DNA sequence analysis of the genetic environment of various blaCTX-M genes

Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains

The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.

Transmission dynamics of ESBL/AmpC and carbapenemase-producing Enterobacterales between companion animals and humans

Antimicrobial resistance mediated by extended-spectrum beta-lactamase (ESBL)- and plasmid-mediated cephalosporinase (AmpC)-producing Enterobacterales, as well as carbapenemase-producing Enterobacterales have globally increased among companion animals, posing a potential health risk to humans in contact with them. This prospective longitudinal study investigates the transfer of ESBL/AmpC- and carbapenemase-producing Enterobacterales between companion animals and their cohabitant humans in Portugal (PT) and the United Kingdom (UK) during animal infection. Fecal samples and nasal swabs collected from dogs and cats with urinary tract infection (UTI) or skin and soft tissue infection (SSTI), and their cohabitant humans were screened for resistant strains. Relatedness between animal and human strains was established by whole-genome sequencing (WGS). ESBL/AmpC-producing Enterobacterales were detected in companion animals (PT = 55.8%; UK = 36.4%) and humans (PT = 35.9%; UK = 12.5%). Carbapenemase-producing Enterobacterales carriage was observed in one dog from Portugal (2.6%) and another dog from the UK (4.5%). Transmission of index clinical ESBL-producing Escherichia coli and Klebsiella pneumoniae strains to cohabitant humans was observed in three Portuguese households (6.9%, n = 43), with repeated isolation of the index strains on fecal samples from the animals and their cohabiting humans. In addition, longitudinal sharing of E. coli strains carried by companion animals and their owners was observed in other two Portuguese households and two households from the UK. Furthermore, a multidrug-resistant ACT-24-producing Enterobacter hormaechei subsp. hoffmannii strains were also shared within another Portuguese household. These results highlight the importance of the household as an epidemiological unit in the efforts to mitigate the spread of antimicrobial resistance, further emphasizing the need for antimicrobial surveillance in this context, capable of producing data that can inform and evaluate public health actions.

Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serovar Typhimurium Isolates from Food Animals During 2010-2021 in South Korea

Extended-spectrum β-lactamase (ESBL)-producing Salmonella is emerging as a worldwide public health concern. In this study, we aimed to investigate the antimicrobial resistance profiles and molecular characteristics of ESBL-producing Salmonella enterica serovar Typhimurium (S. Typhimurium). We obtained a total of 995 S. Typhimurium isolates from the feces and carcasses of pigs (n = 678), chickens (n = 202), and cattle (n = 115) during 2010-2021 in Korea. We found that 35 S. Typhimurium isolates (3.5%) showed resistance to ceftiofur: pigs (51.4%, 18/35) and cattle (42.9%, 15/35). All of the ceftiofur-resistant S. Typhimurium isolates demonstrated multidrug resistance. Moreover, ceftiofur-resistant S. Typhimurium isolates displayed significantly higher rates of resistance to chloramphenicol and trimethoprim/sulfamethoxazole than ceftiofur-susceptible S. Typhimurium isolates (p < 0.05). The ceftiofur-resistant S. Typhimurium isolates produced four different CTX-M-type β-lactamase, comprising blaCTX-M-55 in the majority (51.4%, 18/35), followed by blaCTX-M-65 (28.6%, 10/35), blaCTX-M-14 (17.1%, 6/35), and blaCTX-M-1 (2.9%, 1/35). Among the 35 ceftiofur-resistant S. Typhimurium isolates, 16 blaCTX-M-55-positive isolates and one blaCTX-M-1-positive isolate were transferred to recipient Escherichia coli RG488 by conjugation. The predominantly found transposable units were blaCTX-M-55-orf477 (45.7%, 16/35), followed by blaCTX-M-65-IS903 (28.6%, 10/35) and blaCTX-M-14-IS903 (17.1%, 6/35). Ceftiofur-resistant S. Typhimurium represented 19 types, with types P1-19 (22.9%, 8/35) and P12-34 (22.9%, 8/35) making up the majority and being found in most farms nationwide. Sequence types (STs) were different by animal species: ST19 (48.6%, 17/35) and ST34 (42.9%, 15/35) were mostly found STs in pigs and cattle, respectively. These findings showed that food animals, especially pigs and cattle, act as reservoirs of blaCTX-M-harboring S. Typhimurium that can potentially be spread to humans.

Epidemiology and molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolated from neonatal intensive care units in General Hospital of Ningxia Medical University, China, 2017-2021

OBJECTIVES

This study aimed to retrospectively investigate the epidemiology and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from neonatal intensive care units (NICU) between 2017 and 2021.

METHODS

The antibacterial susceptibility of all strains was assessed using the VITEK 2 compact system. The presence of antibiotic resistance, virulence genes, sequence types (STs), capsular (K) types, and the wzi genes was determined through polymerase chain reaction (PCR). Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) using the restriction enzyme XbaI. Additionally, the virulence potential of peg344-positive strains was evaluated using the string test and mouse intraperitoneal infection models. Whole-genome sequencing was conducted on the DNB system and PacBio platforms.

RESULTS

A total of 46 CRKP isolates were collected during the study period. Out of these, 93.47% (43/46) were identified as CRKP strains belonging to the ST76-K10 type carrying blaNDM-5. It was observed that CRKP infection resulted in more severe clinical symptoms compared to CRKP colonization. Among the CRKP strains, a hypervirulent CRKP strain called KP-63, belonging to the ST23 type, was identified. This strain exhibited high mortality in the mouse infection model and was found to possess virulence genes. Genomic alignment analysis revealed a significant similarity between the virulence plasmid from KP-63 strain (pKP-63) and pK2044 from the hypervirulent K. pneumoniae strain NTUH-2044.

CONCLUSIONS

There has been a potential dissemination of ST76-K10 type CRKP carrying blaNDM-5 in the NICU at Ningxia Hospital. Neonatal CRKP infection has been found to cause more severe clinical symptoms than colonization. Furthermore, we have discovered a CR-hvKP strain of ST23 with serotype K1, which exhibits a significant resemblance in its virulent plasmid to pK2044. Therefore, it is crucial to enforce effective measures to restrict the spread and hinder the evolution of CRKP within the hospital.

New insights on mcr-1-harboring plasmids from human clinical Escherichia coli isolates

Mobile colistin resistance (mcr) genes were described recently in Gram-negative bacteria including carbapenem-resistant Enterobacterales. There are ten mcr genes described in different Gram-negative bacteria, however, Escherichia coli harboring mcr-1 gene is by far the most frequent combination. In Argentina, mcr-1 gene was characterized only on plasmids belonging to IncI2 group. The aim of this work was to get new insights of mcr-1-harboring plasmids from E. coli. Eight E. coli isolates from a larger collection of 192 clinical E. coli isolates carrying the mcr-1 gene were sequenced using next generation technologies. Three isolates belonged to ST131 high-risk clone, and five to single ST, ST38, ST46, ST226, ST224, and ST405. Eight diverse mcr-1-harboring plasmids were analyzed: IncI2 (1), IncX4 (3), IncHI2/2A (3) and a hybrid IncFIA/HI1A/HI1B (1) plasmid. Plasmids belonging to the IncI2 (n = 1) and IncX4 (n = 3) groups showed high similarity with previously described plasmids. Two IncHI2/HI2A plasmids, showed high identity between them, while the third, showed several differences including additional resistance genes like tet(A) and floR. One IncFIA/H1A/H1B hybrid plasmid was characterized, highly similar to pSRC27-H, a prototype plasmid lacking mcr genes. mcr-1.5 variant was found in four plasmids with three different Inc groups: IncI2, IncHI2/HI2A and the hybrid FIA/HI1A/HI1B plasmid. mcr-1.5 variant is almost exclusively described in our country and with a high frequency. In addition, six E. coli isolates carried three allelic variants codifying for CTX-M-type extended-spectrum-β-lactamases: blaCTX-M-2 (3), blaCTX-M-65 (2), and blaCTX-M-14 (1). It is the first description of mcr-1 harboring plasmids different to IncI2 group in our country. These results represents new insights about mcr-1 harboring plasmids recovered from E. coli human samples from Argentina, showing different plasmid backbones and resistance gene combinations.

IS26 mediated blaCTX-M-65 amplification in Escherichia coli increase the antibiotic resistance to cephalosporin in vivo

OBJECTIVES

To characterize two Escherichia coli strains isolated from a patient pre- and post-treatment, using β-lactams and β-lactam/β-lactamase inhibitor combinations (BLBLIs).

METHODS

A combination of antibiotic susceptibility testing (AST) with whole genome sequencing using Illumina and Oxford Nanopore platforms. Long-read sequencing and reverse transcription-quantitative PCR were performed to determine the copy numbers and expression levels of antibiotic resistance genes (ARGs), respectively. Effect on fitness costs were assessed by growth rate determination.

RESULTS

The strain obtained from the patient after the antibiotic treatment (XH989) exhibited higher resistance to cefepime, BLBLIs and quinolones compared with the pre-treatment strain (XH987). Sequencing revealed IS26-mediated duplications of a IS26-fosA3-blaCTX-M-65 plasmid-embedded element in strain XH989. Long-read sequencing (7.4 G data volume) indicated a variation in copy numbers of blaCTX-M-65 within one single culture of strain XH989. Increased copy numbers of the IS26-fosA3-blaCTX-M-65 element were correlated with higher CTX-M-65 expression level and did not impose fitness costs, while facilitating faster growth under high antibiotic concentrations.

CONCLUSION

Our study is an example from the clinic how BLBLIs and β-lactams exposure in vivo possibly promoted the amplification of an IS26-multiple drug resistance (MDR) region. The observation of a copy number variation seen with the blaCTX-M-65 gene in the plasmid of the post-treatment strain expands our knowledge of insertion sequence dynamics and evolution during treatment.

Emergence of OXA-48-producing Enterobacter hormaechei in a Swiss companion animal clinic and their genetic relationship to clinical human isolates

BACKGROUND

Enterobacter hormaechei producing the carbapenemase OXA-48 was identified repeatedly in infections in companion animals hospitalized at a Swiss veterinary clinic where OXA-48-producing Klebsiella pneumoniae was previously reported.

