Epidemiology and antimicrobial resistance of Salmonella serovars Typhimurium and 4,[5],12:i- recovered from hospitalized patients in China

Global emergence of multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is a continuing challenge for modern healthcare. However, the knowledge, regarding the epidemiology of salmonellosis caused by the monophasic variant S. 4,[5],12:i:- in hospitalized patients, is limited in China. To bridge this gap, we carried out a retrospective study to determine the antimicrobial resistance, trends, and risk factors of S. Typhimurium and S. 4,[5],12:i:- (n = 329) recovered from patients in Zhejiang province between 2011 and 2019. The results showed that 90.57% (298/329) of the isolates were MDR; among them, 48.94% (161/329) and 12.46% (41/329) were phenotypically resistant to cephalosporins and fluoroquinolones, respectively, which are the drugs of choice used to treat salmonellosis in clinics. Additionally, we observed a higher incidence of infections among the young population (<5 years old). Notably, the higher prevalence of ST34 (sequence type 34) isolates, especially after 2014, with MDR (57.05%, 170/298) phenotype, and incidence of ST34 isolates co-harbouring mcr-1 (mobile colistin resistance gene) and blaCTX-M-14 (β-lactamase gene) suggest an association between STs and drug resistance. Together, the increasing prevalence of MDR ST34 calls for enhanced monitoring strategies to mitigate the spread and dissemination of MDR clones of S. Typhimurium and S. 4,[5],12:i-. Our study provides improved knowledge about non-typhoid Salmonella (NTS) infections, which could help in the effective recommendation of antimicrobials in hospitalized patients.

Repeated Occurrence of Mobile Colistin Resistance Gene-Carrying Plasmids in Pathogenic Escherichia coli from German Pig Farms

The global spread of plasmid-mediated mobile colistin resistance (mcr) genes threatens the vital role of colistin as a drug of last resort. We investigated whether the recurrent occurrence of specific E. coli pathotypes and plasmids in individual pig farms resulted from the continued presence or repeated reintroduction of distinct E. coli strains. E. coli isolates (n = 154) obtained from three pig farms with at least four consecutive years of mcr detection positive for virulence-associated genes (VAGs) predicting an intestinal pathogenic pathotype via polymerase chain reaction were analyzed. Detailed investigation of VAGs, antimicrobial resistance genes and plasmid Inc types was conducted using whole genome sequencing for 87 selected isolates. Sixty-one E. coli isolates harbored mcr-1, and one isolate carried mcr-4. On Farm 1, mcr-positive isolates were either edema disease E. coli (EDEC; 77.3%) or enterotoxigenic E. coli (ETEC; 22.7%). On Farm 2, all mcr-positive strains were ETEC, while mcr-positive isolates from Farm 3 showed a wider range of pathotypes. The mcr-1.1 gene was located on IncHI2 (Farm 1), IncX4 (Farm 2) or IncX4 and IncI2 plasmids (Farm 3). These findings suggest that various pathogenic E. coli strains play an important role in maintaining plasmid-encoded colistin resistance genes in the pig environment over time.

Salmonella Typhimurium with Eight Tandem Copies of blaNDM-1 on a HI2 Plasmid

Carbapenem-resistant Salmonella has recently aroused increasing attention. In this study, a total of four sequence type 36 Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) isolates were consecutively isolated from an 11-month-old female patient with a gastrointestinal infection, of which one was sensitive to carbapenems and three were resistant to carbapenems. Via antibiotic susceptibility testing, a carbapenemases screening test, plasmid conjugation experiments, Illumina short-reads, and PacBio HiFi sequencing, we found that all four S. Typhimurium isolates contained a blaCTX-M-14-positive IncI1 plasmid. One carbapenem-sensitive S. Typhimurium isolate then obtained an IncHI2 plasmid carrying blaNDM-1 and an IncP plasmid without any resistance genes during the disease progression. The blaNDM-1 gene was located on a new 30 kb multiple drug resistance region, which is flanked by IS26 and TnAs2, respectively. In addition, the ST_F0903R isolate contained eight tandem copies of the ISCR1 unit (ISCR1-dsbD-trpF-ble-blaNDM-1-ISAba125Δ1), but an increase in MICs to carbapenems was not observed. Our work further provided evidence of the rapid spread and amplification of blaNDM-1 through plasmid. Prompting the recognition of carbapenem-resistant Enterobacterales and the initiation of appropriate infection control measures are essential to avoid the spread of these organisms.

Characteristics of Two mcr-1-Harboring IncHI2 Plasmids from Clinical Salmonella Isolates in Jiaxing City

Salmonella is a primary cause of foodborne diseases, and the increasing prevalence of mcr-1-carrying plasmids, which confer colistin resistance to Salmonella, poses significant global health concerns. As the frequency of occurrence of the mcr-1 gene is increasing globally, we studied the prevalence of mcr-1 in clinical Salmonella isolates by analyzing 195 clinical strains isolated in 2020. Of the 195 Salmonella isolates, 41 isolates were resistant to colistin. We found mcr-1 in two strains (Salmonella Typhimurium ZJJX20006 and Salmonella Kentucky ZJJX20014), which we analyzed in detail via whole-genome sequencing and antibiotic susceptibility testing. Two strains displayed resistance to ampicillin, ampicillin-sulbactam, tetracycline, chloramphenicol, and cotrimoxazole, while ZJJX20006 displayed resistance to colistin and ZJJX20014 was sensitive. Genomic analysis revealed that these strains had plasmid-encoded mcr-1 in IncHI2 plasmids, which were not similar to the mcr-1-IncX4 identified in 2016. These two strains also harbored other drug resistance genes, including blaOXA-1 and blaCTX-M-14. Our findings may help clarify the molecular mechanisms of mcr-1 dissemination among Salmonella strains in Jiaxing City and offer insights into the evolution of mcr-1 in Salmonella.

Clinically relevant antibiotic resistance in Escherichia coli from black kites in southwestern Siberia: a genetic and phenotypic investigation

Wild birds including raptors can act as vectors of clinically relevant bacteria with antibiotic resistance. The aim of this study was to investigate the occurrence of antibiotic-resistant Escherichia coli in black kites (Milvus migrans) inhabiting localities in proximity to human-influenced environments in southwestern Siberia and investigate their virulence and plasmid contents. A total of 51 E. coli isolates mostly with multidrug resistance (MDR) profiles were obtained from cloacal swabs of 35 (64%, n = 55) kites. Genomic analyses of 36 whole genome sequenced E. coli isolates showed: (i) high prevalence and diversity of their antibiotic resistance genes (ARGs) and common association with ESBL/AmpC production (27/36, 75%), (ii) carriage of mcr-1 for colistin resistance on IncI2 plasmids in kites residing in proximity of two large cities, (iii) frequent association with class one integrase (IntI1, 22/36, 61%), and (iv) presence of sequence types (STs) linked to avian-pathogenic (APEC) and extra-intestinal pathogenic E. coli (ExPEC). Notably, numerous isolates had significant virulence content. One E. coli with APEC-associated ST354 carried qnrE1 encoding fluoroquinolone resistance on IncHI2-ST3 plasmid, the first detection of such a gene in E. coli from wildlife. Our results implicate black kites in southwestern Siberia as reservoirs for antibiotic-resistant E. coli. It also highlights the existing link between proximity of wildlife to human activities and their carriage of MDR bacteria including pathogenic STs with significant and clinically relevant antibiotic resistance determinants. IMPORTANCE Migratory birds have the potential to acquire and disperse clinically relevant antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs) through vast geographical regions. The opportunistic feeding behavior associated with some raptors including black kites and the growing anthropogenic influence on their natural habitats increase the transmission risk of multidrug resistance (MDR) and pathogenic bacteria from human and agricultural sources into the environment and wildlife. Thus, monitoring studies investigating antibiotic resistance in raptors may provide essential data that facilitate understanding the fate and evolution of ARB and ARGs in the environment and possible health risks for humans and animals associated with the acquisition of these resistance determinants by wildlife.

