First Report of a Foodborne Salmonella enterica Serovar Gloucester (4:i:l,w) ST34 Strain Harboring bla CTX-M- 55 and qnrS Genes Located in IS26-Mediated Composite Transposon

Dissemination of Ceftriaxone-Resistant Salmonella Enteritidis Harboring Plasmids Encoding blaCTX-M-55 or blaCTX-M-14 Gene in China

Salmonella Enteritidis was the primary foodborne pathogen responsible for acute gastroenteritis. The growing ceftriaxone resistance poses a significant threat to public health. Infection with S. Enteritidis has emerged as a major public health concern, particularly in developing countries. However, research on ceftriaxone-resistant S. Enteritidis (CRO-RSE) remains limited, particularly concerning its resistance mechanism, plasmid structure, and transmission characteristics. This study aims to address these gaps comprehensively. We collected 235 S. Enteritidis isolates from Hangzhou First People's Hospital between 2010 and 2020. Among these, 8.51% (20/235) exhibited resistance to ceftriaxone. Whole-genome analysis revealed that 20 CRO-RSE isolates harbored blaCTX-M-55 or blaCTX-M-14 on the plasmid. Moreover, the dissemination of the blaCTX-M-type gene was associated with IS26 and ISEcp1. Plasmid fusion entailing the integration of the p1 plasmid with antibiotic resistance genes and the p2 (pSEV) virulence plasmid was observed in certain CRO-RSE. Additionally, the structural analysis of the plasmids unveiled two types carrying the blaCTX-M-type gene: type A with multiple replicons and type B with IncI1 (Alpha) replicon. Type B plasmids exhibited superior adaptability and stability compared to type A plasmids within Enterobacteriaceae. Interestingly, although the type B (S808-p1) plasmid displayed the potential to spread to Acinetobacter baumannii, it failed to maintain stability in this species.

Molecular characterization of IncFII plasmid carrying blaNDM-5 in a Salmonella enterica serovar Typhimurium ST34 clinical isolate in China

IMPORTANCE

In this study, an IncFII plasmid pIncFII-NDM5 carrying blaNDM-5 was found in carbapenem-resistant Salmonella enterica serovar Typhimurium (S. enterica serovar Typhimurium), which has conjugative transferability and carried blaNDM-5, bleMBL, mph(A), and blaTEM-1 four resistance genes that can mediate resistance to multiple antibiotics including cephalosporins, beta-lactamase inhibitor combinations, carbapenems, and macrolides. Phylogenetic analysis showed that 1104-65 and 1104-75 were closely related to other S. enterica serovar Typhimurium in this area. The above-mentioned S. enterica serovar Typhimurium chromosome carries blaCTX-M-55, qnrS1, and tet(A) genes, so the antibiotic resistance of isolates will be further enhanced after obtaining the pIncFII_NDM5-like plasmid. Meanwhile, we discovered a novel genetic structure of blaNDM-5 mediated by the IS26 composite transposon, which will expand our understanding of the emergence and spread of carbapenem-resistance genes. Altogether, the presence of the IncFII plasmid pIncFII-NDM5 further underscores the need for vigilant surveillance and appropriate infection control measures to mitigate the impact of carbapenem-resistant S. enterica serovar Typhimurium in clinical settings.

Multidrug-Resistant Escherichia coli Isolate of Chinese Bovine Origin Carrying the blaCTX-M-55 Gene Located in IS26-Mediated Composite Translocatable Units

Elevated detection rates of the blaCTX-M-55 gene in animals have been reported as a result of antibiotic misuse in clinics. To investigate the horizontal transfer mechanism of blaCTX-M-55 and its associated mobile genetic elements (MGEs), we isolated 318 nonrepetitive strains of Escherichia coli (E. coli) from bovine samples in Xinjiang and Gansu provinces, China. All E. coli strains were screened for the CTX-M-55 gene using PCR. The complete genomic data were sequenced using the PacBio triplet sequencing platform and corrected using the Illumina data platform. The genetic environment of the plasmids carrying the resistance blaCTX-M-55 gene was mapped using the software Easyfig2.2.3 for comparison. The results showed that all blaCTX-M-55-positive strains were resistant to multiple antibiotics. Five strains of Escherichia coli carry the blaCTX-M-55 gene, which is adjacent to other resistance genes and is located on the IncHI2-type plasmid. Four of the five blaCTX-M-55-harbor strains carried translocatable units (TUs). All the donor bacteria carrying the blaCTX-M-55 genes could transfer horizontally to the recipient (E. coli J53 Azr). This study demonstrates that the transmission of blaCTX-M-55 is localized on IS26-flanked composite transposons. The cotransmission and prevalence of blaCTX-M-55 with other MDR resistance genes on epidemic plasmids require enhanced monitoring and control.