OBJECTIVES

To determine the genetic relatedness of animal and human E. hormaechei strains collected in Switzerland during 2017-22 and their mobile genetic elements.

METHODS

Hybrid assemblies for phylogenetic and comparative analysis of animal (n = 9) and human (n = 25) isolates were obtained by sequencing with Illumina, PacBio and Oxford Nanopore Technologies. Antimicrobial susceptibility was tested by broth microdilution.

RESULTS

The animal strains were identified as E. hormaechei subsp. xiangfangensis ST114 (n = 6) and ST418 (n = 2), and E. hormaechei subsp. hoffmannii ST78 (n = 1). Human E. hormaechei belonged to subspecies steigerwaltii (n = 10), xiangfangensis (n = 13), hoffmannii (n = 1) and hormaechei (n = 1), with a heterogeneous ST distribution differing from the animal strains, except for two ST114. Core-gene SNP analysis confirmed the clonality of the animal ST114 and ST418 isolates (0 to 10 SNPs), and close relatedness of animal and human ST114 strains (80-120 SNPs). The strains harboured the blaOXA-48 gene on ca. 63 kb IncL-type plasmids (n = 27); on ca. 72 kb IncL plasmids co-harbouring blaCTX-M-14 (n = 2); and on ca. 150-180 kb IncFIB (n = 4) or hybrid IncFIB/IncL (n = 1) plasmids. The blaOXA-48-harbouring plasmids and the blaDHA-1-carrying ISCR1 element in one animal ST114 and both ST418 clones were likely acquired from previously spreading K. pneumoniae strains.

CONCLUSIONS

Common ecological niches favour the spread of plasmid-borne carbapenemases among Enterobacterales and the emergence of MDR E. hormaechei clones.

Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador

The increasing abundance of extended spectrum (β-lactamase (ESBL) genes in E. coli, and other commensal and pathogenic bacteria, endangers the utility of third or more recent generation cephalosporins, which are major tools for fighting deadly infections. The role of domestic animals in the transmission of ESBL carrying bacteria has been recognized, especially in low- and middle-income countries, however the horizontal gene transfer of these genes is difficult to assess. Here we investigate blaCTX-M gene diversity (and flanking nucleotide sequences) in E. coli from chicken and humans, in an Ecuadorian rural community and from chickens in another location in Ecuador. The blaCTX-M associated sequences in isolates from humans and chickens in the same remote community showed greater similarity than those found in E. coli in a chicken industrial operation 200 km away. Our study may provide evidence of blaCTX-M transfer between chickens and humans in the community.

Implications of different waterfowl farming on cephalosporin resistance: Investigating the role of blaCTX-M-55

We investigated the cephalosporin resistance of Escherichia coli from waterfowl among different breeding mode farms. In 2021, we isolated 200 strains of E. coli from waterfowl feces samples collected from Sichuan, Heilongjiang, and Anhui provinces. The key findings are: Out of the 200 strains, 80, 80, and 40 strains were isolated from waterfowl feces samples in intensive, courtyard, and outdoor breeding mode farms, respectively. The overall positive rate of the ESBL phenotype, detecting by the double disk diffusion method, was 68.00% (136/200). In particular, the rates for intensive, courtyard, and outdoor breeding modes were 98.75%, 36.25%, and 70.00%, respectively. Results of MIC test showed drug resistance rates in the intensive breeding mode: 100.00% for cephalothin, 38.75% for cefoxitin, 100.00% for cefotaxime, and 100.00% for cefepime. In courtyard breeding mode, the corresponding rates were 100.00%, 40.00%, 63.75%, and 45.00%, respectively. In outdoor breeding mode, the corresponding rates were 100.00%, 52.50%, 82.50%, and 77.50%, respectively. The PCR results for blaCTX-M, blaTEM, blaOXA, and blaSHV showed the detection rate of blaCTX-M was highest at 75.50%, with blaCTX-M-55 is the main subtype gene, followed by blaTEM at 73.50%. We screened 58 donor strains carrying blaCTX-M-55, including 52 strains from the intensive breeding mode. These donor bacteria can transfer different plasmids to recipient E. coli J53, resulting in recipient bacteria acquiring cephalosporin resistance, and the conjugational transfer frequency ranged from 1.01 × 10-5 to 6.56 × 10-2. The transferred plasmids remained stable in recipient bacteria for up to several days without significant adaptation costs observed. During molecular typing of E. coli with conjugational transfer ability, the blaCTX-M-55 was found to be widely present in different ST strains with several phylogenetic groups. In summary, cephalosporin resistance of E. coli carried by waterfowl birds in intensive breeding mode farm was significantly higher than in courtyard and outdoor mode farms. The blaCTX-M-55 subtype gene was the prevalent ARGs and can be horizontally transferred through plasmids, which plays a key role in the spread of cephalosporin drug resistance.

Characterization of plasmids carrying blaCTX-M genes among extra-intestinal Escherichia coli clinical isolates in Ethiopia

CTX-Ms are encoded by bla_CTX-M genes and are widely distributed extended-spectrum β-lactamases (ESBLs). They are the most important antimicrobial resistance (AMR) mechanism to β-lactam antibiotics in the Enterobacteriaceae. However, the role of transmissible AMR plasmids in the dissemination of bla_CTX-M genes has scarcely been studied in Africa where the burden of AMR is high and rapidly spreading. In this study, AMR plasmid transmissibility, replicon types and addiction systems were analysed in CTX-M-producing Escherichia coli clinical isolates in Ethiopia with a goal to provide molecular insight into mechanisms underlying such high prevalence and rapid dissemination. Of 100 CTX-Ms-producing isolates obtained from urine (84), pus (10) and blood (6) from four geographically distinct healthcare settings, 75% carried transmissible plasmids encoding for CTX-Ms, with CTX-M-15 being predominant (n = 51). Single IncF plasmids with the combination of F-FIA-FIB (n = 17) carried the bulk of bla_CTX-M-15 genes. In addition, IncF plasmids were associated with multiple addiction systems, ISEcp1 and various resistance phenotypes for non-cephalosporin antibiotics. Moreover, IncF plasmid carriage is associated with the international pandemic E. coli ST131 lineage. Furthermore, several CTX-M encoding plasmids were associated with serum survival of the strains, but less so with biofilm formation. Hence, both horizontal gene transfer and clonal expansion may contribute to the rapid and widespread distribution of bla_CTX-M genes among E. coli populations in Ethiopian clinical settings. This information is relevant for local epidemiology and surveillance, but also for global understanding of the successful dissemination of AMR gene carrying plasmids.

Characterization of a Tigecycline-Resistant and blaCTX-M-Bearing Klebsiella pneumoniae Strain from a Peacock in a Chinese Zoo

In Chinese zoos, there are usually specially designed bird parks, similar to petting zoos, that allow children and adults to interact with diverse birds. However, such behaviors present a risk for the transmission of zoonotic pathogens. Recently, we isolated eight strains of Klebsiella pneumoniae and identified two blaCTX-M-positive strains from 110 birds, including parrots, peacocks, and ostriches, using anal or nasal swabs in a bird park of a zoo in China. There, K. pneumoniae LYS105A was obtained from a diseased peacock with chronic respiratory diseases by a nasal swab, which harbored the blaCTX-M-3 gene and exhibited resistance to amoxicillin, cefotaxime, gentamicin, oxytetracycline, doxycycline, tigecycline, florfenicol, and enrofloxacin. According to an analysis by whole-genome sequencing, K. pneumoniae LYS105A belongs to serotype ST859 (sequence type 859)-K19 (capsular serotype 19) and contains two plasmids, of which pLYS105A-2 can be transferred by electrotransformation and harbors numerous resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91. The above-mentioned genes are located in a novel mobile composite transposon, Tn7131, which makes horizontal transfer more flexible. Although no known genes were identified in the chromosome, a significant increase in SoxS upregulated the expression levels of phoPQ, acrEF-tolC, and oqxAB, which contributed to strain LYS105A acquiring resistance to tigecycline (MIC = 4 mg/L) and intermediate resistance to colistin (MIC = 2 mg/L). Altogether, our findings show that bird parks in zoos may act as important vehicles for the spread of multidrug-resistant bacteria from birds to humans and vice versa. IMPORTANCE A multidrug-resistant ST859-K19 K. pneumoniae strain, LYS105A, was obtained from a diseased peacock in a Chinese zoo. In addition, multiple resistance genes such as blaCTX-M-3, aac(6')-Ib-cr5, and qnrB91 were located in a novel composite transposon, Tn7131, of a mobile plasmid, implying that most of the resistance genes in strain LYS105A can be moved easily via horizontal gene transfer. Meanwhile, an increase in SoxS can further positively regulate the expression of phoPQ, acrEF-tolC, and oqxAB, which is the key factor for strain LYS105A to develop resistance to tigecycline and colistin. Taken together, these findings enrich our understanding of the horizontal cross-species spread of drug resistance genes, which will help us curb the development of bacterial resistance.

Increased clonal dissemination of OXA-232-producing ST15 Klebsiella pneumoniae in Zhejiang, China from 2018 to 2021

BACKGROUND

OXA-232-producing Klebsiella pneumoniae was first identified in China in 2016, and its clonal transmission was reported in 2019. However, there are no prevalence and genotypic surveillance data available for OXA-232 in China. Therefore, we investigated the trends and characteristics of OXA-232 type carbapenemase in Zhejiang Province, China from 2018 to 2021.

METHODS

A total of 3278 samples from 1666 patients in the intensive care units were collected from hospitals in Zhejiang Province from 2018 to 2021. Carbapenem-resistant isolates were initially selected by China Blue agar plates supplemented with 0.3 μg/ml meropenem, and further analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry identification, immune colloidal gold technique, conjugation experiment, antimicrobial susceptibility testing and whole genome sequencing.

RESULTS

A total of 79 OXA-producing strains were recovered, with the prevalence increased from 1.8% [95% confidence interval (CI): 0.7-3.7%] in 2018 to 6.0% (95% CI: 4.4-7.9%) in 2021. Seventy-eight strains produced OXA-232 and one produced OXA-181. The bla_OXA-232 gene in all strains was located in a 6141-bp ColKP3-type non-conjugative plasmid and the bla_OXA-181 gene was located in a 51,391-bp ColKP3/IncX3-type non-conjugative plasmid. The bla_OXA-232-producing K. pneumoniae was dominated (75/76) by isolates of sequence type 15 (ST15) that differed by less than 80 SNPs. All OXA-producing strains (100%, 95% CI: 95.4-100.0%) were multidrug-resistant.