The first description of the complete genome sequence of multidrug-resistant Salmonella enterica serovar monophasic Typhimurium (1,4,[5],12:i:-) isolate with the mcr-1.1 gene on IncHI2 found in pig in Poland

Monophasic Salmonella Typhimurium (1,4,[5],12:i:-) is one of the leading Salmonella serovars causing human salmonellosis in Europe. It has been observed in Poland since 2008. This serovar is considered the one with the highest rate of mcr prevalence. This report presents a sequence characteristic of the multidrug-resistant (MDR) monophasic S. Typhimurium isolated from a pig faecal sample with the confirmed presence of the mcr-1.1 gene. The genome was assembled into the complete chromosome and 4 plasmids: IncHI2 (232 119 bp), IncFIB/IncFIC (133 901 bp), ColRNAI (6659 bp), and Col8282 (4066bp). The strain identified as ST34 carried multiple antimicrobial resistance genes located both on chromosome (tet(B)) and plasmids: mcr-1.1 and blaTEM-1B on ST4-IncHI2, and mef(B), blaTEM-1B, aadA1, qacL, dfrA12, aadA2, cmlA1, sul3, tet(M) on IncFIB/FIC. The mcr-1.1 gene was previously identified in E. coli deriving mainly from poultry, but this is the first case of the occurrence of mcr-positive Salmonella in Poland. The obtained results of analysis of the genome content draw attention to the problem of multidrug-resistant pathogens, especially in the context of resistance to colistin which is a last-resort antimicrobial.

High-risk international clones ST66, ST171 and ST78 of Enterobacter cloacae complex causing blood stream infections in Spain and carrying blaOXA-48 with or without mcr-9

BACKGROUND

In the last years, Enterobacter cloacae complex has become an important threat associated with nosocomial infections (including bacteraemia). These bacteria have the ability to acquire mobile genetic elements with antimicrobial resistance genes, reducing the number of therapies available for treatment of the infections they cause. Multidrug resistant isolates of the E. cloacae complex have been causing blood stream infections in a hospital in northern Spain. The aim of this study was to report the spread of E. cloacae complex isolates carrying bla_OXA-48 with or without mcr-9 which were involved in blood stream infections, in a Spanish hospital.

METHODS

All Enterobacter spp. isolates recovered from blood cultures of patients admitted to a tertiary Spanish hospital, over a five-year period were recovered. Of those, OXA-48-producing isolates were selected for further analysis (19 E. xiangfangensis isolates and a single E. hoffmannii). Bacterial identification, antimicrobial susceptibility, DNA sequencing, molecular typing, resistome analysis and plasmid characterization was performed.

RESULTS

20 isolates were positive for bla_OXA-48, harbored by IncL/M plasmids. They belonged to the international high-risk clones ST66, ST171 and ST78. They produced the extended-spectrum β-lactamases CTX-M-15 and/or CTX-M-9 and 40 % of them (n = 8) also carried the mcr-9 gene, located on IncHI2 plasmids. However, they were susceptible to colistin.

CONCLUSION

The presence of bla_OXA-48, together with at least one bla_CTX-M gene in our multidrug resistant high-risk E. cloacae complex clones is worrisome. Also, the additional presence of mcr-9 in some of them is of concern as it could potentially be transferred into other hosts or acquire mutations that might led to emerging colistin resistance. Surveillance systems are essential to detect these difficult-to-treat bacteria which, apart from causing live-threatening infections, can spread important resistance threats.

Spread of the mcr-1 colistin-resistance gene in Escherichia coli through plasmid transmission and chromosomal transposition in French goats

Introduction

Colistin-resistance widely disseminated in food-producing animals due to decades of colistin use to treat diarrhea. The plasmid-borne mcr-1 gene has been extensively reported from bovine, swine and chicken worldwide, but smaller productions such as the goat farming sector were much less surveyed.

Methods

We looked for colistin-resistant isolates presenting plasmid-borne genes of the mcr family in both breeding (n=80) and fattening farms (n=5). Localization of the mcr-1 gene was performed using Southern blot analysis coupled to short-read and long-read sequencing.

Results

Only the mcr-1 gene was identified in 10% (8/80) of the breeding farms and four over the five fattening farms. In total, 4.2% (65/1561) of the animals tested in breeding farms and 60.0% (84/140) of those tested in fattening farms presented a mcr-1-positive E. coli. The mcr-1 gene was located either on the chromosome (32.2%) or on IncX4 (38.9%) and IncHI2 (26.8%) plasmids. As expected, both clonal expansion and plasmidic transfers were observed in farms where the mcr-1 gene was carried by plasmids. Tn6330 transposition was observed in the chromosome of diverse E. coli sequence types within the same farm.

Discussion

Our results show that the mcr-1 gene is circulating in goat production and is located either on plasmids or on the chromosome. Evidence of Tn6330 transposition highlighted the fact that chromosomal insertion does not impair the transmission capability of the mcr-1 gene. Only strict hygiene and biosecurity procedures in breeding farms, as well as a prudent use of antibiotics in fattening farms, can avoid such complex contamination pathways.

Prevalence of Chromosomally Located blaCTX-M-55 in Salmonella Typhimurium ST34 Isolates Recovered from a Tertiary Hospital in Guangzhou, China

Nontyphoidal Salmonella (NTS) is one of the most prevalent bacterial causes of gastrointestinal infections worldwide. Meanwhile, the detection rate of CTX-M-55 ESBL-positive has increased gradually in China. To identify the molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying nontyphoidal Salmonella (NTS) clinical isolates, a total of 105 NTS isolates were collected from a Chinese tertiary hospital. Antimicrobial susceptibility testing was performed to determine the resistance phenotype. Whole-genome sequencing and bioinformatics analysis were used to determine the antimicrobial resistance genes, serotypes, phylogenetic relationships, and the genetic environment of the blaCTX-M-55 gene. The results showed that among the 22 ceftriaxone resistant isolates, the blaCTX-M-55 was the most common β-Lactamase gene carried by 14 isolates, including serotypes S. Typhimurium (10/14), S. Muenster (2/14), S. Rissen (1/14), and S. Saintpaul (1/14). Phylogenetic analysis shows that 10 blaCTX-M-55-positive S. Typhimurium ST34 isolates were divided into two clusters. The genetic relationship of isolates in each cluster was very close (≤10 cgMLST loci). The blaCTX-M-55 gene was located on the chromosome in 10 isolates, on IncI1 plasmid in three isolates, and IncHI2 plasmid in one isolate. In conclusion, the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, close attention to the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings must be monitored carefully. IMPORTANCE ESCs are the first choice for treating NTS infections. However, ESBLs and AmpC β-lactamases are the most typical cause for ESCs resistance. The CTX-M-55 ESBL-positive rate has gradually increased in the clinic in recent years. At present, the research about blaCTX-M-55-positive Salmonella mainly focuses on the foodborne animals or the environment while less on clinical patients. Thus, this study was carried out for identifying molecular epidemiological and genomic characteristics of blaCTX-M-55-carrying NTS clinical isolates. The results showed that the blaCTX-M-55 gene, mainly located on the chromosome of S. Typhimurium ST34 isolates from Conghua District, was the main driving force associated with the resistance of NTS to cephalosporins. Therefore, our work highlights the importance of monitoring the clonal dissemination of blaCTX-M-55-carrying S. Typhimurium ST34 in clinical settings.

