes were identified in 40 Salmonella, and S. Enteritidis (CB: 15/21, 71.4%; SH: 10/19, 52.6%) was the dominant serotype, followed by S. Typhimurium (CB: 4/21, 19%; SH: 6/19, 31.6%) and S. Derby (CB: 2/21, 9.5%; SH: 3/19, 15.8%). Among 21 Salmonella isolated from CB, high antibiotic resistance rates were found for ampicillin (20/21, 95.2%), nalidixic acid (18/21, 85.7%), cefotaxime (17/21, 81%), and tetracycline (13/21, 61.9%); class 1 integron was observed in seven isolates (7/21, 33.3%), and gene cassettes included an empty integron (0.15 kb, n = 1), aadA2 (1.2 kb, n = 3), drfA1-aadA1 (1.4 kb, n = 1), and drfA17-aadA5 (1.7 kb, n = 2); bla_TEM-1 was the dominant β-lactamase gene (21/21, 100%), followed by bla_CTX-M-55 (7/21, 33.3%). Among 19 Salmonella isolated from SH, high antibiotic resistance rates were found for nalidixic acid (19/19, 100%), tetracycline (19/19, 100%), ampicillin (18/19, 94.7%), and ciprofloxacin (13/19, 68.4%); class 1 integron was observed in two isolates (2/19, 10.5%), and gene cassettes included drfA17-aadA5 (1.7 kb, n = 1) and drfA1-aadA1 (1.4 kb, n = 1); bla_TEM-1 was the dominant β-lactamase gene (19/19, 100%), followed by bla_CTX-M-55 (2/19, 10.5%) and bla_CMY-2 (1/19, 5.3%). Collectively, antibiotic-resistant Salmonella can be widely detected in retail raw chicken carcasses of CB and SH, and therefore can pose a serious risk to public health.

Prevalence and Antimicrobial Resistance of Salmonella Isolates Recovered from Retail Pork in Major Village Markets in Tai'an Region, China

The current study was undertaken to evaluate Salmonella contamination in retail pork at major village markets of the Tai'an region, China. In total, 200 retail pork samples were collected from four village markets between June 2015 and February 2016, of which 69 samples (34.5%) were determined to be positive for Salmonella. Eleven serotypes were identified from the 69 Salmonella isolates, and Salmonella Derby was the most common (18 of 69, 26.1%), followed by Typhimurium (17 of 69, 24.6%) and Meleagridis (11 of 69, 15.9%). Antimicrobial susceptibility testing showed that antimicrobial resistance against tetracycline was the most prevalent (42 of 69, 60.9%), but antimicrobial resistance against both ceftriaxone and cefotaxime was 1.4% (1 of 69) and 2.9% (2 of 69), respectively. Multilocus sequence typing revealed that the 69 Salmonella isolates were divided into 11 sequence types (STs), among which ST40 (18 of 69, 26.1%) was the most common, followed by ST34 (15 of 69, 21.7%) and ST64 (13 of 69, 18.8%). Collectively, retail pork at village markets in the Tai'an region has a high Salmonella contamination rate, and these isolates exhibit broad-spectrum antimicrobial resistance. However, the absence of a dominant ST demonstrates that the Salmonella isolates from retail pork may be of diverse origins.

Population dynamics and antimicrobial resistance of the most prevalent poultry-associated Salmonella serotypes

Salmonella spp. is the most predominant bacterial cause of foodborne gastroenteritis in humans. Due to the risk of human infection associated with poultry products and the prevalence of antimicrobial resistance, Salmonella also poses a significant challenge to commercial poultry production. During the last decade (2002 to 2012), the 12 most prevalent poultry-associated Salmonella serotypes (MPPSTs) were frequently and consistently isolated from poultry products in the United States. These MPPSTs and their percent prevalence in poultry products include Kentucky (4%), Enteritidis (2%) Heidelberg (2%), Typhimurium (2%), S. I 4,[5],12:i:- (0.31%), Montevideo (0.20%), Infantis (0.16%) Schwarzengrund (0.15%), Hadar (0.15%), Mbandaka (0.13%), Thompson (0.12%), and Senftenberg (0.04%). All MPPSTs except Kentucky are among the top 30 clinically significant serotypes that cause human illnesses in the United States. However with the exception of a few widely studied serotypes such as S. Enteritidis and Typhimurium, the ecology and epidemiology of the majority of MPPSTs still remain poorly investigated. Published data from the United States suggests that MPPSTs such as Heidelberg, Typhimurium, Kentucky, and Sentfenberg are more likely to be multi-drug resistant (MDR, ≥3 antimicobial classes) whereas Enteritidis, Montevideo, Schwarzengrund, Hadar, Infantis, Thompson, and Mbandaka are generally pan-susceptible or display resistance to fewer antimicobials. In contrast, the majority of MPPSTs isolated globally have been reported to display MDR phenotype. There also appears to be an international spread of a few MDR serotypes including Kentucky, Schwarzengrund, Hadar, Thomson, Sentfenberg, and Enteritidis, which may pose significant challenges to the public health. The current knowledge gaps on the ecology, epidemiology, and antimicrobial resistance of MPPSTs are discussed.

Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken

Numerous studies have examined the prevalence of pathogenic Escherichia coli in poultry and poultry products; however, limited data are available regarding their resistance- and virulence-associated gene expression profiles. This study was designed to examine the resistance and virulence of poultry E. coli strains in vitro and in vivo via antibiotic susceptibility, biofilm formation and adhesion, and invasion and intracellular survivability assays in Caco-2 and Raw 264.7 cell lines as well as the determination of the median lethal dose in two-day old chickens. A clinical pathogenic multidrug-resistant isolate, E. coli 381, isolated from broilers, was found to be highly virulent in cell culture and 1000-fold more virulent in a chicken model than other strains; accordingly, the isolate was subsequently selected for transcriptome analysis. The comparative gene expression profile of MDR E. coli 381 and the reference human strain E. coli ATCC 25922 was completed with Illumina HiSeq. 2500 transcriptome analysis. Differential gene expression analysis indicates that there are multiple pathways involved in the resistance and virulence of this highly virulent strain. The results garnered from this study provide critical information about the highly virulent MDR E. coli strain of poultry origin and warrant further investigation due to its significant threat to public health.

Serotype Distribution, Antimicrobial Resistance, and Class 1 Integrons Profiles of Salmonella from Animals in Slaughterhouses in Shandong Province, China

The current study aimed to analyze the prevalence and characterization of Salmonella enterica isolated from animals in slaughterhouses before slaughter. A total of 143 non-duplicate Salmonella were recovered from 1,000 fresh fecal swabs collected from four major pig slaughterhouses (49/600, 8.2%) and four major chicken slaughterhouses (94/400, 23.5%) between March and July 2016. Among Salmonella isolates from pigs, the predominant serovars were Salmonella Rissen (28/49, 57.1%) and Typhimurium (14/49, 28.6%), and high antimicrobial resistance rates were observed for tetracycline (44/49, 89.8%) and ampicillin (16/49, 32.7%). Class 1 integrons were detected in 10.2% (5/49) of these isolates and all contained gene cassettes aadA2 (0.65 kb). Two β-lactamase genes were detected among these isolates, and most of these isolates carried blaTEM-1 (46/49), followed by blaOXA-1(4/49). Seven STs (MLST/ST, multilocus sequence typing) were detected in these isolates, and the predominant type was ST469 (19.6%). Among Salmonella isolates from chickens, the predominant serovars were Salmonella Indiana (67/94, 71.3%) and Enteritidis (23/94, 24.5%), and high antimicrobial resistance rates were observed for nalidixic acid (89/94, 94.7%), ampicillin (88/94, 93.6%) and tetracycline (81/94, 86.2%). Class 1 integrons were detected in 23 isolates (23/94, 24.5%), which contained empty integrons (0.15 kb, n = 6) or gene cassettes drfA17-aadA5 (1.7 kb, n = 6), aadA2 (1.2 kb, n = 5), drfA16-blaPSE-1-aadA2-ereA2 (1.6 kb, n = 5) or drfA1-aadA1 (1.4 kb, n = 1). Three β-lactamase genes were detected, and all 94 isolates carried blaTEM-1, followed by blaCTX-M-55 (n = 19) and blaSPE-1 (n = 3). Five STs were found in these isolates, and the predominant type was ST17 (71.3%). Our findings indicated that Salmonella was widespread in animals at slaughter and may be transmitted from animal to fork.