CONCLUSIONS

From 2018 to 2021, OXA-232 is the most prevalent OXA-48-like derivative in Zhejiang Province, and ST15 K. pneumoniae isolates belonging to the same clone are the major carriers. The transmission of ColKP3-type plasmid to E. coli highlighted that understanding the transmission mechanism is of great importance to delay or arrest the propagation of OXA-232 to other species.

Effect of high-copper diet on transference of blaCTX−M genes among Escherichia coli strains in rats' intestine

Both ceftiofur (CTO) and high copper are widely utilized in animal production in China, and the occurrence of CTX-M-carrying Escherichia coli in food-producing animals is increasing. There are some specific associations between in-feed high-level copper and antibiotic resistance, but research in Gram-negative bacteria such as E. coli remains scarce. This study aimed to evaluate the effect of high-copper diet on the horizontal transfer of blaCTX−M−1 among E. coli. A total of 32 male SPF rats aged 21 days were randomly assigned to the following four groups: control (6 mg/kg in-feed copper, C−), high copper (240 mg/kg in-feed copper, H−), CTO (6 mg/kg in-feed copper with oral CTO administration, C+), and high copper plus CTO (240 mg/kg in-feed copper with oral CTO administration, H+). All rats were orally inoculated with an E. coli strain harboring a conjugative plasmid carrying blaCTX−M−1, and the C+ and H+ groups were given 10 mg/kg of body weight (BW) CTO hydrochloride at 26, 27, and 28 days, while the C− and H− groups were given salad oil at the same dose. Fecal samples collected at different time points were used for the enumeration of E. coli on Mac plates or for molecular analysis using PCR, pulsed-field gel electrophoresis (PFGE), S1-PFGE, and Southern-blot hybridization. The results showed that the number of the blaCTX−M−1 gene in the H− group was higher and that the loss speed of this gene was slower compared with the C− group. After administration of CTO, the counts of cefotaxime-resistant E. coli were significantly higher in the C+ group than that in the corresponding control group (C+ vs. C−; H+ vs. H−). In the in vitro test, the results showed that the transfer rates of the conjugation induced by the H− (12 mmol/L) group were significantly higher than that of low copper (2 mmol/L) group. The indigenous sensitive isolates, which were homologous to the blaCTX−M-positive isolates of rat feces, were found by PFGE. The further analysis of S1-PFGE and Southern-blot hybridization confirmed that the blaCTX−M−1 gene in new transconjugants was derived from the inoculated strain. Taken together, high-copper diet facilitates the horizontal transfer and maintenance of the resistant genes in the intestine of rats, although the effects of antibiotics on bacterial resistance appearance and maintenance are more obvious.

Antimicrobial Resistance Profiles and Molecular Characteristics of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Healthy Cattle and Pigs in Korea

Antimicrobial-resistant bacteria isolated from food animals pose a major health threat to the public on this planet. This study aimed to determine the susceptibility profiles of Escherichia coli isolated from cattle and pig fecal samples and investigate the molecular characteristics of extended-spectrum β-lactamase (ESBL)-producing E. coli using gene identification, conjugation, and Southern blot approach. Overall 293 E. coli were recovered from cattle (120 isolates) and pigs (173 isolates) in 7 provinces of Korea during 2017-2018. Ampicillin, chloramphenicol, streptomycin, and sulfisoxazole resistance rates were the highest in pigs' isolates (>60%, p ≤ 0.001) compared to that in cattle (3-39%). Multidrug resistance (MDR) was higher in pig isolates (73%) than in cattle (31%), and the MDR profile usually includes streptomycin, sulfisoxazole, and tetracycline. Resistance to critically important antimicrobials such as ceftiofur, colistin, and ciprofloxacin was higher in weaners than those from finishers in pigs. The qnrS gene was detected in 13% of the pig isolates. Eight isolates from pigs and one isolate from cattle were identified as ESBL-producers and ESBL genes belonged to bla_CTX-M-55 (n = 4), bla_CTX-M-14 (n = 3), and bla_CTX-M-65 (n = 2). Notably, the bla_CTX-M-65 and qnrS1 genes were found to be carried together in an identical plasmid (IncHI2) in two isolates from finisher pigs. The bla_CTX-M-carrying isolates belonged to phylogenetic groups B1 (n = 4), B2 (n = 2), A (n = 2), and D (n = 1). The bla_CTX-M genes and non-β-lactam resistance traits were transferred to the E. coli J53 recipient from seven bla_CTX-M-positive strains isolated from pigs. The bla_CTX-M genes belonged to the IncI1α, IncFII, and IncHI2 plasmids and are also associated with the ISEcp1, IS26, IS903, and orf477 elements. These findings suggested the possibility of bla_CTX-M-carrying E. coli transmission to humans through direct contact with cattle and pigs or contamination of food products.

Detection and characterization of ESBL-producing Escherichia coli and additional co-existence with mcr genes from river water in northern Thailand

Background

Extended-spectrum β-lactamase producing Escherichia coli (ESBL-producing E. coli) have emerged, causing human and animal infections worldwide. This study was conducted to investigate the prevalence and molecular genetic features of ESBL-producing and multidrug-resistant (MDR) E. coli in river water.

Methods

A total of 172 E. coli samples were collected from the Kok River and Kham River in Chiang Rai, Thailand, during a 10-month period (2020-2021).

Results

We detected 45.3% of E. coli to be MDR. The prevalence of ESBL-producers was 22%. Among those ESBL-producing strains, CTX-M-15 (44.7%) was predominantly found, followed by CTX-M-55 (26.3%), CTX-M-14 (18.4%), and CTX-M-27 (10.5%). The bla _TEM-1 and bla _TEM-116 genes were found to be co-harbored with the bla _CTX-M genes. Mobile elements, i.e., ISEcp1 and Tn3, were observed. Twelve plasmid replicons were found, predominantly being IncF (76.3%) and IncFIB (52.6%). Whole genome sequencing of ten selected isolates revealed the co-existence of ESBL with mcr genes in two ESBL-producing E. coli. A wide diversity of MLST classifications was observed. An mcr-1.1-pap2 gene cassette was found to disrupt the PUF2806 domain-containing gene, while an mcr-3.4 contig on another isolate contained the nimC/nimA-mcr-3.4-dgkA core segment.

Discussion

In conclusion, our data provides compelling evidence of MDR and ESBL-producing E. coli, co-existing with mcr genes in river water in northern Thailand, which may be disseminated into other environments and so cause increased risks to public health.

CTX-M-Producing Bacteria Isolated from a Highly Polluted River System in Portugal

Enterobacteriaceae resistant to third-generation cephalosporins are a great concern for public health, as these are first-line drugs to treat infections. The production of carbapenemases and extended spectrum beta-lactamases (ESBLs) and/or the overexpression of AmpC β-lactamases are the main mechanisms of resistance to these antibiotics. Among the ESBLs, CTX-M β-lactamases are the most prevalent worldwide. Our aims were to determine the prevalence of cefotaxime-resistant Enterobacteriaceae along a heavily polluted river and characterize bla_CTX-M carriers. River water was collected in 11 sites along the main course and tributaries, in two sampling moments. Water quality was evaluated and a collection of cefotaxime-resistant isolates was obtained. bla_CTX-M carriers were characterized regarding phylogenetic affiliation, clonality, antibiotic susceptibility, gene diversity, and context. Water presented very low quality in all sites. From 147 cefotaxime-resistant isolates, 46% carried bla_CTX-M and were affiliated with Escherichia, Klebsiella, Enterobacter, and Citrobacter. Molecular typing revealed clonal isolates in different sites and over the two years, suggesting survival of the strains in the river or continuous pollution inputs from the same sources. Eight variants of bla_CTX-M were found, with bla_CTX-M-15 being the most prevalent (52.5%). Sites with a lower water quality showed the highest resistance rates and prevalence of bla_CTX-M, suggesting that river water may embody human health risks.

Antibiotic Resistance Profiles and Molecular Characteristics of blaCTX-M-15-Carrying Salmonella enterica Serovar Enteritidis Isolates from Healthy and Diseased Chickens in Korea

Extended-spectrum β-lactamase (ESBL)-producing Salmonella enterica serovar Enteritidis has emerged as a public health concern. The main objectives of this study were therefore to determine the antimicrobial susceptibility profiles of Salmonella Enteritidis and to investigate the molecular characteristics of identified ESBL-producing isolates. In the study, 237 Salmonella Enteritidis isolates (232 isolates from chickens, 4 from cattle, and 1 from a pig) were recovered from carcasses and fecal samples of healthy and diseased food animals between 2010 and 2017. Ceftiofur resistance was noted only in chicken isolates (43%, 102/237), with the highest in healthy chickens and their carcasses (48.3%, 83/172) compared with that in diseased chickens (31.7%, 19/60). All of the ceftiofur-resistant isolates exhibited resistance to multiple antimicrobials. Indeed, a relatively higher percentage of ceftiofur-resistant isolates demonstrated resistance to the tested aminoglycosides and tetracycline compared with the ceftiofur-susceptible strains. In this study, bla_CTX-M-15 was the only ESBL gene detected in all of the ceftiofur-resistant isolates. The bla_CTX-M-15-carrying isolates belonged to 11 different pulsotypes. The bla_CTX-M-15 gene was transferred from 20.6% (21/102) of the bla_CTX-M-15-harboring isolates to a recipient Escherichia coli J53. The coexistence of IncHI2/ST2 and IncFIIs/ST1 plasmids was noted in the majority (81.8%, 18/22) of the transconjugants. E. coli J53 transconjugants carrying bla_CTX-M-15 gene showed distinct genetic environments, predominantly ISEcp1-bla_CTX-M-15-orf477 (15/21, 71.4%). This study demonstrated that healthy chickens and their carcasses act as reservoirs of bla_CTX-M-15-carrying Salmonella Enteritidis that can potentially be transmitted to humans.