Characterization of a Multidrug-Resistant Salmonella Enteritidis Clinical Strain Carrying a Novel Hybrid Plasmid

A Salmonella Enteritidis clinical strain SAL045 isolated from an infant patient in China was subjected to whole genome sequencing. Strain SAL045 is resistant to 12 antibiotics tested including ampicillin and polymyxin E. A novel hybrid plasmid pS045A harboring 22 antibiotic resistance genes and 10 virulence genes was characterized. There were no sequences in the NCBI nucleotide database that completely covered the pS045A sequence. Sequence analysis indicated that pS045A was formed by IS26-mediated recombination of two plasmids. Plasmid pS045A was transferred to E. coli EC600 recipient strain at a frequency of 1.76 × 10^-6 per donor cell. Plasmid pS045A is a novel conjugative plasmid and might cause dissemination of drug-resistance and virulence genes within enterobacterial species.

Co-occurrence of bla NDM-1 and mcr-9 in a Conjugative IncHI2/HI2A Plasmid From a Bloodstream Infection-Causing Carbapenem-Resistant Klebsiella pneumoniae

Spread of the carbapenemase-encoding and mobilized colistin resistance (mcr) genes among Enterobacteriales poses a great threat to global public health, especially when the both genes are transferred by a single plasmid. Here, we identified a bla _NDM-1- and mcr-9-co-encoding plasmid harbored by a clinical isolate of Klebsiella pneumoniae (KPN710429). KPN710429 was recovered from a blood sample from an inpatient in a tertiary hospital in China, and antimicrobial susceptibility testing showed that it was multidrug-resistant and only susceptible to aztreonam, colistin, and tigecycline. KPN710429 belongs to sequence type (ST) 1308 and capsular serotype KL144. The string test of KPN710429 was negative, and this strain didn't exhibit a hypervirulent phenotype according to serum-killing and Galleria mellonella lethality assessments. Whole-genome sequencing revealed the KPN710429 genome comprises a single chromosome and three plasmids. All virulence associated genes were harbored by chromosome. Most of its antimicrobial resistance genes, including bla _NDM-1 and mcr-9 were carried by plasmid pK701429_2, belonging to the incompatibility (Inc) HI2/HI2A group and ST1. Comparative genomics assays indicates that pK710429_2 could be a hybrid plasmid, formed by a Tn6696-like bla _NDM-1 region inserting into a mcr-9-positive-IncHI2/HI2A plasmid. pK710429_2 contained the conjugative transfer gene regions, Tra1 and Tra2, with some structural variations, and conjugation assays revealed that pK710429_2 was transferable. Although pK710429_2 lacked the qseB-qseC regulatory genes, mcr-9 expression was upregulated after pretreatment with colistin for 6 h, leading to colistin resistance in KPN710429. To our knowledge, this is the first report of a bla _NDM-1- and mcr-9-co-encoding transferable plasmid harbored by a bloodstream-infection-causing K. pneumoniae strain in China. Effective surveillance should be implemented to assess the prevalence of the plasmid co-harboring carbapenemase-encoding gene and mcr-9.

Corrigendum: First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

[This corrects the article DOI: 10.3389/fmicb.2021.676113.].

First Report of Coexistence of bla SFO-1 and bla NDM-1 β-Lactamase Genes as Well as Colistin Resistance Gene mcr-9 in a Transferrable Plasmid of a Clinical Isolate of Enterobacter hormaechei

Many antimicrobial resistance genes usually located on transferable plasmids are responsible for multiple antimicrobial resistance among multidrug-resistant (MDR) Gram-negative bacteria. The aim of this study is to characterize a carbapenemase-producing Enterobacter hormaechei 1575 isolate from the blood sample in a tertiary hospital in Wuhan, Hubei Province, China. Antimicrobial susceptibility test showed that 1575 was an MDR isolate. The whole genome sequencing (WGS) and comparative genomics were used to deeply analyze the molecular information of the 1575 and to explore the location and structure of antibiotic resistance genes. The three key resistance genes (bla_SFO–1, bla_NDM–1, and mcr-9) were verified by PCR, and the amplicons were subsequently sequenced. Moreover, the conjugation assay was also performed to determine the transferability of those resistance genes. Plasmid files were determined by the S1 nuclease pulsed-field gel electrophoresis (S1-PFGE). WGS revealed that p1575-1 plasmid was a conjugative plasmid that possessed the rare coexistence of bla_SFO–1, bla_NDM–1, and mcr-9 genes and complete conjugative systems. And p1575-1 belonged to the plasmid incompatibility group IncHI2 and multilocus sequence typing ST102. Meanwhile, the pMLST type of p1575-1 was IncHI2-ST1. Conjugation assay proved that the MDR p1575-1 plasmid could be transferred to other recipients. S1-PFGE confirmed the location of plasmid with molecular weight of 342,447 bp. All these three resistant genes were flanked by various mobile elements, indicating that the bla_SFO–1, bla_NDM–1, and mcr-9 could be transferred not only by the p1575-1 plasmid but also by these mobile elements. Taken together, we report for the first time the coexistence of bla_SFO–1, bla_NDM–1, and mcr-9 on a transferable plasmid in a MDR clinical isolate E. hormaechei, which indicates the possibility of horizontal transfer of antibiotic resistance genes.

Dissemination of Extended-Spectrum-β-Lactamase-Producing Enterobacter cloacae Complex from a Hospital to the Nearby Environment in Guadeloupe (French West Indies): ST114 Lineage Coding for a Successful IncHI2/ST1 Plasmid

Wastewater treatment plants are considered hot spots for antibiotic resistance. Most studies have addressed the impact on the aquatic environment, as water is an important source of anthropogenic pollutants.

Wastewater treatment plants are considered hot spots for antibiotic resistance. Most studies have addressed the impact on the aquatic environment, as water is an important source of anthropogenic pollutants. Few investigations have been conducted on terrestrial animals living near treatment ponds. We isolated extended-spectrum-β-lactamase Enterobacter cloacae complex-producing strains from 35 clinical isolates, 29 samples of wastewater, 19 wild animals, and 10 domestic animals living in the hospital sewers and at or near a wastewater treatment plant to study the dissemination of clinically relevant resistance through hospital and urban effluents. After comparison of the antibiotic-resistant profiles of E. cloacae complex strains, a more detailed analysis of 41 whole-genome-sequenced strains demonstrated that the most common sequence type, ST114 (n = 20), was present in human (n = 9) and nonhuman (n = 11) samples, with a close genetic relatedness. Whole-genome sequencing confirmed local circulation of this pathogenic lineage in diverse animal species. In addition, nanopore sequencing and specific synteny of an IncHI2/ST1/bla_CTX-M-15 plasmid recovered on the majority of these ST114 clones (n = 18) indicated successful worldwide diffusion of this mobile genetic element.