The first description of the extended-spectrum beta-lactamase blaSHV-12 gene in a Salmonella monophasic Typhimurium strain isolated from acute gastroenteritis in a kidney transplant recipient in Southeast Spain

Acute gastroenteritis (AGE) is a common disease within the population. Most cases are self-limited. However, intensive treatment is sometimes necessary to ensure patient integrity. This disease is characterized by vomiting and/or diarrhea with blood or mucus, discomfort, fever, and nonspecific abdominal pain. Commonly involved pathogens in the developed world include: viruses, bacteria, and parasites. In this paper we report a rare cause of AGE.

Enteropathogens and antibiotics

Infectious gastroenteritis remains a public health problem. The most severe cases are of bacterial origin. In Spain, Campylobacter and Salmonella are the most prevalent bacterial genus, while Yersinia and Shigella are much less frequent. Most cases are usually self-limiting and antibiotic therapy is not generally indicated, unless patients have risk factors for severe infection and shigellosis. Ciprofloxacin, third generation cephalosporins, azithromycin, ampicillin, cotrimoxazole and doxycycline are the most recommended drugs. The susceptibility pattern of the different bacteria determines the choice of the most appropriate treatment. The aim of this review is to analyse the current situation, developments, and evolution of resistance and multidrug resistance in these 4 enteric pathogens.

First detection of CMY-2 plasmid mediated β-lactamase in Salmonella Heidelberg in South America

Salmonella enterica serovar Heidelberg ranks among the most prevalent causes of human salmonellosis in the United States and Canada, although it has been infrequently reported in South American and European countries. Most Salmonella infections are self-limiting; however, some invasive infections require antimicrobial therapy. In this work we characterized an oxyimino-cephalosporin resistant S. Heidelberg isolate recovered from an inpatient in a Buenos Aires hospital. CMY-2 was responsible for the β-lactam resistance profile. S. Heidelberg contained a 97kb plasmid belonging to the Inc N group harboring blaCMY-2. ISEcp1 was located upstream blaCMY-2 driving its expression and mobilization. The isolate belonged to sequence type 15 and virotyping revealed the presence of sopE gene. In this study we identified the first CMY-2 producing isolate of S. Heidelberg in Argentina and even in South America.

Plasmid-mediated AmpC β-lactamase (CMY-2) gene in Salmonella typhimurium isolated from diarrheic pigs in South Korea

Abstracts

β-Lactamase production in key gram-negative pathogen isolates from the Arabian Peninsula

SUMMARY Infections due to Gram-negative bacilli (GNB) are a leading cause of morbidity and mortality worldwide. The extent of antibiotic resistance in GNB in countries of the Gulf Cooperation Council (GCC), namely, Saudi Arabia, United Arab Emirates, Kuwait, Qatar, Oman, and Bahrain, has not been previously reviewed. These countries share a high prevalence of extended-spectrum-β-lactamase (ESBL)- and carbapenemase-producing GNB, most of which are associated with nosocomial infections. Well-known and widespread β-lactamases genes (such as those for CTX-M-15, OXA-48, and NDM-1) have found their way into isolates from the GCC states. However, less common and unique enzymes have also been identified. These include PER-7, GES-11, and PME-1. Several potential risk factors unique to the GCC states may have contributed to the emergence and spread of β-lactamases, including the unnecessary use of antibiotics and the large population of migrant workers, particularly from the Indian subcontinent. It is clear that active surveillance of antimicrobial resistance in the GCC states is urgently needed to address regional interventions that can contain the antimicrobial resistance issue.

Resistance to third-generation cephalosporins in human non-typhoidal Salmonella enterica isolates from England and Wales, 2010-12

OBJECTIVES

To identify the mechanism(s) underlying cefotaxime resistance in 118 of 21,641 (0.55%) non-typhoidal Salmonella enterica isolates collected from humans throughout England and Wales from January 2010 to September 2012.

METHODS

Non-duplicate isolates (n = 118) resistant to cefotaxime (MICs >1 mg/L) were screened by PCR for genes encoding CTX-M extended-spectrum β-lactamases (ESBLs) and associated ISEcp1-like elements, and for genes encoding acquired AmpC, SHV, TEM, VEB, PER and GES β-lactamases. Sequencing was used to identify specific alleles in selected isolates. Carbapenem resistance was sought by ertapenem disc screening.