Rectal and Tracheal Carriage of Carbapenemase Genes and Class 1 and 2 Integrons in Patients in Neurosurgery Intensive Care Unit

The spread of multidrug-resistant Gram-negative bacteria, which is associated with the distribution of beta-lactamase genes and class 1 and 2 integrons, is a global problem. In this study, in the Moscow neurosurgery intensive care unit (neuro-ICU), the high prevalence of the above-stated genes was found to be associated with intestinal and tracheal carriage. Seven-point prevalence surveys, which included 60 patients in the neuro-ICU, were conducted weekly in the period from Oct. to Nov. 2019. A total of 293 clinical samples were analyzed, including 146 rectal and 147 tracheal swabs; 344 Gram-negative bacteria isolates were collected. Beta-lactamase genes (n = 837) were detected in the isolates, including beta-lactamase blaTEM (n = 162), blaSHV (n = 145), cephalosporinase blaCTX-M (n = 228), carbapenemase blaNDM (n = 44), blaKPC (n = 25), blaOXA-48 (n = 126), blaOXA-51-like (n = 54), blaOXA-40-like (n = 43), blaOXA-23-like (n = 8), and blaVIM (n = 2), as well as class 1 (n = 189) and class 2 (n = 12) integrons. One extensively drug-resistant Klebsiella pneumoniae strain (sequence type ST39 and capsular type K23), simultaneously carried beta-lactamase genes, blaSHV-40 and blaTEM-1B, three carbapenemase genes, blaNDM, blaKPC, and blaOXA-48, the cephalosporinase gene blaCTX-M, and two class 1 integrons. Before this study, such heavily armed strains have not been reported, suggesting the ongoing evolution of antibiotic resistance.

Molecular characterization of resistance determinants and mobile genetic elements of ESBL producing multidrug-resistant bacteria from freshwater lakes in Kashmir, India

BACKGROUND

Antibiotic resistance conceded as a global concern is a phenomenon that emerged from the bacterial response to the extensive utilization of antimicrobials. The expansion of resistance determinants through horizontal transfer is linked with mobile genetic elements (MGEs) like transposons, insertion sequences, and integrons. Heavy metals also create consequential health hazards. Metal resistance gene in alliance with antibiotic resistance genes (ARGs) and MGEs is assisting bacteria to attain exalted quantity of resistance.

METHODOLOGY

The present work was carried out to study ARGs blaCTX-M, AmpC, qnrS, MGEs like ISecp1, TN3, TN21, and Int I by performing PCR and sequencing from Wular and Dal lakes of Kashmir; India. The genetic environment analysis of blaCTX-M-15 was carried out using PCR amplification, and sequencing approach followed by in-silico docking and mutational studies. Co-occurrence of ARGs and HMRGs was determined. Plasmid typing was done using PCR-based replicon typing (PBRT) and conjugation assay was also performed.

RESULTS

Out of 201 isolates attained from 16 locations, 33 were ESBLs producers. 30 ESBL displaying isolates were perceived positive for CTX-M gene, followed by AmpC (17), qnrS (13), ISecp1 (15), TN3 (11), TN21 (11), Int I (18), and SulI (14). The genetic environment of blaCTX-M-15 was observed as (ISEcp1-blaCTX-M-15-orf477), classical promoter-10 TACAAT and -35 TTGAA was found at the 3' region. The 3D structure of CTX-M-15 and ISEcp1 was generated and CTX-M-15-ISEcp1 (R299L) docking and mutation showed a reduction in hydrogen bonds. Co-occurrence of antibiotics and HMRGs (mer, sil, and ars) was found in 18, 14, and 8 isolates. PBRT analysis showed the presence of Inc. groups- B/O, F, I1, HI1, FIA, HI2, N, FIB, L/M. Molecular analysis of transconjugants showed the successful transfer of ARGs, MGEs, and HMRGs in the E. coli J53 AZ^R strain.

CONCLUSION

This study highlights the occurrence of ESBL producing bacteria in the aquatic environment of Kashmir India that can serve as a reservoir of ARGs. It also discussed the molecular mechanisms of MGEs which can help in containing the spread of antibiotic resistance.

First Record of Dissemination of BLBLI-Resistant Enterobacter cloacae from Public Hospitals in Baghdad, Iraq

Background:

Enterobacter cloacae are most frequently isolated from human clinical specimens.

Objective:

This cross-sectional study aimed to investigate the dissemination of E. cloacae clinical isolates resistant to β-lactam-β-lactamase inhibitor (BLBLI) combinations from different clinical specimens of hospitalized patients.

Methods:

E. cloacae isolates were recovered from different clinical samples of hospitalized patients in three main hospitals in Baghdad city. E. cloacae isolates were identified based on their morphology and biochemical tests, and the identification was confirmed using Vitek-2 system. The antibiotic susceptibility testing of E. cloacae isolates to a variety of antibiotics was achieved using disc diffusion test (DDT) and Vitek-2 system.

Results:

Results found that among 335 culture-positive samples, 30 isolates (8.9%) belonged to E. cloacae. A high rate of isolation was observed in urine isolates (46.6%), followed by wounds (burns) isolates (26.6%). Out of 30 E. cloacae strains isolated during this study, 18 (60%) showed reduced susceptibility to BLBLI combinations. TEM genes (TEM-1 and TEM-2) were successfully amplified from 7/18 isolates (38.8%) and high rate of BLBLI genes was detected (CTX-M, bla-SHV, SHV-2, and OXA-1). However, no BLBLI genes of bla-AmpC, bla- OXA-2, and bla- OXA-10 were found in E. cloacae isolates when tested using specific primers for bla-AmpC and bla-OXA genes.

Conclusion:

From this study, we can conclude that the production of inhibitor-resistant β-lactamases by E. cloacae isolates could be increasingly common in nosocomial pathogens other than E. coli or K. pneumoniae in public hospitals in Baghdad, Iraq.

Phenotyping and genotyping studies on extended-spectrum β-lactamase-producing Escherichia coli isolates from mastitic cows on dairy farms in Egypt

Background and Aim: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have become a serious public health hazard worldwide. This importance is derived from the increase of new variants, particularly blaTEM, blaSHV, and blaCTX-M genes. This study aimed to examine ESBL-producing Escherichia coli isolated from different governorates in Egypt from dairy cows infected with subclinical and clinical mastitis. Materials and Methods: This study examined 207 milk samples for the resistance of isolates against 14 different antibiotics and ran serological identification of ESBL-producing E. coli isolates with complete antibiotic resistance. Genotypic and sequencing analyses of several resistance genes were conducted using a polymerase chain reaction. Results: E. coli was identified in cases with subclinical mastitis (80.5%) and clinical mastitis (85.7%). ESBL-producing E. coli was isolated from 38.2% of subclinical mastitic milk compared to 39.3% in clinical cases, where O26:k60, O125:k70, and O25:k11 were the serotypes with complete resistance to antibiotics. ESBL-producing E. coli isolates were resistant to cefotaxime, amoxicillin, cloxacillin, oxacillin, rifampicin, and penicillin in 100% but susceptible to amoxicillin and clavulanic acid in 82.5% of the cases. Results also revealed that 51.25%, 52.5%, 66.25%, 77.5% and 60% of ESBL-producing E. coli isolates were responsive to ciprofloxacin, ofloxacin, norfloxacin, levofloxacin, and gentamycin, respectively. The detected genes were registered in GenBank as MW345819.1 and MW345820.1 for the E. coli blaTEM gene and MW295407 for the E. coli blaSHV gene. Conclusion: This study found ESBL-producing E. coli in mastitic milk samples from Egyptian dairy farms and confirmed the occurrence and circulation of the main antibiotic genes (blaTEM and blaSHV) in the samples. Regular and thorough surveillance of ESBL-producing E. coli and subsequent preventive actions are essential for preventing the spread of these resistance genes in the future, which could pose serious and catastrophic health risks. Authorities should cling to the concept of One Health to minimize the risk of new varieties.

Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province

Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.

Similarities in Virulence and Extended Spectrum Beta-Lactamase Gene Profiles among Cefotaxime-Resistant Escherichia coli Wastewater and Clinical Isolates

The World Health Organization has identified antibiotic resistance as one of the largest threats to human health and food security. In this study, we compared antibiotic resistance patterns between ESBL-producing Escherichia coli from human clinical diseases and cefotaxime-resistant environmental strains, as well as their potential to be pathogenic. Antibiotic susceptibility was tested amongst clinical isolates (n = 11), hospital wastewater (n = 22), and urban wastewater (n = 36, both influent and treated effluents). Multi-drug resistance predominated (>70%) among hospitalwastewater and urban wastewater influent isolates. Interestingly, isolates from clinical and urban treated effluents showed similar multi-drug resistance rates (~50%). Most hospital wastewater isolates were Phylogroup A, while clinical isolates were predominately B2, with a more diverse phylogroup population in urban wastewater. ESBL characterization of cefotaxime-resistant populations identified blaCTX-M-1 subgroup as the most common, whereby blaKPC was more associated with ceftazidime and ertapenem resistance. Whole-genome sequencing of a carbapenemase-producing hospital wastewater E. coli strain revealed plasmid-mediated blaKPC-2. Among cefotaxime-resistant populations, over 60% of clinical and 30% of treated effluent E. coli encoded three or more virulence genes exhibiting a pathogenic potential. Together, the similarity among treated effluent E. coli populations and clinical strains suggest effluents could serve as a reservoir for future multi-drug resistant E. coli clinical infections.

Emergence and Genomic Characterization of a KPC-2-, NDM-1-, and IMP-4-Producing Klebsiella michiganensis Isolate

A rectal swab sample was collected from a patient with Guillain–Barré syndrome and enriched in lysogeny broth. Carbapenem-resistant bacteria were selected by China Blue agar plates containing 0.3 μg/ml meropenem. Carbapenemase-producing Klebsiella michiganensis was identified and characterized by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF), immune colloidal gold technique, a conjugation experiment, PCR analysis, and antimicrobial susceptibility testing. The genome of K. michiganensis was determined by whole genome sequencing. Antimicrobial susceptibility testing showed that the K. michiganensis was resistant to imipenem, meropenem, ertapenem, cefmetazole, ceftazidime, cefotaxime, piperacillin/tazobactam, sulbactam/cefoperazone, ceftazidime/avibactam, cefepime, and aztreonam while susceptible to polymyxin B, ciprofloxacin, tigecycline, and amikacin. Immune colloidal gold technique suggested that this strain co-produced three different carbapenemases [Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), and Imipenem (IMP)]. Whole genome sequencing analysis indicated that this strain belonged to ST91, and bla_KPC–2, bla_NDM–1, and bla_IMP–4 were carried on different conjugative plasmids. Besides, the co-existence and transferability of bla_KPC–2, bla_NDM–1, and bla_IMP–4 in K. michiganensis facilitates the potential horizontal dissemination and nosocomial spread of resistance genes among multidrug-resistant organisms.