Characterization of the Complete Nucleotide Sequences of mcr-1-Encoding Plasmids From Enterobacterales Isolates in Retailed Raw Meat Products From the Czech Republic

The aim of our study was to determine complete nucleotide sequence of mcr-1-carrying plasmids from Enterobacterales isolates recovered from domestic and imported raw retailed meat and compare them with plasmids available at the GenBank sequence database. A set of 16 plasmids originating from Escherichia coli (n = 13), Klebsiella pneumoniae (n = 2), and Citrobacter braakii (n = 1) were analyzed. In our previous study, data from whole genome sequencing showed that mcr-1 gene was located on plasmids of different incompatibility groups (IncHI2, IncI2, and IncX4). The IncI2 (n = 3) and IncX4 (n = 8) plasmids harbored mcr-1.1 gene only, whereas IncHI2 sequence type 4 plasmids (n = 5) carried large multidrug resistance (MDR) regions. MDR regions of IncHI2 plasmids included additional antimicrobial resistance genes conferring resistance to β-lactams (bla_TEM−1), aminoglycosides [aadA1, aadA2, and aph(6)-Id], macrolides [mef (B)], tetracycline (tetA, tetR), and sulphonamides (sul1, sul2, and sul3). Likewise, IncHI2 plasmids carried several insertion sequences including IS1, IS3, IS26, IS1326, and ISApl1. In conclusion, our findings confirmed the involvement of IncX4, IncI2, and IncHI2 plasmids in the dissemination of mcr-1.1 gene in several environmental niches, as in samples of retail meat originating from different geographical regions. In contrast to IncX4 and IncI2, IncHI2 plasmids were more diverse and carried additional genes for resistance to heavy metals and multiple antimicrobials.

Detection of Five mcr-9-Carrying Enterobacterales Isolates in Four Czech Hospitals

Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the “last-resort” antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published.

The aim of this study was to report the characterization of the first mcr-positive Enterobacterales isolated from Czech hospitals. In 2019, one Citrobacter freundii and four Enterobacter isolates were recovered from Czech hospitals. The production of carbapenemases was examined by a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) imipenem hydrolysis assay. Additionally, bacteria were screened for the presence of carbapenemase-encoding genes and plasmid-mediated colistin resistance genes by PCR. To define the genetic units carrying mcr genes, the genomic DNAs of mcr-carrying clinical isolates were sequenced on the PacBio Sequel I platform. Results showed that all isolates carried bla_VIM- and mcr-like genes. Analysis of whole-genome sequencing (WGS) data revealed that all isolates carried mcr-9-like alleles. Furthermore, the three sequence type 106 (ST106) Enterobacter hormaechei isolates harbored the bla_VIM-1 gene, while the ST764 E. hormaechei and ST95 C. freundii included bla_VIM-4. Analysis of plasmid sequences showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. Additionally, at least one multidrug resistance (MDR) region was identified in each mcr-9-carrying IncHI2 plasmid. The bla_VIM-4 gene was found in the MDR regions of p48880_MCR_VIM and p51929_MCR_VIM. In the three remaining isolates, bla_VIM-1 was localized on plasmids (∼55 kb) exhibiting repA-like sequences 99% identical to the respective gene of pKPC-CAV1193. In conclusion, to the best of our knowledge, these 5 isolates were the first mcr-9-positive bacteria of clinical origin identified in the Czech Republic. Additionally, the carriage of the bla_VIM-1 on pKPC-CAV1193-like plasmids is described for the first time. Thus, our findings underline the ongoing evolution of mobile elements implicated in the dissemination of clinically important resistance determinants.

IMPORTANCE Infections caused by carbapenemase-producing bacteria have led to the revival of polymyxins as the “last-resort” antibiotic. Since 2016, several reports describing the presence of plasmid-mediated colistin resistance genes, mcr, in different host species and geographic areas were published. Here, we report the first detection of Enterobacterales carrying mcr-9-like alleles isolated from Czech hospitals in 2019. Furthermore, the three ST106 Enterobacter hormaechei isolates harbored bla_VIM-1, while the ST764 E. hormaechei and ST95 Citrobacter freundii isolates included bla_VIM-4. Analysis of WGS data showed that, in all isolates, mcr-9 was carried on IncHI2 plasmids. bla_VIM-4 was found in the MDR regions of IncHI2 plasmids, while bla_VIM-1 was localized on pKPC-CAV1193-like plasmids, described here for the first time. These findings underline the ongoing evolution of mobile elements implicated in dissemination of clinically important resistance determinants. Thus, WGS characterization of MDR bacteria is crucial to unravel the mechanisms involved in dissemination of resistance mechanisms.

Whole-Genome Sequence Analysis of an Extensively Drug-Resistant Salmonella enterica Serovar Agona Isolate from an Australian Silver Gull (Chroicocephalus novaehollandiae) Reveals the Acquisition of Multidrug Resistance Plasmids

Although most of the approximately 94 million annual human cases of gastroenteritis due to Salmonella enterica resolve without medical intervention, antimicrobial therapy is recommended for patients with severe disease. Wild birds can be natural hosts of Salmonella that pose a threat to human health; however, multiple-drug-resistant serovars of S. enterica have rarely been described. In 2012, silver gull (Chroicocephalus novaehollandiae) chicks at a major breeding colony were shown to host Salmonella, most isolates of which were susceptible to antibiotics. However, multiple-drug-resistant (MDR) Escherichia coli with resistance to carbapenems, ceftazidime, and fluoroquinolones was reported from this breeding colony. In this paper, we describe a novel MDR Salmonella strain subsequently isolated from the same breeding colony. SG17-135, an isolate of S. enterica with phenotypic resistance to 12 individual antibiotics but only nine antibiotic classes including penicillins, cephalosporins, monobactams, macrolides, fluoroquinolones, aminoglycosides, dihydrofolate reductase inhibitors (trimethoprim), sulfonamides, and glycylcyclines was recovered from a gull chick in 2017. Whole-genome sequence (WGS) analysis of SG17-135 identified it as Salmonella enterica serovar Agona (S Agona) with a chromosome comprising 4,813,284 bp, an IncHI2 ST2 plasmid (pSG17-135-HI2) of 311,615 bp, and an IncX1 plasmid (pSG17-135-X) of 27,511 bp. pSG17-135-HI2 housed a complex resistance region comprising 16 antimicrobial resistance genes including bla _CTX-M-55 The acquisition of MDR plasmids by S. enterica described here poses a serious threat to human health. Our study highlights the importance of taking a One Health approach to identify environmental reservoirs of drug-resistant pathogens and MDR plasmids.IMPORTANCE Defining environmental reservoirs hosting mobile genetic elements that shuttle critically important antibiotic resistance genes is key to understanding antimicrobial resistance (AMR) from a One Health perspective. Gulls frequent public amenities, parklands, and sewage and other waste disposal sites and carry drug-resistant Escherichia coli Here, we report on SG17-135, a strain of Salmonella enterica serovar Agona isolated from the cloaca of a silver gull chick nesting on an island in geographic proximity to the greater metropolitan area of Sydney, Australia. SG17-135 is closely related to pathogenic strains of S Agona, displays resistance to nine antimicrobial classes, and carries important virulence gene cargo. Most of the antibiotic resistance genes hosted by SG17-135 are clustered on a large IncHI2 plasmid and are flanked by copies of IS26 Wild birds represent an important link in the evolution and transmission of resistance plasmids, and an understanding of their behavior is needed to expose the interplay between clinical and environmental microbial communities.