RESULTS

Seventy-nine isolates (0.37% of all referred S. enterica) produced ESBLs, 37 isolates (0.17%) produced CMY-type AmpC enzymes, and 1 isolate had both enzyme types; the mechanism of cefotaxime resistance in 3 isolates could not be identified. Group 1 CTX-M genes were identified in 57 isolates belonging to 22 serotypes, with CTX-M-1 (n = 11), -15 (n = 9) and -55/57 (n = 8) the most prevalent alleles among the 29 (51%) investigated. CTX-M-2 (n = 5), -14 (n = 5), -8 (n = 1) and -65 (n = 1) were also identified. TEM-52 was identified in two isolates and SHV-12 in seven isolates. There was no evidence of carbapenem resistance. ESBL and AmpC genes were detected in both domestically acquired and travel-associated salmonellae. Eighty-nine isolates (75%) were multidrug resistant (resistant to at least three antimicrobial classes) and 42 (36%) had decreased susceptibility to ciprofloxacin (MICs 0.25-1 mg/L), with a further 13 (11%) isolates resistant (MICs >1 mg/L).

CONCLUSIONS

The prevalence of CTX-M and acquired AmpC genes in human non-typhoidal S. enterica from England and Wales is still low, but has increased from 0.03% in 2001-03 to 0.49% in 2010-12. Resistance to third-generation cephalosporins requires monitoring as it may reduce therapeutic options.

Characterisation of plasmids implicated in the mobilisation of extended-spectrum and AmpC β-lactamase genes in clinical Salmonella enterica isolates and temporal stability of the resistance genotype

Plasmids implicated in the mobilisation of β-lactamase genes in extended-spectrum β-lactamase (ESBL)- and AmpC-producing Salmonella enterica isolates recovered from three Spanish hospitals were characterised. The temporal stability of these plasmids and of the resistance phenotype without antimicrobial pressure was also assessed in the laboratory setting. The resistance determinants and their genetic environments were characterised by PCR sequencing, and their genomic location was analysed by S1 nuclease pulsed-field gel electrophoresis (PFGE) and I-CeuI PFGE, followed by Southern blot hybridisation. The 11 S. enterica studied strains carried blaCTX-M-9 (serovar Virchow, 2 isolates), blaCTX-M-10 (Virchow, 2), blaCTX-M-14 (Enteritidis, 1), blaCTX-M-15 (Gnesta and S. enterica group C, 2), blaSHV-2 (Livingstone, 1), blaSHV-12 (Enteritidis, 1) and blaCMY-2 (Bredeney, 2). The ISEcp1-blaCTX-M-14-IS903 and ISEcp1-blaCTX-M-15-orf477 genetic structures were detected. IncI1 and IncA/C plasmids carried blaCTX-M-14, blaCTX-M-15, blaSHV-2, blaSHV-12 and blaCMY-2 genes. blaCTX-M-9 included in an In60 complex integron and blaCTX-M-10 linked to a phage-related element were found in non-typeable plasmids. Conjugation and temporal stability experiments were performed in vitro through daily passages (100 days) in the absence of antimicrobial pressure. In the stability experiments, 5 of the 11 tested isolates lost the ESBL or AmpC plasmidic genes and this was associated with concomitant loss of the whole or partial plasmid. In conclusion, successful plasmids belonging to different Inc groups mobilise ESBL- and AmpC-encoding genes in S. enterica. Loss of ESBL/AmpC genes in the absence of antimicrobial pressure might explain the low prevalence of these β-lactamases among Salmonella isolates.

Prevalence and characterization of Salmonella species isolated from pigs, ducks and chickens in Sichuan Province, China