The emergence of CTX-M-55 in ESBL-producing Escherichia coli from vegetables sold in local markets of northern Thailand

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are spreading worldwide and pose a public health issue. An assessment of their presence in the environment and in food chain products would clarify the pathway of this foodborne transmission. Here, we investigated the prevalence of ESBL-producing E. coli in fresh vegetables purchased from fresh markets in Chiang Rai, Thailand. Overall, 8.8% of the samples collected contained ESBL-producing E. coli, of which 81.3% were multidrug-resistant. All isolates carried the bla_CTX-M-55 gene, and 10 isolates contained the ISEcp1 gene. One E. coli strain carried bla_CTX-M-55 coexisting with bla_TEM-1. Thirteen different sequence types (ST48, ST101, ST155, ST165, ST398, ST414, ST457, ST515, ST542, ST1081, ST3045, ST7538 and ST10651) were identified. One strain belonged to ST101, which is one of the most prevalent STs among human isolates. Our study thus demonstrated the spread of CTX-M-55 on non-ST131 vegetable isolates that are not global pandemic strains and suggests that they may be a source of antibiotic resistance gene transfer from agricultural foods to humans. Further studies are needed to investigate the possibility that these ESBL producers could transfer resistance genes to commensal E. coli and cause severe disease.

Prevalence of β-lactamase-encoding genes and molecular typing of Acinetobacter baumannii isolates carrying carbapenemase OXA-24 in children

Background

β-Lactam antibiotics have been broadly used for the treatment of Acinetobacter baumannii infections, resulting in development of β-lactam inactivating β-lactamases. Here, we described antibiotic resistance rate, prevalence of β-lactamase-encoding genes, and clonal relationships of A. baumannii strains isolated from children referred to Children’s Medical Center in Tehran, Iran, during 2019–2020.

Methods

A total of 60 non-replicate A. baumannii isolates were recovered from clinical specimens of pediatric patients. Antibiotic susceptibility testing was done by the disc diffusion method. Colistin susceptibility of isolates was performed by the broth microdilution method. β-lactamase-encoding genes were characterized by PCR. The presence of ISAba1 element upstream of the several oxacillinase genes was also checked. Genetic relatedness of isolates was determined by using random amplification of polymorphic DNA (RAPD) typing.

Results

The antimicrobial susceptibility tests showed that 83.3% of A. baumannii isolates were MDR, and 40% XDR. Both MDR and XDR A. baumannii isolates were susceptible to colistin. The frequency of bla_OXA-51-like, bla_OXA-23-like, bla_TEM, bla_OXA-24-like, bla_PER, bla_SHV, bla_CTX-M, bla_OXA-58-like, and bla_IMP was 100, 93.33, 60, 36.67, 28.33, 8.33, 5, 3.33, and 1.67%, respectively. Coexistence of ISAba1/bla_OXA-23-like and ISAba1/bla_OXA-51-like was observed in 65% and 85% of isolates, respectively. RAPD analysis revealed 4 common types and 2 single types of A. baumannii isolates.

Conclusions

The multiple clones harboring bla_OXA-23-like, ISAba1-bla_OXA-51-like, and ISAba1-bla_OXA-23-like were responsible for the spread of A. baumannii isolates in our clinical wards. Dissemination of the well-established clones is worrisome and would become therapeutic challenges due to the possible transferring genetic elements associated with resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00480-5.

Analysis of the upstream genetic structures of the ISEcp1-blaCTX-M transposition units in Escherichia coli isolates carrying blaCTX-M obtained from the Indonesian and Vietnamese communities

Extended spectrum β-lactamase (ESBL)-producing Escherichia coli have been found in healthy individuals in Indonesia and Vietnam. The ISEcp1-bla_CTX-M transposition unit of ESBL-producing bacterial isolates has been considered responsible for the production of CTX-M type ESBL and it is important for the dissemination of bla_CTX-M . This study aimed to characterize the upstream genetic structure (UGS) of E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes obtained from healthy individuals in Indonesia and Vietnam. A total of 501 CTX-M type ESBL-producing E. coli isolates possessing bla_CTX-M-1 group and/or bla_CTX-M-9 group genes were obtained from healthy individuals of the two countries in 2018. The UGSs of the ISEcp1-bla_CTX-M transposition unit of the 501 ESBL-producing E. coli isolates were amplified by barcode-adaptor-ligation-mediated PCR and analyzed using the Nanopore sequencer. The obtained sequence information was used to classify the UGSs of the ISEcp1-bla_CTX-M transposition unit. From the 501 ESBL-producing E. coli isolates, 502 UGSs were obtained, which were classified into 85 UGS types based on the sequence. ISEcp1 of 359 (71.5%) of the 502 UGSs was disrupted by gene insertion, and ISEcp1-bla_CTX-M transposition unit of most (87.1%) of the determined UGSs was confirmed as plasmidic. Only 6 (7.1%) of the 85 UGS types were common to both countries. Our results indicated that many different UGSs of ISEcp1-bla_CTX-M transposition units were detected in Indonesia and Vietnam; hence, we suggest that structurally different kinds of plasmids harboring bla_CTX-M were separately distributed in the two countries.

Multidrug-Resistant Klebsiella pneumoniae Causing Severe Infections in the Neuro-ICU

The purpose of this study was the identification of genetic lineages and antimicrobial resistance (AMR) and virulence genes in Klebsiella pneumoniae isolates associated with severe infections in the neuro-ICU. Susceptibility to antimicrobials was determined using the Vitek-2 instrument. AMR and virulence genes, sequence types (STs), and capsular types were identified by PCR. Whole-genome sequencing was conducted on the Illumina MiSeq platform. It was shown that K. pneumoniae isolates of ST14^K2, ST23^K57, ST39^K23, ST76^K23, ST86^K2, ST218^K57, ST219^KL125/114, ST268^K20, and ST2674^K47 caused severe systemic infections, including ST14^K2, ST39^K23, and ST268^K20 that were associated with fatal incomes. Moreover, eight isolates of ST395^K2 and ST307^{KL102/149/155} were associated with manifestations of vasculitis and microcirculation disorders. Another 12 K. pneumoniae isolates of ST395^K2,KL39, ST307^{KL102/149/155}, and ST147^K14/64 were collected from patients without severe systemic infections. Major isolates (n = 38) were XDR and MDR. Beta-lactamase genes were identified: bla_SHV (n = 41), bla_CTX-M (n = 28), bla_TEM (n = 21), bla_OXA-48 (n = 21), bla_NDM (n = 1), and bla_KPC (n = 1). The prevalent virulence genes were wabG (n = 41), fimH (n = 41), allS (n = 41), and uge (n = 34), and rarer, detected only in the genomes of the isolates causing severe systemic infections-rmpA (n = 8), kfu (n = 6), iroN (n = 5), and iroD (n = 5) indicating high potential of the isolates for hypervirulence.

Extended-spectrum β-lactamases: an update on their characteristics, epidemiology and detection

Extended-spectrum β-lactamase (ESBL)-producing Gram-negative pathogens are a major cause of resistance to expanded-spectrum β-lactam antibiotics. Since their discovery in the early 1980s, they have spread worldwide and an are now endemic in Enterobacterales isolated from both hospital-associated and community-acquired infections. As a result, they are a global public health concern. In the past, TEM- and SHV-type ESBLs were the predominant families of ESBLs. Today CTX-M-type enzymes are the most commonly found ESBL type with the CTX-M-15 variant dominating worldwide, followed in prevalence by CTX-M-14, and CTX-M-27 is emerging in certain parts of the world. The genes encoding ESBLs are often found on plasmids and harboured within transposons or insertion sequences, which has enabled their spread. In addition, the population of ESBL-producing Escherichia coli is dominated globally by a highly virulent and successful clone belonging to ST131. Today, there are many diagnostic tools available to the clinical microbiology laboratory and include both phenotypic and genotypic tests to detect β-lactamases. Unfortunately, when ESBLs are not identified in a timely manner, appropriate antimicrobial therapy is frequently delayed, resulting in poor clinical outcomes. Several analyses of clinical trials have shown mixed results with regards to whether a carbapenem must be used to treat serious infections caused by ESBLs or whether some of the older β-lactam-β-lactamase combinations such as piperacillin/tazobactam are appropriate. Some of the newer combinations such as ceftazidime/avibactam have demonstrated efficacy in patients. ESBL-producing Gram-negative pathogens will continue to be major contributor to antimicrobial resistance worldwide. It is essential that we remain vigilant about identifying them both in patient isolates and through surveillance studies.

Molecular characterization of a carbapenem-resistant Enterobacter hormaechei ssp. xiangfangensis co-harbouring blaNDM-1 and a chromosomally encoded phage-linked blaCTX-M-15 genes

Enterobacter cloacae complex (ECC) members are rapidly emerging as successful nosocomial pathogens, especially, with the emergence of carbapenem-resistant clones. In this study, we performed a comprehensive molecular characterization of a carbapenem-resistant E. hormaechei ssp. xiangfangensis LAU_ENC1. hsp60 and average nucleotide identity (ANI) were used for its identification. The repertoire of resistance genes and phage content were analyzed. Plasmid sequences were extracted and compared to closest references. The isolate LAU_ENC1 was identified as an E. hormaechei ssp. xiangfangensis and belonged to ST-114A sub-cluster. bla_NDM-1, bla_CTX-M-15, bla_OXA-1, and bla_ACT-16 genes were detected as β-lactam resistance determinants. A chromosomal hybrid intact phage, Enterobacter phage LAU1, with bla_CTX-M-15 integrated in its direct vicinity within an ISEcp1 - bla_CTX-M-15 - wbuC - ∆Tn2 rare cassette was detected. bla_NDM-1 was integrated within a novel IncFII conjugative plasmid, pLAU_ENC1, through an IS3000- ΔISAba125-bla_NDM-1-ble_MBL-//-Tn5403 cassette. To our knowledge, this is the first report of a multi-drug resistant (MDR) E. hormaechei ssp. xiangfangensis carrying a bla_CTX-M-15 integrated within the proximity of a provirus chromosomal region. Treatment options for MDR ECC members are becoming scarce, thus warranting an increased monitoring of the dissemination of these pathogens in clinical settings.