Wide Spread of bla CTX-M-9/mcr-9 IncHI2/ST1 Plasmids and CTX-M-9-Producing Escherichia coli and Enterobacter cloacae in Rescued Wild Animals

Wildlife has recently been pinpointed as one of the drivers of dissemination of genes conferring resistances to clinically important antimicrobials. The presence of both extended-spectrum beta-lactamase- (ESBL) and carbapenemase-encoding genes has notably been reported in wild birds, that can act as sentinels of antimicrobial resistance (AMR) contamination but also as long-distance spreaders in case of migratory birds. Here, 424 wild birds brought to a rescue center in France were sampled over a 6-month period. These birds encompassed 62 different sedentary or migratory species. A further 16 wild mammals present in the center were also investigated. No carbapenemase-producer was found, but we identified a surprisingly high proportion (24.1%) of ESBL-positive isolates. A total of 144 non-duplicate isolates were collected, including Escherichia coli (n = 88), Enterobacter cloacae (n = 51), and Citrobacter freundii (n = 5), of which 123 carried the bla_CTX–M–9 gene. PFGE, phylogroup, and MLST revealed the presence of a limited number of ESBL-positive clones circulating in these animals, all presenting multiple associated resistances. Next-generation sequencing on a subset of isolates, followed by Southern blot hybridization, showed the wide dissemination of an IncHI2/ST1 plasmid carrying the bla_CTX–M–9, bla_SHV–12 and mcr-9 genes. In all, our results undoubtedly reflect cross transmissions of ESC-resistance (ESC-R) Enterobacteriaceae within the rescue center – similarly to nosocomial spreads observed at hospital, rather than the true bacterial flora of birds. We also showed that the spread of ESC-R in this rescue center did not only rely on clonal but also on a highly successful plasmidic transmission. Since most animals are intended to get back to nature after a few days or weeks, this is obviously an issue with regard to ESBL dissemination in natural environments.

First Genomic Characterization of blaVIM-1 and mcr-9-Coharbouring Enterobacter hormaechei Isolated from Food of Animal Origin

We describe here the complete genome sequence of an Enterobacter hormaechei ST279 coharbouring bla_VIM-1 and mcr-9 recovered from uncooked beef patty in June 2017, Egypt. The tested isolate was resistant to carbapenem but susceptible to colistin (minimum inhibitory concentration (MIC), 0.5 μg/mL). The antimicrobial susceptibility profile and conjugation experiments were performed. The entire genome was sequenced by the Illumina MiniSeq and Oxford Nanopore methods. The bla_VIM-1 and mcr-9 genes are carried on the same IncHI2/pMLST1 plasmid, pMS37a (Size of 270.9 kb). The mcr-9 gene was located within the physical boundaries demarcated by two insertion elements IS903 (upstream) and IS1 (downstream) but did not possess the downstream regulatory genes (qseC/qseB) which regulate the expression of mcr-9. Therefore, the mcr-9 might be silently disseminated among carbapenem-resistant Enterobacterales. In addition to bla_VIM-1 and mcr-9, plasmid pMS37a harbored various antibiotic resistance genes including aac(6’)-Il, ΔaadA22, aac(6’)-Ib-cr, sul1, dfrA1 and tetA. To the best of our knowledge, this is the first report of a bla_VIM-1 and mcr-9-coharbouring E. hormaechei isolate of food origin worldwide. The identification of a multidrug-resistant VIM-1 and mcr-9 positive Enterobacter hormaechei isolate from food is worrisome as retail meat and meat products could serve as a vehicle for these MDR bacteria, which could be transferred between animals and humans through the food chain. It further highlights that Enterobacterales co-producing MCR and carbapenemases being found in the food chain indeed correspond to a One-Health issue, highlighting the need for serious steps to prevent their further dissemination.

Two IncHI2 Plasmid-Mediated Colistin-Resistant Escherichia coli Strains from the Broiler Chicken Supply Chain in Zhejiang Province, China

ABSTRACT

Colistin is used as one of the last-resort drugs against lethal infections caused by carbapenem-resistant pathogens of the Enterobacteriaceae family. Enterobacteriaceae bacteria carrying the mcr-1 colistin resistance gene are emerging in livestock and poultry, posing a serious threat to human health. However, there have been few reports about the prevalence and transmission of mcr-1 along the regional chicken supply chain. In this study, the complete sequences of mcr-1-positive Escherichia coli ST2705 and ST206 isolates obtained by screening 129 chilled chicken samples and 251 chicken fecal samples were investigated. Both of these isolates showed resistance to colistin, and importantly, the complete sequence of the mcr-1-positive E. coli ST2705 in China was reported for the first time. The mcr-1 gene was located on the IncHI2 plasmids pTBMCR421 (254,365 bp) and pTBMCR401 (230,964 bp) in strains ECCNB20-2 and ECZP248, respectively. Comparative analysis of mcr-1-bearing IncHI2 plasmids showed a marked similarity, indicating that these plasmids are very common and have the ability to be efficient vehicles for mcr-1 dissemination among humans, animals, and food. Furthermore, an insertion (ISKpn26) in Tn6330 (ISApl1-mcr-1-pap2-ISApl1) was identified in the plasmid pTBMCR401 and then compared; this insertion might affect the adaptability and stability of Tn6330. Taken together, these findings suggest that the IncHI2 plasmid might be a main factor affecting the transmission of mcr-1 in the chicken supply chain and that the genetic context of the mcr-1-bearing IncHI2 plasmid is constantly evolving.

HIGHLIGHTS

Genomic Characterisation of a Multiple Drug Resistant IncHI2 ST4 Plasmid in Escherichia coli ST744 in Australia

Antibiotic resistance genes (ARGs) including those from the bla_CTX-M family and mcr-1 that encode resistance to extended spectrum β–lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal E. coli from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides. The ARGs reside within a complex resistance locus (CRL) that shows considerable sequence identity to a CRL in pSDE_SvHI2, an IncHI2:ST3 plasmid from an enterotoxigenic E. coli with serotype O157:H19 of porcine origin that caused substantial losses to swine production operations in Australia in 2007. pTZ41_1P is closely related to IncHI2 plasmids found in E. coli and Salmonella enterica from porcine, avian and human sources in Europe and China but it does not carry genes encoding resistance to clinically-important antibiotics. We identified regions of IncHI2 plasmids that contribute to the genetic plasticity of this group of plasmids and highlight how they may readily acquire new resistance gene cargo. Genomic surveillance should be improved to monitor IncHI2 plasmids.