This study aimed to analyze the prevalence of Salmonella isolated from different parts of the food production chain, and to characterize these isolates. A total of 165 Salmonella enterica isolates were identified from 1382 samples taken from conventional farms, abattoirs and retail markets from 2010 to 2011 in Sichuan, China. The Salmonella isolates were assayed for serotype, antimicrobial susceptibility, prevalence of class 1 integrons and β-lactamase genes, and subtyped using pulsed-field gel electrophoresis. Among these isolates, S. enterica serotypes Derby (76 isolates, 46%) and Typhimurium (16 isolates, 10%) were the most prevalent, and high antimicrobial resistance rates were observed for tetracycline (77%), sulfamethoxazole/trimethoprim (43%), nalidixic acid (41%) and spectinomycin (41%). Class 1 integrons were detected in 21% of these isolates, and contained gene cassettes dfrA12-aadA2, dfrA1-aadA1, dfrA1, blaPSE-1 and dfrA1/aadA2. blaOXA-1 was the most commonly identified β-lactamase gene (n=14), followed by blaTEM-1 (n=6), blaPSE-1 (n=4) and blaCMY-2 (n=1). A S. enterica serotype Indiana isolate derived from chicken from a market was positive for both blaOXA-1 and blaCMY-2, and resistant to nine tested antibiotics. The PFGE patterns were diverse. Our findings indicated that most isolates from different sampling sites were phenotypically and genetically diverse, and Salmonella was widespread and may transmit along the food production chain from farm to market. Isolates with decreased susceptibility to fluoroquinolones and extended-spectrum cephalosporins, which are used to fight foodborne Salmonella, pose a serious threat to public health.

Transfer of multidrug-resistant bacteria between intermingled ecological niches: the interface between humans, animals and the environment

The use of antimicrobial agents has been claimed to be the driving force for the emergence and spread of microbial resistance. However, several studies have reported the presence of multidrug-resistant bacteria in populations exposed to low levels of antimicrobial drugs or even never exposed. For many pathogens, especially those organisms for which asymptomatic colonization typically precedes infection (e.g., Enterococcus spp. and Escherichia coli), the selective effects of antimicrobial use can only be understood if we considerer all biological and environmental pathways which enable these bacteria, and the genes they carry, to spread between different biomes. This ecological framework provides an essential perspective for formulating antimicrobial use policies, precisely because it encompasses the root causes of these problems rather than merely their consequences.

First human isolate of Salmonella enterica serotype Enteritidis harboring blaCTX-M-14 in South America

We studied a clinical isolate of Salmonella enterica serotype Enteritidis showing resistance to oxyiminocephalosporins. PCR analysis confirmed the presence of bla(CTX-M-14) linked to IS903 in a 95-kb IncI1 conjugative plasmid. Such a plasmid is maintained on account of the presence of a pndAC addiction system. Multilocus sequence typing (MLST) analysis indicated that the strain belongs to ST11. This is the first report of bla(CTX-M-14) in Salmonella Enteritidis of human origin in South America.

Molecular characterization of resistance to extended-spectrum cephalosporins in clinical Escherichia coli isolates from companion animals in the United States

Resistance to extended-spectrum cephalosporins (ESC) among members of the family Enterobacteriaceae occurs worldwide; however, little is known about ESC resistance in Escherichia coli strains from companion animals. Clinical isolates of E. coli were collected from veterinary diagnostic laboratories throughout the United States from 2008 to 2009. E. coli isolates (n = 54) with reduced susceptibility to ceftazidime or cefotaxime (MIC ≥ 16 μg/ml) and extended-spectrum-β-lactamase (ESBL) phenotypes were analyzed. PCR and sequencing were used to detect mutations in ESBL-encoding genes and the regulatory region of the chromosomal gene ampC. Conjugation experiments and plasmid identification were conducted to examine the transferability of resistance to ESCs. All isolates carried the bla(CTX-M-1)-group β-lactamase genes in addition to one or more of the following β-lactamase genes: bla(TEM), bla(SHV-3), bla(CMY-2), bla(CTX-M-14-like), and bla(OXA-1.) Different bla(TEM) sequence variants were detected in some isolates (n = 40). Three isolates harbored a bla(TEM-181) gene with a novel mutation resulting in an Ala184Val substitution. Approximately 78% of the isolates had mutations in promoter/attenuator regions of the chromosomal gene ampC, one of which was a novel insertion of adenine between bases -28 and -29. Plasmids ranging in size from 11 to 233 kbp were detected in the isolates, with a common plasmid size of 93 kbp identified in 60% of isolates. Plasmid-mediated transfer of β-lactamase genes increased the MICs (≥ 16-fold) of ESCs for transconjugants. Replicon typing among isolates revealed the predominance of IncI and IncFIA plasmids, followed by IncFIB plasmids. This study shows the emergence of conjugative plasmid-borne ESBLs among E. coli strains from companion animals in the United States, which may compromise the effective therapeutic use of ESCs in veterinary medicine.