Genetic Environments of Plasmid-Mediated blaCTXM-15 Beta-Lactamase Gene in Enterobacteriaceae from Africa

The most widely distributed blaCTX-M gene on a global scale is blaCTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the blaCTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of blaCTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of blaCTX-M-15 in Africa. Seven different genetic patterns were seen in the blaCTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the blaCTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of blaCTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with blaCTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the blaCTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the blaCTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the blaCTX-M-15 gene in Africa.

Extended-spectrum β-lactamase blaCTX-M-1 group in gram-negative bacteria colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital in Morogoro, Tanzania

Objective

The objective of this study was to determine the proportion of extended spectrum β-lactamase producing gram-negative bacteria (ESBL-GNB) colonizing patients admitted at Mazimbu hospital and Morogoro Regional hospital, in Morogoro, Tanzania. Rectal colonization with ESBL-GNB increases the risks of developing bacterial infections by extra-intestinal pathogenic ESBL-GNB.

Results

Of the 285 patients investigated, 123 (43.2%) carried ESBL-GNB in their intestines. Five of the 123 ESBL positive patients were colonized with two different bacteria, making a total of 128 ESBL producing isolates. Escherichia coli (n = 95, 74.2%) formed the majority of ESBL isolates. The proportion of CTX-M-1 group genes among ESBL isolates tested was 94.9% (93/98). History of antibiotic use (OR: 1.83, 95% CI: 1.1–3.2, P = 0.03), being on antibiotic treatment (OR: 2.61, 95% CI: 1.5–4.53, P = 0.001), duration of hospital stay (OR: 1.2, 95% CI: 1.1–1.3, P < 0.001) and history of previous admission (OR: 2.24, 95% CI: 1.2–4.1, P = 0.009) independently predicted ESBL-GNB carriage.

High Prevalence of Drug Resistance and Class 1 Integrons in Escherichia coli Isolated From River Yamuna, India: A Serious Public Health Risk

Globally, urban water bodies have emerged as an environmental reservoir of antimicrobial resistance (AMR) genes because resistant bacteria residing here might easily disseminate these traits to other waterborne pathogens. In the present study, we have investigated the AMR phenotypes, prevalent plasmid-mediated AMR genes, and integrons in commensal strains of Escherichia coli, the predominant fecal indicator bacteria isolated from a major urban river of northern India Yamuna. The genetic environment of bla_CTX–M–15 was also investigated. Our results indicated that 57.5% of the E. coli strains were resistant to at least two antibiotic classes and 20% strains were multidrug resistant, i.e., resistant to three or more antibiotic classes. The multiple antibiotic resistance index of about one-third of the E. coli strains was quite high (>0.2), reflecting high contamination of river Yamuna with antibiotics. With regard to plasmid-mediated AMR genes, bla_TEM–1 was present in 95% of the strains, followed by qnrS1 and armA (17% each), bla_CTX–M–15 (15%), strA-strB (12%), and tetA (7%). Contrary to the earlier reports where bla_CTX–M–15 was mostly associated with pathogenic phylogroup B2, our study revealed that the CTX-M-15 type extended-spectrum β-lactamases (ESBLs) were present in the commensal phylogroups A and B1, also. The genetic organization of bla_CTX–M–15 was similar to that reported for E. coli, isolated from other parts of the world; and ISEcp1 was present upstream of bla_CTX–M–15. The integrons of classes 2 and 3 were absent, but class 1 integron gene intI1 was present in 75% of the isolates, denoting its high prevalence in E. coli of river Yamuna. These evidences indicate that due to high prevalence of plasmid-mediated AMR genes and intI1, commensal E. coli can become vehicles for widespread dissemination of AMR in the environment. Thus, regular surveillance and management of urban rivers is necessary to curtail the spread of AMR and associated health risks.

Genomic characteristics of mcr-1 and blaCTX-M-type in a single multidrug-resistant Escherichia coli ST93 from chicken in China

This study was undertaken to discern the transmission characteristics of mcr-1 and bla_CTX-M-type in one multidrug-resistant Escherichia coli LWY24 from chicken in China. The genetic profiles of LWY24 isolate were determined by conjugation, S1-pulsed-field gel electrophoresis, southern blot hybridization, and whole genome sequencing analysis. Meanwhile, co-transfer of plasmids in LWY24 isolate was screened by dual conjugation assays. The LWY24 isolate was identified as ST93, and harbored 3 conjugative plasmids, pLWY24J-3 (bla_CTX-M-55-bearing IncFⅡ), pLWY24J-mcr-1 (mcr-1-carrying IncI2), and pLWY24J-4 (non-resistance-conferring IncI1), and one nonconjugative plasmid pLWY24 (bla_CTX-M-14-containing IncHI2/IncHI2A). Numerous resistance genes, insertion sequences (especially IS26), and transposons were found in the 4 plasmids, suggesting that horizontal transmission have occurred by plasmid mating, homologous recombination, and transpositions. Under the selection pressure of cefotaxime and colistin or cefotaxime alone, the mcr-1-bearing plasmid and the bla_CTX-M-55-harboring plasmid could be co-transferred at a similar frequency, with 8.00 × 10⁻⁴ or 9.00 × 10⁻⁴ transconjugants per donor cell, respectively. The specific shufflon region in mcr-1-encoding plasmid could generate up to 6 diverse PilV structures, which may further accelerate the horizontal transfer of plasmid. In conclusion, the transmission characteristics of mcr-1 and bla_CTX-M-type in LWY24 isolate could due to clonal spread of ST93, selective pressure of cefotaxime, IS26-mediate homologous recombination and transposition, and the specific shufflon region.

Whole-genome analyses of extended-spectrum or AmpC β-lactamase-producing Escherichia coli isolates from companion dogs in Japan

The emergence and global spread of extended-spectrum or AmpC β-lactamase (ESBL/AmpC)-producing Enterobacteriaceae in companion animals have led to the hypothesis that companion animals might be reservoirs for cross-species transmission because of their close contact with humans. However, current knowledge in this field is limited; therefore, the role of companion animals in cross-species transmission remains to be elucidated. Herein, we studied ESBL/AmpC-producing Enterobacteriaceae, Escherichia coli in particular, isolated from extraintestinal sites and feces of companion dogs. Whole-genome sequencing analysis revealed that (i) extraintestinal E. coli isolates were most closely related to those isolated from feces from the same dog, (ii) chromosomal sequences in the ST131/C1-M27 clade isolated from companion dogs were highly similar to those in the ST131/C1-M27 clade of human origin, (iii) certain plasmids, such as IncFII/pMLST F1:A2:B20/bla_CTX-M-27, IncI1/pMLST16/bla_CTX-M-15, or IncI1/bla_CMY-2 from dog-derived E. coli isolates, shared high homology with those from several human-derived Enterobacteriaceae, (iv) chromosomal bla_CTX-M-14 was identified in the ST38 isolate from a companion dog, and (v) eight out of 14 tested ESBL/AmpC-producing E. coli isolates (i.e., ST131, ST68, ST405, and ST998) belonged to the human extraintestinal pathogenic E. coli (ExPEC) group. All of the bla-coding plasmids that were sequenced genome-wide were capable of horizontal transfer. These results suggest that companion dogs can spread ESBL/AmpC-producing ExPEC via their feces. Furthermore, at least some ESBL/AmpC-producing ExPECs and bla-coding plasmids can be transmitted between humans and companion dogs. Thus, companion dogs can act as an important reservoir for ESBL/AmpC-producing E. coli in the community.

Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

BACKGROUND

Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars.

RESULTS

Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility.

CONCLUSIONS

This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors. Video abstract.

Shared Extended-Spectrum β-Lactamase-Producing Salmonella Serovars between Agricultural and Aquatic Environments Revealed through invA Amplicon Sequencing

The presence of antibiotic-resistant Salmonella spp. in the environment is of great public health interest, worldwide. Furthermore, its extended-spectrum β-lactamase (ESBL)-producing strains constitute an emerging global health concern due to their limited treatment options in hospital. Therefore, this study aimed at characterising and tracking nonresistant and ESBL-producing Salmonella spp. from agricultural settings to nearby water sources highlighting their antibiotic resistance genes (ARG) and virulence factor (VF) distribution using a combination of both culture-dependent and independent methods. Furthermore, this study investigated the diversity and shared serovars among sampled matrices using amplicon sequencing of the invasion gene A (invA) of Salmonella spp. The results showed that soil had the highest prevalence of Salmonella spp. (62.5%, 65/104) and ESBL-producing Salmonella (34.6%, 36/104). For typed ARG, the most commonly detected gene was blaOXA with 75% (30/40), followed by blaCTX-M 67.5% (27/40),blaTEM 40% (16/40) and sul1 30% (12/40) gene; blaSHV gene was not detected in isolated ESBL-producing Salmonella spp. For VF, the most detected gene was invA (96.9%, 38/40), followed by spaM (17.5%, 7/40), spiC (40%, 16/40), orfL (32.5%, 13/40), misL 32.5% (13/40) and pipD 32.5 (13/40). For diversity analysis, soil, manure, irrigation water and nearby freshwater revealed 81, 68, 12 and 9 serovars, respectively. Soil, manure, irrigation water and freshwater stream samples shared five serovars, which indicated circulation of ESBL-producing Salmonella spp. within the agricultural environment and nearby water sources. Soil is therefore identified as one of the major reservoirs of ESBL-producing Salmonella spp. It is concluded that agricultural environment contamination may have a direct relationship with the presence of antibiotic-producing Salmonella in freshwater streams.