Plugging the leaks: antibiotic resistance at human-animal interfaces in low-resource settings

Antibiotic resistance is one of the greatest public health challenges of our time. International efforts to curb resistance have largely focused on drug development and limiting unnecessary antibiotic use. However, in areas where water, sanitation, and hygiene infrastructure is lacking, we propose that bacterial flow between humans and animals can exacerbate the emergence and spread of resistant pathogens. Here, we describe the consequences of poor environmental controls by comparing mobile resistance elements among Escherichia coli recovered from humans and meat in Cambodia, a middle-income country with substantial human-animal connectivity and unregulated antibiotic use. We identified identical mobile resistance elements and a conserved transposon region that were widely dispersed in both humans and animals, a phenomenon rarely observed in high-income settings. Our findings indicate that plugging leaks at human-animal interfaces should be a critical part of addressing antibiotic resistance in low- and especially middle-income countries.

Prevalence and molecular characterization of cefotaxime-resistant Salmonella strains recovered from retail meat samples in Shenzhen, China, during 2014-2017

In this work, we collected foodborne Salmonella strains in Shenzhen, China, during 2014-2017 and investigated the genetic profile of all cefotaxime-resistant isolates in the collection. The strains were subjected to antimicrobial susceptibility tests, whole-genome sequencing, bioinformatics analysis, and conjugation studies. A total of 79 cefotaxime-resistant Salmonella were identified and found to exhibit multidrug resistance. Resistance rate recorded during the study period increased from 1.9% to 9.1%. Salmonella Typhimurium was the predominant serovar, and CTX-M family genes were dominant among the ESBLs genes detected. Notably, CTX-M-bearing plasmids or transposons often contain other drug resistance genes. Furthermore, a combination of CTX-M-55 and CTX-M-65 genes was detected for the first time in foodborne Salmonella strains. Our findings reveal the prevalence and molecular characteristics of cefotaxime-resistant foodborne Salmonella strains in southern China. IMPORTANCE Cefotaxime-resistant Salmonella strains pose an increasing threat to human health by causing infections with limited treatment options. It is therefore necessary to undertake a surveillance on the prevalence of such strains and investigate the resistance and transmission mechanisms. In this work, various ESBL genes flanked by different IS located in different mobile genetic elements were detectable among cefotaxime-resistant Salmonella strains. These data show that the high prevalence and genotypic diversity of cefotaxime-resistant foodborne Salmonella strains in China are possibly attributed to the evolution and transmission of a wide range of multidrug resistance-encoding mobile genetic elements.

Isolation and characterization of multidrug resistant Gallibacterium anatis biovar haemolytica strains from Polish geese and hens

Gallibacterium anatis biovar haemolytica is a bacterium that is frequently associated with infections of the reproductive tract and respiratory system in poultry. To assess the current prevalence and resistance profile of these bacteria in Poland, we collected and investigated 63 strains of Gallibacterium from diseased domestic poultry flocks including geese, laying hens, breeding hens and an ornamental hen. Detailed characterization of the isolates included the analysis of phenotypic antimicrobial resistance profiles and biofilm formation ability. Furthermore, the genetic background of 40 selected isolates regarding the presence of virulence and antimicrobial resistance genes and mobile genetic elements was determined. All investigated isolates were multidrug resistant, most prominently to β-lactams, fluoroquinolones, sulfonamides and macrolides. A total of 48 different resistance profiles were detected. Of all isolates, 50.8% formed a strong biofilm, where strains isolated from geese appeared to be better at biofilm formation than strains isolated from laying and breeding hens. Single-nucleotide polymorphism genotyping revealed that G. anatis bv. haemolytica strains are restricted in host and geographical distribution, and the geese isolates showed greater phylogenetic similarity. Whole genome sequencing enabled identification of 25 different antimicrobial resistance determinants. The most common resistance genes were tetB, blaROB-1, and blaTEM-1 which may be located on mobile genetic elements. All isolates possessed the toxin gene gtxA, and the fimbrial gene flfA was identified in 95% of strains. Our results indicated that all G. anatis bv. haemolytica isolates showed multidrug resistant phenotypes. Strains isolated from geese were characterized by the highest percentage of isolates resistant to selected antimicrobials, probably reflecting host-related adaptations.