Comparative genomics of multidrug resistance-encoding IncA/C plasmids from commensal and pathogenic Escherichia coli from multiple animal sources

Incompatibility group A/C (IncA/C) plasmids have received recent attention for their broad host range and ability to confer resistance to multiple antimicrobial agents. Due to the potential spread of multidrug resistance (MDR) phenotypes from foodborne pathogens to human pathogens, the dissemination of these plasmids represents a public health risk. In this study, four animal-source IncA/C plasmids isolated from Escherichia coli were sequenced and analyzed, including isolates from commercial dairy cows, pigs and turkeys in the U.S. and Chile. These plasmids were initially selected because they either contained the floR and tetA genes encoding for florfenicol and tetracycline resistance, respectively, and/or the bla_CMY-2 gene encoding for extended spectrum β-lactamase resistance. Overall, sequence analysis revealed that each of the four plasmids retained a remarkably stable and conserved backbone sequence, with differences observed primarily within their accessory regions, which presumably have evolved via horizontal gene transfer events involving multiple modules. Comparison of these plasmids with other available IncA/C plasmid sequences further defined the core and accessory elements of these plasmids in E. coli and Salmonella. Our results suggest that the bla_CMY-2 plasmid lineage appears to have derived from an ancestral IncA/C plasmid type harboring floR-tetAR-strAB and Tn21-like accessory modules. Evidence is mounting that IncA/C plasmids are widespread among enteric bacteria of production animals and these emergent plasmids have flexibility in their acquisition of MDR-encoding modules, necessitating further study to understand the evolutionary mechanisms involved in their dissemination and stability in bacterial populations.

Population dynamics of Salmonella enterica serotypes in commercial egg and poultry production

Fresh and processed poultry have been frequently implicated in cases of human salmonellosis. Furthermore, increased consumption of meat and poultry has increased the potential for exposure to Salmonella enterica. While advances have been made in reducing the prevalence and frequency of Salmonella contamination in processed poultry, there is mounting pressure on commercial growers to prevent and/or eliminate these human pathogens in preharvest production facilities. Several factors contribute to Salmonella colonization in commercial poultry, including the serovar and the infectious dose. In the early 1900s, Salmonella enterica serovars Pullorum and Gallinarum caused widespread diseases in poultry, but vaccination and other voluntary programs helped eradicate pullorum disease and fowl typhoid from commercial flocks. However, the niche created by the eradication of these serovars was likely filled by S. Enteritidis, which proliferated in the bird populations. While this pathogen remains a significant problem in commercial egg and poultry production, its prevalence among poultry has been declining since the 1990s. Coinciding with the decrease of S. Enteritidis, S. Heidelberg and S. Kentucky have emerged as the predominant serovars in commercial broilers. In this review, we have highlighted bacterial genetic and host-related factors that may contribute to such shifts in Salmonella populations in commercial poultry and intervention strategies that could limit their colonization.

The expression levels of outer membrane proteins STM1530 and OmpD, which are influenced by the CpxAR and BaeSR two-component systems, play important roles in the ceftriaxone resistance of Salmonella enterica serovar Typhimurium

Significant increases in STM3031, STM1530, and AcrD protein levels and significant decreases in OmpC and OmpD protein levels are present when the ceftriaxone-resistant Salmonella enterica serovar Typhimurium R200 strain is compared with the ceftriaxone-susceptible strain 01-4. AcrD is known to be involved in drug export, and STM3031 seems to play a key role in ceftriaxone resistance. Here, we examine the roles of STM1530, OmpC, and OmpD in ceftriaxone resistance. An ompD gene deletion mutant showed 4-fold higher ceftriaxone resistance than 01-4. An ompC gene deletion mutant showed 4-fold higher cephalothin and erythromycin resistance than 01-4, but there was no effect on ceftriaxone resistance. However, a stm1530 deletion mutant did show >64-fold lower ceftriaxone resistance than R200. Moreover, the STM3031 protein was significantly decreased in R200(Δstm1530) compared to R200. STM3031 expression has been shown to be influenced by the two-component system regulator gene baeR. CpxR seems to modulate BaeR. A cpxA-cpxR gene deletion mutant showed >2,048-fold lower ceftriaxone resistance than R200. The outer membrane protein profile of R200(ΔcpxAR) showed significant decreases in STM3031 and STM1530 compared to R200, while OmpD had returned to the level found in 01-4. Furthermore, the stm3031, stm1530, and ompD mRNA levels were correlated with their protein expression levels in these strains, while decreases in the mRNA levels of the efflux pump acrB, acrD, and acrF genes were found in R200(ΔcpxAR). Findings similar to those for R200(ΔcpxAR) were found for R200(ΔbaeSR). These results, together with those for STM3031 and the fact that STM1530 is an outer membrane protein, suggest that STM1530 and OmpD are influenced by the CpxAR and BaeSR two-component systems and that this contributes to S. enterica serovar Typhimurium ceftriaxone resistance.