A hybrid plasmid formed by recombination of a virulence plasmid and a resistance plasmid in Klebsiella pneumoniae

OBJECTIVE

The emergence of multidrug-resistant (MDR) and hypervirulent Klebsiella pneumoniae (hvKP) facilitates simultaneous dissemination of virulence and resistance in a single event, which poses serious threat to public health.

METHODS

This study characterized the multidrug-resistant and moderately virulent ST11 K64 K. pneumoniae strain HB25-1 from a clinical case with microbiological and genomic approaches. Plasmids from strain HB25-1 were subjected to whole plasmid sequencing using both the Illumina NextSeq 500 sequencing platform and Nanopore MinION sequencer platforms. Klebsiella pneumoniae HB25-1 was subjected to a conjugation experiment and Galleria mellonella infection model to evaluate the transmission and virulence potential.

RESULTS

We report the emergence of an ST11, serotype K64 K. pneumoniae isolate, which is resistant to third-generation cephalosporin and exhibited a moderate level of virulence. WGS revealed that this strain harboured a plasmid, pHB25-1, which carried multidrug resistance genes (bla_DHA-1, qnrB4, dfrA12, aadA2, sul1, aac(3)-lld, bla_TEM-1, mph(E)) and virulence-encoding genes (the regulator of mucoid phenotype A gene rmpA2 and the aerobactin gene cluster iutAiucABCD). Genomic analysis indicated that pHB25-1 was formed through co-integration of structural regions located in two different plasmids, enabling it to encode both resistance and virulent phenotypes.

CONCLUSION

Findings in this study provide evidence of active plasmid evolution in K. pneumoniae and suggest that surveillance of multidrug-resistant and hypervirulent K. pneumoniae is urgently needed.

Resistance Profiling and Molecular Characterization of Extended-Spectrum/Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli Isolated from Healthy Broiler Chickens in South Korea

We aimed to identify and characterize extended-spectrum β-lactamase (ESBL)-and/or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli isolated from healthy broiler chickens slaughtered for human consumption in Korea. A total of 332 E. coli isolates were identified from 339 cloacal swabs in 2019. More than 90% of the isolates were resistant to multiple antimicrobials. ESBL/pAmpC-production was noted in 14% (46/332) of the isolates. Six of the CTX-M-β-lactamase-producing isolates were found to co-harbor at least one plasmid-mediated quinolone resistance gene. We observed the co-existence of blaCMY-2 and mcr-1 genes in the same isolate for the first time in Korea. Phylogenetic analysis demonstrated that the majority of blaCMY-2-carrying isolates belonged to subgroup D. Conjugation confirmed the transferability of blaCTX-M and blaCMY-2 genes, as well as non-β-lactam resistance traits from 60.9% (28/46) of the ESBL/pAmpC-producing isolates to a recipient E. coli J53. The ISECP, IS903, and orf477 elements were detected in the upstream or downstream regions. The blaCTX-M and blaCMY-2 genes mainly belonged to the IncI1, IncHI2, and/or IncFII plasmids. Additionally, the majority of ESBL/pAmpC-producing isolates exhibited heterogeneous PFGE profiles. This study showed that healthy chickens act as reservoirs of ESBL/pAmpC-producing E. coli that can potentially be transmitted to humans.

The occurrence of CTX-M-producing E. coli in the broiler parent stock in Korea

A large number of antimicrobials are used for the treatment of bacterial infections, and the emergence of antimicrobial-resistant Escherichia coli (E. coli) in livestock and the transfer of resistant isolates to humans poses a serious potential risk to public health. In particular, broiler parent stock produce thousands of eggs for commercial broiler chickens and can transfer antimicrobial-resistant bacteria and drug-resistance genes to chicks. This study was conducted to investigate the prevalence and characteristics of third-generation cephalosporin-resistant and extended-spectrum β-lactamases (ESBL)-producing E. coli isolated from the broiler parent stock in Korea. Among 51 cefotaxime-resistant E. coli isolates, 45 (88.2%) isolates were identified as multidrug resistant and 21 isolates showed phenotypic and genotypic characteristics of CTX-M-producing E. coli. The CTX-M genes CTX-M-14, CTX-M-15, CTX-M-1, and CTX-M-1 were detected in 10, 7, 3, and 1 isolates, respectively. ISEcp1 or IS26 + ISEcp1 were identified upstream of all CTX-M-type genes, and orf477 and IS903 were detected downstream of 9 and 10 CTX-M-type genes, respectively. Thirteen (61.9%) of the 21 CTX-M-producing E. coli isolates harbored class 1 integrons with 4 different gene cassette arrangements. Among the plasmid replicons, CTX-M-1 was located on I1, F, and FIB; CTX-M-14 on F and FII; CTX-M-15 on FII, FIA, and FIB; and CTX-M-65 on FIB. This is the first study to investigate the presence and distribution of third-generation cephalosporin-resistant and CTX-M-producing E. coli isolated from the broiler parent stock level in Korea, and the results indicate that comprehensive surveillance and persistent monitoring systems in broiler parent stock farms are necessary to prevent the dissemination of resistant isolates.

Urban brown rats (Rattus norvegicus) as possible source of multidrug-resistant Enterobacteriaceae and meticillin-resistant Staphylococcus spp., Vienna, Austria, 2016 and 2017

Background

Brown rats (Rattus norvegicus) are an important wildlife species in cities, where they live in close proximity to humans. However, few studies have investigated their role as reservoir of antimicrobial-resistant bacteria.

Aim

We intended to determine whether urban rats at two highly frequented sites in Vienna, Austria, carry extended-spectrum β-lactamase-producing Enterobacteriaceae, fluoroquinolone-resistant Enterobacteriaceae and meticillin-resistant (MR) Staphylococcus spp. (MRS).

Methods

We surveyed the presence of antimicrobial resistance in 62 urban brown rats captured in 2016 and 2017 in Vienna, Austria. Intestinal and nasopharyngeal samples were cultured on selective media. We characterised the isolates and their antimicrobial properties using microbiological and genetic methods including disk diffusion, microarray analysis, sequencing, and detection and characterisation of plasmids.

Results

Eight multidrug-resistant Escherichia coli and two extensively drug-resistant New Delhi metallo-β-lactamases-1 (NDM-1)-producing Enterobacter xiangfangensis ST114 (En. cloacae complex) were isolated from nine of 62 rats. Nine Enterobacteriaceae isolates harboured the bla_CTX-M gene and one carried a plasmid-encoded ampC gene (bla_CMY-2). Forty-four MRS were isolated from 37 rats; they belonged to seven different staphylococcal species: S. fleurettii, S. sciuri, S. aureus, S. pseudintermedius, S. epidermidis, S. haemolyticus (all mecA-positive) and mecC-positive S. xylosus.

Conclusion

Our findings suggest that brown rats in cities are a potential source of multidrug-resistant bacteria, including carbapenem-resistant En. xiangfangensis ST114. Considering the increasing worldwide urbanisation, rodent control remains an important priority for health in modern cities.

Horizontal Plasmid Transfer among Klebsiella pneumoniae Isolates Is the Key Factor for Dissemination of Extended-Spectrum β-Lactamases among Children in Tanzania

Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.

Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations. We therefore studied the dissemination of the bla_CTX-M-15 extended-spectrum-β-lactamase (ESBL) gene in Klebsiella pneumoniae isolates obtained from stool samples from hospitalized children and healthy controls below 2 years of age in Dar es Salaam, Tanzania, from August 2010 to July 2011. We performed Illumina whole-genome sequencing (WGS) to characterize resistance genes, multilocus sequence type (MLST), plasmid incompatibility group (Inc), and plasmid MLST of 128 isolates of K. pneumoniae with bla_CTX-M-15 recovered from both healthy and hospitalized children. We assessed the phylogenetic relationship using single nucleotide polymorphism (SNP)-based analysis and resolved the sequences of five reference plasmids by Oxford Nanopore technology to investigate plasmid dissemination. The WGS analyses revealed the presence of a bla_CTX-M-15-positive IncFII_K5/IncR plasmid with a highly conserved backbone in 70% (90/128) of the isolates. This plasmid, harboring genes encoding resistance to most β-lactams, aminoglycosides, trimethoprim-sulfamethoxazole, and chloramphenicol, was present in phylogenetically very diverse K. pneumoniae strains (48 different MLSTs) carried by both hospitalized and healthy children. Our data strongly suggest widespread horizontal transfer of this ESBL-carrying plasmid both in hospitals and in the general population.

IMPORTANCE Horizontal spread of plasmids carrying multiple resistance genes is considered an important mechanism behind the global health problem caused by multidrug-resistant bacteria. Nevertheless, knowledge about spread of plasmids in a community is limited. Our detailed molecular analyses of K. pneumoniae isolated from hospitalized and healthy children in Tanzania disclosed an epidemic spread of a resistance plasmid. In this study population, we revealed horizontal plasmid transfer among K. pneumoniae as the key factor for dissemination of ESBLs. Traditional outbreak investigation and surveillance focus on the spread of bacterial clones, and short-read sequencing can result in erroneous plasmid composition. Our approach using long-read sequencing reveals horizontal gene transfer of antimicrobial resistance, and therefore has a potential impact on outbreak investigations and approaches to limit spread of AMR.

Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Fresh Produce and Agricultural Environments in Korea

ABSTRACT

This study was conducted to characterize Escherichia coli strains and evaluate the spread of antimicrobial resistance among these strains from fresh produce and farm environments in Korea. We then conducted phenotypic and genetic studies on antimicrobial-resistant isolates. We determined the genetic epidemiological characteristics of isolates that produced extended-spectrum β-lactamase (ESBL) and confirmed plasmid transfer in isolates that carried blaCTX-M-type genes. E. coli strains were isolated from 8 samples of fresh produce and 152 samples from the farm environment collected from May 2014 to June 2016. Cephalosporin resistance was the most prevalent (61.8%) type of resistance among the isolates. Five ESBL-producing strains with high genetic homology with E. coli of human or livestock origin were identified. Lateral transfer of plasmids harboring blaCTX-M-type genes to transconjugants was successful. Two isolates from Chinese cabbage and from water samples collected from a nearby stream harbored the ISEcp1-blaCTX-M-55-orf477 operon and were confirmed as sequence type 1196 and the same type of plasmid replicon, suggesting that cross-contamination was highly likely. A high-risk clone of sequence type 69 (clonal complex 69) isolates was also recovered from the farm environment. This study provides genetic evidence that antimicrobial resistance factors in E. coli from farm environments originate in the clinic or in livestock, highlighting the fact that good agricultural practices in farming are important to inhibit the spread of antimicrobial resistance to bacteria on fresh produce.