Antimicrobial Resistance in Salmonella enterica Serovar Paratyphi B Variant Java in Poultry from Europe and Latin America

Salmonella enterica serovar Paratyphi B variant Java sequence type 28 is prevalent in poultry and poultry meat. We investigated the evolutionary relatedness between sequence type 28 strains from Europe and Latin America using time-resolved phylogeny and principal component analysis. We sequenced isolates from Colombia, Guatemala, Costa Rica, and the Netherlands and complemented them with publicly available genomes from Europe, Africa, and the Middle East. Phylogenetic time trees and effective population sizes (N_e) showed separate clustering of strains from Latin America and Europe. The separation is estimated to have occurred during the 1980s. N_e of strains increased sharply in Europe around 1995 and in Latin America around 2005. Principal component analysis on noncore genes showed a clear distinction between strains from Europe and Latin America, whereas the plasmid gene content was similar. Regardless of the evolutionary separation, similar features of resistance to β-lactams and quinolones/fluoroquinolones indicated parallel evolution of antimicrobial resistance in both regions.

Emergence of a Multidrug-Resistant Enterobacter hormaechei Clinical Isolate from Egypt Co-Harboring mcr-9 and blaVIM-4

This study describes the first full genomic sequence of an mcr-9 and bla_VIM-4-carrying multidrug-resistant Enterobacter hormaechei clinical isolate from Egypt. The strain was isolated in April 2015 from the sputum of a patient in Cairo, Egypt. The mcr-9 and bla_VIM-4 genes were identified by PCR screening and DNA sequencing; the isolate was subjected to antimicrobial susceptibility testing, conjugation experiments, and whole genomic sequencing. mcr-9 and bla_VIM-4 were carried by an IncHI2 plasmid, pAMS-38a (281,121 bp in size); the plasmid also carried genes conferring resistance against sulfonamides (sul1), quinolones (qnrA1), trimethoprim (dfrA1), β-lactams (bla_TEM-1B), aminoglycosides (aac (6’)-II, aadA23, aadA2b, and ant(2’’)-Ia). The strain was susceptible to colistin (MIC, <0.25 μg/mL); this could be due to the absence of the qseC/qseB regulatory system located downstream of mcr-9 in Enterobacterales, which is involved in the induction of colistin-resistance. The genetic context of mcr-9 and bla_VIM-4 was identified as IS1-mcr-9-IS903-pcoS-∆pcoE-rcnA and intI1-bla_VIM-4—aac (6’)-II-dfrA1-∆aadA23-smr-ISPa21-qacE∆1, respectively. This is the first report of an mcr-9 and bla_VIM-4 /IncHI2-carrying multidrug-resistant E. hormaechei clinical isolate from Africa and the Middle East. Plasmids of the IncHI2 group and the two insertion sequences (IS1, and IS903) might be the main vehicles for dissemination of mcr-9. Further screening for mcr-9 is essential for identifying its incidence and to prevent its dissemination.

Molecular characteristics of extended-spectrum β-lactamase/AmpC-producing Salmonella enterica serovar Virchow isolated from food-producing animals during 2010-2017 in South Korea

Global dissemination of non-typhoidal Salmonella producing extended-spectrum β-lactamase (ESBL) is a public-health concern. Recently, the prevalence of Salmonella spp. resistant to third-generation cephalosporins has been increasing in food-producing animals in Korea. In this study, we investigated resistance mechanisms and molecular characteristics of S. Virchow isolates resistant to extended-spectrum cephalosporins (ESCs). We obtained 265 S. Virchow isolates from fecal and carcasses samples of cattle (n = 2), pigs (n = 7), and chickens (n = 256) during 2010-2017, and observed high ESC-resistance (63.8%, 169/265); most of the resistant isolates (96.4%) were obtained from chickens. ESC-resistant S. Virchow isolates (n = 169) showed significantly higher resistance rates to other antimicrobials (especially aminoglycosides and tetracycline, p-value <0.0001), as well as prevalence of multidrug resistance, than did ESC-susceptible S. Virchow isolates (n = 96). All ESC-resistant S. Virchow produced CTX-M-15-type ESBL (n = 147) and/or CMY-2-type AmpC β-lactamase (n = 23). ESC-resistant S. Virchow represented seven pulsotypes, predominantly composed of type II (58.6%) and III (26.0%), detected in 69 farms in 10 provinces, and 33 farms in 7 provinces, respectively. Genes encoding ESC-resistance were horizontally transferred by conjugation to recipient E. coli J53; this was demonstrated in 28.8% (42/146) of bla_CTX-M-15-positive isolates and in 50.0% (11/22) of bla_CMY-2-positive isolates. All conjugative plasmids carrying bla_CTX-M-15 and bla_CMY-2 genes belonged to ST2-IncHI2 and ST12/CC12-IncI1, respectively. Genetic features of transferred bla genes were involved with ISEcp1 in both bla_CTX-M-15 and bla_CMY-2; ISEcp1 plays a critical role in the efficient capture, expression, and mobilization of bla genes. In addition to bla_CTX-M-15 genes, resistance markers to aminoglycosides and/or tetracycline were co-transferred to recipient E. coli J53. Our results show a high prevalence of ESBL-producing S. Virchow in chickens and chicken carcasses. Specific bla_CTX-M-15 and bla_CMY-2-carrying S. Virchow clones and plasmids were predominant in food-producing animals nationwide. Restriction of antimicrobial use and proper biosecurity practices at the farm level should be urgently implemented in the poultry industry.

Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of blaIMP-4 on an IncHI2 plasmid

Carbapenemase-producing Enterobacteriaceae (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare exposure. blaIMP-4 is the most frequently detected carbapenemase gene in Enterobacteriaceae within Australia, but little is known about the mechanisms behind its persistence. Here we used whole genome sequencing (WGS) to investigate the molecular epidemiology of blaIMP-4 in Queensland, Australia. In total, 107 CPE were collected between 2014 and 2017 and sent for WGS on an Illumina NextSeq500. Resistance genes and plasmid types were detected using a combination of read mapping and nucleotide comparison of de novo assemblies. Six isolates were additionally sequenced using Oxford Nanopore MinION to generate long-reads and fully characterize the context of the blaIMP-4 gene. Of 107 CPE, 93 carried the blaIMP-4 gene; 74/107 also carried an IncHI2 plasmid, suggesting carriage of the blaIMP-4 gene on an IncHI2 plasmid. Comparison of these isolates to a previously characterized IncHI2 plasmid pMS7884A (isolated from an Enterobacter hormaechei strain in Brisbane) suggested that all isolates carried a similar plasmid. Five of six representative isolates sequenced using Nanopore long-read technology carried IncHI2 plasmids harbouring the blaIMP-4 gene. While the vast majority of isolates represented E. hormaechei, several other species were also found to carry the IncHI2 plasmid, including Klebsiella species, Escherichia coli and Citrobacter species. Several clonal groups of E. hormaechei were also identified, suggesting that persistence of blaIMP-4 is driven by both presence on a common plasmid and clonal spread of certain E. hormaechei lineages.

Corrigendum: Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011-2016

[This corrects the article DOI: 10.3389/fmicb.2019.01753.].

Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011-2016

The emergence of plasmid-mediated colistin resistance (mcr genes) threatens the effectiveness of polymyxins, which are last-resort drugs to treat infections by multidrug- and carbapenem-resistant Gram-negative bacteria. Based on the occurrence of colistin resistance the aims of the study were to determine possible resistance mechanisms and then characterize the mcr-positive Escherichia coli. The research used material from the Polish national and EU harmonized antimicrobial resistance (AMR) monitoring programs. A total of 5,878 commensal E. coli from fecal samples of turkeys, chickens, pigs, and cattle collected in 2011-2016 were screened by minimum inhibitory concentration (MIC) determination for the presence of resistance to colistin (R) defined as R > 2 mg/L. Strains with MIC = 2 mg/L isolated in 2014-2016 were also included. A total of 128 isolates were obtained, and most (66.3%) had colistin MIC of 2 mg/L. PCR revealed mcr-1 in 80 (62.5%) isolates recovered from 61 turkeys, 11 broilers, 2 laying hens, 1 pig, and 1 bovine. No other mcr-type genes (including mcr-2 to -5) were detected. Whole-genome sequencing (WGS) of the mcr-1-positive isolates showed high diversity in the multi-locus sequence types (MLST) of E. coli, plasmid replicons, and AMR and virulence genes. Generally mcr-1.1 was detected on the same contig as the IncX4 (76.3%) and IncHI2 (6.3%) replicons. One isolate harbored mcr-1.1 on the chromosome. Various extended-spectrum beta-lactamase (bla SHV-12, bla CTX-M-1, bla CTX-M-15, bla TEM-30, bla TEM-52, and bla TEM-135) and quinolone resistance genes (qnrS1, qnrB19, and chromosomal gyrA, parC, and parE mutations) were present in the mcr-1.1-positive E. coli. A total of 49 sequence types (ST) were identified, ST354, ST359, ST48, and ST617 predominating. One isolate, identified as ST189, belonged to atypical enteropathogenic E. coli. Our findings show that mcr-1.1 has spread widely among production animals in Poland, particularly in turkeys and appears to be transferable mainly by IncX4 and IncHI2 plasmids spread across diverse E. coli lineages. Interestingly, most of these mcr-1-positive E. coli would remain undetected using phenotypic methods with the current epidemiological cut-off value (ECOFF). The appearance and spread of mcr-1 among various animals, but notably in turkeys, might be considered a food chain, and public health hazard.

oqxAB-Positive IncHI2 Plasmid pHXY0908 Increase Salmonella enterica Serotype Typhimurium Strains Tolerance to Ciprofloxacin

Salmonella enterica serotype Typhimurium is a major global food-borne pathogen and causes life-threatening infections. Although the resistance mechanisms to fluoroquinolones in S. Typhimurium had been well-defined, tolerance to fluoroquinolones and the associated mechanism for this are obscure. In the current work, we investigated an oqxAB-positive plasmid pHXY0908 and analyzed its role in S. Typhimurium tolerance to ciprofloxacin using time-kill, transcriptome sequencing and real-time PCR. S. Typhimurium ATCC14028 could survive under lethal concentrations of ciprofloxacin after acquiring plasmid pHXY0908. Transcriptome sequence analysis showed the chromosomal genes were systematically regulated after acquiring this plasmid suggesting an interaction between chromosome and plasmid. Additionally, the chromosomal efflux pump genes acrB, acrA, tolC, and yceE were up-regulated after acquiring plasmid pHXY0908 suggesting that these efflux pumps may contribute to the survival of ATCC14028 exposed to the lethal concentrations of ciprofloxacin. In conclusion, this is the first known report demonstrating that an IncHI2 type plasmid harboring oqxAB could assist S. Typhimurium survival under lethal concentrations of ciprofloxacin.

Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human

A colistin-resistant Salmonella enterica 4, [5],12:i:- sequence type (ST) 34 harbouring mcr-3.1 was recovered from a patient who travelled to China 2 weeks prior to diarrhoea onset. Genomic analysis revealed the presence of the mcr-3.1 gene located in the globally disseminated IncHI2 plasmid, highlighting the intercontinental dissemination of the colistin-resistant S. enterica 4, [5],12:i:- ST34 pandemic clone.

Co-Occurrence of mcr-1 and qnrS1 on an IncHI2 Plasmid in Clinical Isolates of Salmonella Typhimurium in Spain

Salmonella enterica is a well-adapted zoonotic bacterium associated to cases of gastroenteritis and bacteremia with increased morbidity and mortality. In this study, three isolates of Salmonella Typhimurium obtained from human clinical samples, showing colistin resistance and low-level resistance to quinolones, have been genetically characterized. We detected the co-occurrence of mcr-1 and qnrS1 on a single IncHI2 plasmid in isolates of Salmonella Typhimurium obtained from Spanish children without a travel history. The multiresistant region contained numerous resistance genes. Isolates were clonally related, which suggests the presence of these clones in the community and the potential to cause outbreaks affecting the most susceptible population. It is necessary to monitor the presence of these plasmid-mediated resistance genes in human European strains of Salmonella spp. because of the risk of producing outbreaks of community-acquired infections.

Transmissible ST3-IncHI2 Plasmids Are Predominant Carriers of Diverse Complex IS26-Class 1 Integron Arrangements in Multidrug-Resistant Salmonella

Diverse mobile genetic elements (MGEs) including plasmids, insertion sequences, and integrons play an important role in the occurrence and spread of multidrug resistance (MDR) in bacteria. It was found in previous studies that IS26 and class 1 integrons integrated on plasmids to speed the dissemination of antibiotic-resistance genes in Salmonella. It is aimed to figure out the patterns of specific genetic arrangements between IS26 and class 1 integrons located in plasmids in MDR Salmonella in this study. A total of 74 plasmid-harboring Salmonella isolates were screened for the presence of IS26 by PCR amplification, and 39 were IS26-positive. Among them, 37 isolates were resistant to at least one antibiotic. The thirty-seven antibiotic-resistant isolates were further involved in PCR detection of class 1 integrons and variable regions, and all were positive for class 1 integrons. Six IS26-class 1 integron arrangements with IS26 inserted into the upstream or downstream of class 1 integrons were characterized. Eight combinations of these IS26-class 1 integron arrangements were identified among 31 antibiotic-resistant isolates. Multidrug-resistance plasmids of the IncHI2 incompatibility group were dominant, which all belonged to ST3 by plasmid double locus sequence typing. These 21 IncHI2-positive isolates harbored six complex IS26-class 1 integron arrangement patterns. Conjugation assays and Southern blot hybridizations confirmed that conjugative multidrug-resistance IncHI2 plasmids harbored the different complex IS26-class 1 integron arrangements. The conjugation frequency of IncHI2 plasmids transferring alone was 10⁻⁵-10⁻⁶, reflecting that different complex IS26-class 1 integron arrangement patterns didn't significantly affect conjugation frequency (P > 0.05). These data suggested that class 1 integrons represent the hot spot for IS26 insertion, forming diverse MDR loci. And ST3-IncHI2 was the major plasmid lineage contributing to the horizontal transfer of composite IS26-class 1 integron MDR elements in Salmonella.

pSTM6-275, a Conjugative IncHI2 Plasmid of Salmonella enterica That Confers Antibiotic and Heavy-Metal Resistance under Changing Physiological Conditions

Detailed annotation of an IncHI2 plasmid, pSTM6-275, from Salmonella enterica serotype 1,4,5,12:i:- strain TW-Stm6 revealed a composite structure, including antimicrobial resistance genes on mobile genetic elements. The plasmid was thermosensitive for transfer to Escherichia coli and conferred reduced susceptibility to antibiotics, copper sulfate, and silver nitrate. Metal ion susceptibility was dependent on physiological conditions, giving an insight into the environments where this trait might confer a fitness advantage.