High prevalence of extended-spectrum beta lactamases among Salmonella enterica Typhimurium isolates from pediatric patients with diarrhea in China

We investigated the extended-spectrum beta lactamases among 62 Salmonella enterica Typhimurium isolates recovered from children with diarrhea in a Chinese pediatric hospital. A large proportion of S. enterica Typhimurium isolates were resistant to multiple antimicrobial agents, including ampicillin (90.3%), tetracycline (80.6%), trimethoprim/sulfamethoxazole (74.2%), chloramphenicol (66.1%), cefotaxime (27.4%). Forty-nine (79.0%) of S. enterica Typhimurium isolates were positive for bla_TEM-1b and resistant to ampicillin. Thirteen S. enterica Typhimurium isolates (21.0%) were positive for bla_{CTX-M-1-group} and bla_{CTX-M-9-group}, and all isolates harboring bla_CTX-M genes were positive for ISEcp1. Two main clones (PFGE type A and D) accounted for nearly 70% of S. enterica Typhimurium isolates, and 7 CTX-M-producing isolates belonged to PFGE type D. Collectively, our data reveal multi-drug resistance and a high prevalence of extended spectrum beta lactamases among S. enterica Typhimurium isolates from children in China. In addition, we report the first identification of bla_CTX-M-55 within Salmonella spp. Our data also suggest that clonal spread is responsible for the dissemination of S. enterica Typhimurium isolates.

High prevalence of plasmid-mediated quinolone resistance determinant aac(6')-Ib-cr amongst Salmonella enterica serotype Typhimurium isolates from hospitalised paediatric patients with diarrhoea in China

In this study, the antimicrobial susceptibilities and prevalence of plasmid-mediated quinolone resistance determinants amongst Salmonella enterica serotype Typhimurium isolates from hospitalised paediatric patients with diarrhoea in China were investigated. In total, 40 (64.5%) of 62 S. Typhimurium isolates were resistant to ciprofloxacin (minimum inhibitory concentration ≥0.5 μg/mL), comprising 28 isolates with low-level resistance and 12 isolates with high-level resistance. All ciprofloxacin-resistant isolates were multiresistant to other antimicrobial agents. Four pulsed-field gel electrophoresis (PFGE) clusters were found amongst the 40 ciprofloxacin-resistant isolates, amongst which PFGE clusters A, B, E and D accounted for 7, 4, 1 and 28 isolates, respectively. Two isolates with high-level ciprofloxacin resistance had two mutations in the quinolone resistance-determining regions (QRDRs) of gyrA and parC. The remaining ciprofloxacin-resistant isolates had only one mutation in the QRDR of gyrA. All 62 S. Typhimurium isolates were negative for qnr genes and qepA and 23 (37.1%) of the isolates were positive for aac(6')-Ib-cr. Nineteen isolates harbouring aac(6')-Ib-cr belonged to PFGE cluster D. A high prevalence of ciprofloxacin resistance and aac(6')-Ib-cr was found amongst S. Typhimurium isolates in China from hospitalised paediatric patients with diarrhoea not receiving quinolones. A single mutation in the QRDR of gyrA as well as production of AAC(6')-Ib-cr contributed to ciprofloxacin resistance. Clonal spread was responsible for the dissemination of aac(6')-Ib-cr amongst S. Typhimurium isolates.

IncI1 plasmid carrying extended-spectrum-beta-lactamase gene blaCTX-M-1 in Salmonella enterica isolates from poultry and humans in France, 2003 to 2008

We report the dissemination of a conjugative IncI1 plasmid carrying bla(CTX-M-1), conferring resistance to extended-spectrum cephalosporins, in Salmonella enterica isolates from poultry and humans in France from 2003 to 2008. By IncI1 plasmid subtyping, this plasmid was shown to be genetically related to that found in Escherichia coli isolates from healthy poultry in France.