Genetic context of blaCTX–M–55 and qnrS1 genes in a foodborne Salmonella enterica serotype Saintpaul isolate from China

Salmonella enterica resistant to fluoroquinolones (FQs) and extended-spectrum cephalosporins (ESCs) has been deemed a high-priority pathogen by the WHO. Salmonella enterica serovar Saintpaul (S. Saintpaul) co-resistant to ESCs and FQs and harboring corresponding resistance genes (bla_CTX–M–55 and qnrS1) have been previously reported. However, they have not been reported in China. Moreover, the genetic context and transferability of ESCs and FQs resistance genes in S. Saintpaul remain obscure. This study is the first study to characterize a multidrug-resistant (MDR) S. Saintpaul isolate (16Sal016) harboring plasmid-mediated bla_CTX–M–55 and qnrS1 genes recovered from weever fish in China. The whole genome short- and long-read sequencing results identified the presence of 15 acquired antibiotic resistance genes encoding resistance to nine classes of antibiotics, as well as abundant mobile genetic elements residing on a 259,529 bp IncHI2 plasmid. The bla_CTX–M–55 and qnrS1 genes were located in a 12,865 bp region, IS26-orf-orf-ISKpn19-qnrS1-IS3-Tn3-orf-bla_CTX–M–55-ISEc9-orf-IS26. Similar structures have been identified in various bacterial species, indicating a high transferability of bla_CTX–M–55 and qnrS1 genes within this gene cluster. The plasmid was found to be transferable to Escherichia coli (E. coli) J53 by conjugation and resulted in the acquisition of multiple resistances by the transconjugants. Genome sequence comparisons by core genome multilocus sequence typing (cgMLST) based on global 2,947 S. Saintpaul isolates indicated that strain 16Sal016 was epidemiologically linked with an isolate from the United Kingdom (UK). Our findings suggest that plasmids and IS26-mediated mobile genetic elements are carriers of bla_CTX–M–55 and qnrS1 genes in S. Saintpaul, and highlight their potential transmission, which needs continuous investigations.

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

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

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

Escherichia coli sequence type 131 (ST131) is known for its contribution to multidrug resistance and the worldwide spread of this clone has become a global problem. Understanding the trends among ST131 clades will help design strategies to prevent its rapid dissemination. In this study, 72 ST131 strains were subjected to comparative genomic analysis and 64 clade C strains were compared with clade C strains reported from other regions using publicly available whole-genome sequencing data. C1 (n = 31 [48.4%]) and C2 (n = 33 [%51.5]) strains had the same prevalence in our collection, and C1-M27 (n = 22) strains were closely related, carried a unique plasmid type (F1:A2:B20), and exhibited virotype C. Removal of 11 C2 strains with varied virotype patterns and the heterogeneous IncF type identified 22 closely related virotype E/F strains with replicon type F31/F36:A4:B1, forming what we denote as the “C2-subset.” In a global context, the C2-subset constituted a distinct cluster with international virotype E strains and harbored a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements, mostly IS682/ISKpn37 combination within GI-pheU was identified. The C2-subset accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In addition, a conserved chromosomal IS26-mediated composite transposon (IS15DIV-ISEcp1-bla_CTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed in the C2-subset. The local spread of the C2-subset in the hospital studied, with the carriage of higher virulence/resistance markers and a peculiar F-type plasmid, demonstrates the potential for diversification of the ST131 lineage and the emergence of subpopulations with higher survival potential to cause health care-associated outbreaks.

IMPORTANCEEscherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology. This study systematically compared the Iranian ST131 population to those reported from other countries and found a subpopulation harboring virotype E, a homogeneous profile of plasmid Inc-F type F31/F36:A4:B1 harboring cnf1/hemolysin genes on the genomic island GI-pheU, and up to seven mobile genetic elements (MGEs) flanking cnf1/hemolysin virulence markers. The results of this study highlight the importance of MGEs for virulence gene acquisition and the formation of new subpopulations among pandemic clones such as E. coli ST131.

Comparative Genomic Analysis of Extended-spectrum β-lactamase and mcr-1 Positive Escherichia coli from Gut Microbiota of Healthy Singaporeans

Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of bla_CTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. Importance The human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, we found that MDR E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.