Prevalence and Molecular Characterization of mcr-1-Positive Salmonella Strains Recovered from Clinical Specimens in China

The recently discovered colistin resistance element, mcr-1, adds to the list of antimicrobial resistance genes that rapidly erode the antimicrobial efficacy of not only the commonly used antibiotics but also the last-line agents of carbapenems and colistin. This study investigated the prevalence of the mobile colistin resistance determinant mcr-1 in Salmonella strains recovered from clinical settings in China and the transmission potential of mcr-1-bearing mobile elements harbored by such isolates. The mcr-1 gene was recoverable in 1.4% of clinical isolates tested, with the majority of them belonging to Salmonella enterica serotype Typhimurium. These isolates exhibited diverse pulsed-field gel electrophoresis (PFGE) profiles and high resistance to antibiotics other than colistin and particularly to cephalosporins. Plasmid analysis showed that mcr-1 was carried on a variety of plasmids with sizes ranging from ∼30 to ∼250 kb, among which there were conjugative plasmids of ∼30 kb, ∼60 kb, and ∼250 kb and nonconjugative plasmids of ∼140 kb, ∼180 kb, and ∼240 kb. Sequencing of representative mcr-1-carrying plasmids revealed that all conjugative plasmids belonged to the IncX4, IncI2, and IncHI2 types and were highly similar to the corresponding types of plasmids reported previously. Nonconjugative plasmids all belonged to the IncHI2 type, and the nontransferability of these plasmids was attributed to the loss of a region carrying partial or complete tra genes. Our data revealed that, similar to the situation in Escherichia coli, mcr-1 transmission in Salmonella was accelerated by various plasmids, suggesting that transmission of mcr-1-carrying plasmids between different species of Enterobacteriaceae may be a common event.

Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms

Thermal interventions are commonly used in the food industry as a means of mitigating pathogen contamination in food products. Concern over heat-resistant food contaminants has recently increased, with the identification of a conserved locus shown to confer heat resistance in disparate lineages of Gram-negative bacteria. Complete sequence analysis of a historical isolate of Salmonella enterica serovar Senftenberg, used in numerous studies because of its novel heat resistance, revealed that this important strain possesses two distinct copies of this conserved thermotolerance locus, residing on a multireplicon IncHI2/IncHI2A plasmid. Phylogenetic analysis of these loci in comparison with homologs identified in various bacterial genera provides an opportunity to examine the evolution and distribution of loci conferring resistance to environmental stressors, such as heat and desiccation.

Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg 775W (ATCC 43845), demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs. These two loci reside on a large 341.3-kbp plasmid that is similar to the well-studied IncHI2 R478 plasmid but lacks any antibiotic resistance genes found on R478 or other IncHI2 plasmids. As this historical Salmonella isolate has been in use since 1941, comparative analysis of the plasmid and of the thermotolerance loci contained on the plasmid will provide insight into the evolution of heat resistance loci as well as acquisition of resistance determinants in IncHI2 plasmids.

IMPORTANCE Thermal interventions are commonly used in the food industry as a means of mitigating pathogen contamination in food products. Concern over heat-resistant food contaminants has recently increased, with the identification of a conserved locus shown to confer heat resistance in disparate lineages of Gram-negative bacteria. Complete sequence analysis of a historical isolate of Salmonella enterica serovar Senftenberg, used in numerous studies because of its novel heat resistance, revealed that this important strain possesses two distinct copies of this conserved thermotolerance locus, residing on a multireplicon IncHI2/IncHI2A plasmid. Phylogenetic analysis of these loci in comparison with homologs identified in various bacterial genera provides an opportunity to examine the evolution and distribution of loci conferring resistance to environmental stressors, such as heat and desiccation.

IncHI2 Plasmids Are Predominant in Antibiotic-Resistant Salmonella Isolates

The wide usage of antibiotics contributes to the increase in the prevalence of antibiotic-resistant Salmonella. Plasmids play a critical role in horizontal transfer of antibiotic resistance markers in Salmonella. This study aimed to screen and characterize plasmid profiles responsible for antibiotic resistance in Salmonella and ultimately to clarify the molecular mechanism of transferable plasmid-mediated antibiotic resistance. A total of 226 Salmonella isolates were examined for antimicrobial susceptibility by a disk diffusion method. Thirty-two isolates (14.2%) were resistant to at least one antibiotic. The presence of plasmid-mediated quinolone resistance (PMQR) genes and β-lactamase genes were established by PCR amplification. PCR-based replicon typing revealed that these 32 isolates represented seven plasmid incompatibility groups (IncP, HI2, A/C, FIIs, FIA, FIB, and I1), and the IncHI2 (59.4%) was predominant. Antibiotic resistance markers located on plasmids were identified through plasmid curing. Fifteen phenotypic variants were obtained with the curing efficiency of 46.9% (15/32). The cured plasmids mainly belong to the HI2 incompatibility group. The elimination of IncHI2 plasmids correlated with the loss of β-lactamase genes (blaOXA-1 and blaTEM-1) and PMQR genes (qnrA and aac(6')-Ib-cr). Both IncHI2 and IncI1 plasmids in a S. enterica serovar Indiana isolate SJTUF 10584 were lost by curing. The blaCMY -2-carrying plasmid pS10584 from SJTUF 10584 was fully sequenced. Sequence analysis revealed that it possessed a plasmid scaffold typical for IncI1 plasmids with the unique genetic arrangement of IS1294-ΔISEcp1-blaCMY -2-blc-sugE-ΔecnR inserted into the colicin gene cia. These data suggested that IncHI2 was the major plasmid lineage contributing to the dissemination of antibiotic resistance in Salmonella and the activity of multiple mobile genetic elements may contribute to antibiotic resistance evolution and dissemination between different plasmid replicons.

Rapid Emergence and Clonal Dissemination of CTX-M-15-Producing Salmonella enterica Serotype Virchow, South Korea

The prevalence of cefotaxime-resistant Salmonella enterica serotype Virchow has dramatically increased in South Korea since the first isolation in 2011. Of 68 isolates collected over 10 years, 28 cefotaxime-resistant isolates harbored the bla_CTX-M-15 extended-spectrum β-lactamase gene and were closely related genetically, demonstrating the clonal dissemination of CTX-M-15–producing Salmonella Virchow in South Korea.

bloodstream isolates, and support ESBL-transfer to Escherichia coli

We investigated the prevalence of extended-spectrum β-lactamases (ESBLs) in Enterobacter spp. bloodstream isolates from 19 hospital laboratories in Norway during 2011. A total of 62/230 (27%) isolates were resistant to third-generation cephalosporins and four (1.7%) were ESBL-positive; blaCTX -M-15 (n = 3) and blaSHV -12 (n = 1). This is comparable to the prevalence of ESBLs in clinical isolates of Escherichia coli and Klebsiella pneumoniae in Norway during the same period. All ESBL-positive isolates were multidrug resistant (MDR) and harboured plasmid-mediated quinolone resistance. Three isolates supported transfer of large IncHI2-plasmids harbouring ESBL- and MDR-encoding genes to E. coli recipients by in vitro conjugation.