HIGHLIGHTS

Emergence of Five Genetic Lines ST395NDM-1, ST13OXA-48, ST3346OXA-48, ST39CTX-M-14, and Novel ST3551OXA-48 of Multidrug-Resistant Clinical Klebsiella pneumoniae in Russia

Aims: The objective of this study was phenotypic and genotypic characterization of antibacterial-resistant Klebsiella pneumoniae clinical strains isolated in Moscow Transplantology Intensive Care Unit in 2017-2019. Results: Major strains among K. pneumoniae (n = 63) isolated from 30 patients were recognized as extensive drug-resistant (n = 55) pathogens, and remaining strains were recognized as multidrug-resistant (n = 8) pathogens. The beta-lactamase genes bla_{SHV-1,-2a,-11,-27,-67,-187} (n = 63), bla_CTX-M-14,-15 (n = 61), bla_TEM-1 (n = 54), bla_OXA-48 (n = 52), and bla_NDM-1 (n = 2), as well as class 1 integrons (n = 19) carried gene cassette arrays aacA4 (n = 2), dfrA1-orfC (n = 6), aadB-aadA1 (n = 9), dfrA15-aadA1 (n = 3), and dfrA12-orfF-aadA2 (n = 1) were identified in the strains. All strains carried four virulence genes: wabG, fimH, uge, and allS, but two strains had additionally kfu gene. Six known sequence types (STs) of K. pneumoniae ST395 (n = 44), ST377 (n = 3), ST307 (n = 4), ST13 (n = 2), ST39 (n = 2), ST3346 (n = 1), and a novel sequence-type ST3551 (n = 7) were identified. Phylogenetic analysis showed that ST3551 belonged to the cluster of clonal group CG147, and the remaining six STs to the another cluster consisting of four subgroups. The emergence of K. pneumoniae genetic lines carrying epidemiologically significant beta-lactamase genes ST395^NDM-1, ST13^OXA-48, ST3346^{OXA-48/CTX-M-14}, ST3551^OXA-48, and ST39^CTX-M-14 was the first case of detection in Russia. Conclusion: The emergence of novel carbapenemase-producing K. pneumoniae genetic lines in Russia highlights the global negative tendency of multidrug-resistant pathogens spread in high-technological medical centers.

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.

The Occurrence of blaCTX-M-15 extended-spectrum β-lactamase Among Clinical Isolates of Klebsiella pneumoniae in Khorramabad, Iran

OBJECTIVE

During the recent decade, CTX-M-type enzymes, primarily CTX-M-15 extended- spectrum β-lactamase (ESBL) have strikingly developed throughout the world. The objective of this study was to investigate the frequency of CTX-M-type β-lactamases, as well as blaCTXM- 15 among Klebsiella pneumoniae isolates in Khorramabad, Iran.

METHODS

In this cross-sectional study, 60 isolates of K. pneumoniae were collected from selected teaching hospitals in Khorramabad, Iran. ESBLs producing isolates were identified using phenotypic double-disk synergy test. The presence of bla_CTX-M-types, as well as bla_CTX-M-15 gene, were investigated by PCR method.

RESULTS

While the highest resistance rates of isolates were found to nalidixic acid (65%) and trimethoprim/sulfamethoxazole (60%) antibiotics, the least resistance was to imipenem (15%). Moreover, 31(51.7%) isolates were resistant to at least three classes of antibiotics and designated as multidrug resistance (MDR). Fifty-two (86.7%) of 60 isolates were ESBLs positive. Thirty-five (58.3%) isolates harbored CTX-M-type β-lactamases, and also 29 (48.3%) isolates carried blaCTX-M-15.

CONCLUSIONS

This study presents the first report on the frequency of bla_CTX-M-15 in the west of Iran, so that our results showed ESBL of CTX-M-15 may partly account for hydrolyzing thirdgeneration cephalosporins.

First Report of KPC-2 and KPC-3-Producing Enterobacteriaceae in Wild Birds in Africa

The increased incidence of antibiotic-resistant Enterobacteriaceae is a public health problem worldwide. The aim of this study was to analyze the potential role of wild birds, given their capacity of migrating over long distances, in the spreading of carbapenemase, extended-spectrum β-lactamase (ESBL), and acquired-AmpC beta-lactamase-producing Enterobacteriaceae in the environment. Fecal and pellet samples were recovered from 150 wild birds in seven Tunisian regions and were inoculated in MacConkey-agar plates for Enterobacteriaceae recovery (one isolate/animal). Ninety-nine isolates were obtained and acquired resistance mechanisms were characterized in the five detected imipenem-resistant and/or cefotaxime-resistant isolates, by PCR and sequencing. The following ESBL, carbapenemase, and acquired-AmpC beta-lactamase genes were detected: bla_CTX-M-15 (two Escherichia fergusonii and one Klebsiella oxytoca isolates), bla_KPC-2 (one K. oxytoca), bla_KPC-3 (one E. fergusonii), bla_ACT-36, and bla_ACC-2 (two K. oxytoca, four E. fergusonii, and two E. coli). The IncFIIs, IncF, IncFIB, IncK, IncP, and IncX replicons were detected among these beta-lactamase Enterobacteriaceae producers. The bla_KPC-2, tetA, sul3, qnrB, and cmlA determinants were co-transferred by conjugation from K. oxytoca strain to E. coli J153, in association with IncK and IncF replicons. Our results support the implication of wild birds as a biological vector for carbapenemase, ESBL, and acquired-AmpC-producing Enterobacteriaceae.

Molecular characteristics of carbapenem-resistant Acinetobacter spp. from clinical infection samples and fecal survey samples in Southern China

Background

Carbapenem resistance among Acinetobacter species has become a life-threatening problem. As a last resort in the treatment of gram-negative bacteria infection, resistance to colistin is also a serious problem. The aim of study was to analyze the mechanism of resistance and perform genotyping of carbapenem-resistant Acinetobacter from clinical infection and fecal survey samples in Southern China.

Methods

One hundred seventy and 74 carbapenem-resistant Acinetobacter were isolated from clinical infection samples and fecal survey samples, respectively. We detected the related genes, including carbapenemase genes (bla_KPC, bla_IMP, bla_SPM, bla_VIM, bla_NDM, bla_OXA-23-like, bla_{OXA-24/40-like}, bla_OXA-51-like, and bla_OXA-58-like), colistin resistance-related genes (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5), a porin gene (carO), efflux pump genes (adeA, adeB, adeC, adeI, adeJ, and adeK), mobile genetic element genes (intI1, intI2, intI3, tnpU, tnp513, IS26, ISAba1, and ISAba125), and the integron variable region. Genotyping was analyzed by enterobacterial repetitive intergenic consensus (ERIC)-PCR and dendrogram cluster analysis.

Results

Among the 244 carbapenem-resistant Acinetobacter, the common carbapenemase-positive genes included the following: bla_OXA-51-like, 183 (75.00%); bla_OXA-23-like, 174 (71.30%); bla_NDM-1, 57 (23.40%); and bla_OXA-58-like, 30 (12.30%). The coexistence of mcr-1 and bla_NDM-1 in five strains of A. junii was found for the first time. Eleven distinct carO gene variants were detected in 164 (67.20%) strains, and ten novel variants, which shared 92–99% identity with sequences in the Genbank database, were first reported. Efflux system genes were present in approximately 70% of the isolates; adeABC and adeIJK were observed in 76.23 and 72.13%, respectively. Class 1 integrons were detected in 180 (73.80%) strains and revealed that four gene cassette arrays contained 11 distinct genes. The genotyping by ERIC-PCR demonstrated a high genetic diversity of non-baumannii Acinetobacter, and greater than 90% similarity to A. baumannii.

Conclusions

The bla_NDM-1 gene was identified in up to 77% of the carbapenem-resistant Acinetobacter isolated from fecal survey samples, indicating that the gut might be a reservoir of resistant opportunistic bacteria. Intestinal bacteria can be transmitted through the fecal-hand, which is a clinical threat, thus, the monitoring of carbapenem-resistant bacteria from inpatients’ feces should be improved, especially for patients who have been using antibiotics for a long time.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4423-3) contains supplementary material, which is available to authorized users.

Plasmid and chromosomal integration of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp

Objectives

To provide detailed genetic characterization of four novel blaIMP-carrying transposons from Pseudomonas aeruginosa, Klebsiella pneumoniae and an Enterobacter sp.

Methods

P. aeruginosa 60512, K. pneumoniae 447, P. aeruginosa 12939 and Enterobacter sp. A1137 were subjected to genome sequencing. The complete nucleotide sequences of two plasmids (p60512-IMP from the 60512 isolate and p447-IMP from the 447 isolate) and two chromosomes (the 12939 and A1137 isolates) were determined, then a genomic comparison of p60512-IMP, p447-IMP and four novel blaIMP-carrying transposons (Tn6394, Tn6375, Tn6411 and Tn6397) with related sequences was performed. Transferability of the blaIMP gene and bacterial antimicrobial susceptibility were tested.

Results

Tn6394 and Tn6375 were located in p60512-IMP and p447-IMP, respectively, while Tn6411 and Tn6397 were integrated into the 12939 and A1137 chromosomes, respectively. Tn6394 was an ISPa17-based transposition unit that harboured the integron In992 (carrying blaIMP-1). In73 (carrying blaIMP-8), In73 and In992, together with the ISEcp1:IS1R-blaCTX-M-14-IS903D unit, the macAB-tolC region and the truncated aacC2-tmrB region, respectively, were integrated into the prototype transposons Tn1722, Tn1696 and Tn7, respectively, generating the Tn3-family unit transposons, Tn6375 and Tn6378, and the Tn7-family unit transposon Tn6411, respectively. Tn6397 was a large integrative and conjugative element carrying Tn6378.

Conclusions

Complex events of transposition and homologous recombination have occurred during the original formation and further plasmid and chromosomal integration of these four transposons, promoting accumulation and spread of antimicrobial resistance genes.