BacWGSTdb, a database for genotyping and source tracking bacterial pathogens

Global Emergence and Genomic Epidemiology of blaNDM-Carrying Klebsiella variicola

Purpose

Klebsiella variicola has emerged as a human pathogen in the past decade. Here, we present findings related to a K. variicola strain carrying the blaNDM-1 gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of blaNDM-carrying K. variicola were further investigated.

Material and Methods

The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 and Nanopore MinION sequencer. Genomic features and resistance mechanisms were analyzed through diverse bioinformatics approaches. Additionally, genome sequences of K. variicola strains carrying blaNDM were retrieved from the NCBI database, and a comprehensive analysis of the global dissemination trends of these strains was conducted.

Results

K. variicola strain 353 demonstrated resistance to multiple antimicrobials, including carbapenems. Within its genome, we identified fourteen antimicrobial resistance genes associated with β-lactam, aminoglycoside, fosfomycin, quinolone, trimethoprim, rifamycin, and sulfonamide resistance. The carbapenem-resistant gene blaNDM-1 was located on an IncU-type plasmid spanning 294,608 bp and flanked by ISCR1 and IS26. Downstream of blaNDM-1, we identified an Intl1 element housing numerous antibiotic resistance genes. A comprehensive search of the NCBI database revealed 72 K. variicola strains carrying blaNDM from twelve different countries, predominantly from clinical sources, with the highest prevalence observed in the USA and China. A total of 28 distinct sequence types (STs) were identified, with ST115 being the most prevalent, followed by ST60.

Conclusion

In summary, this study presents the genomic characterization of a K. variicola strain carrying blaNDM-1 on an IncU-type plasmid. The research highlights the global dissemination of blaNDM-carrying K. variicola, observed in both healthcare settings and natural environments. Our data have revealed a diverse array of antimicrobial resistance determinants in K. variicola, providing valuable insights that could aid in the development of strategies for the prevention, diagnosis, and treatment of K. variicola infections.

First detection and characterization of mcr-1 colistin resistant E. coli from wild rat in Bangladesh

Colistin resistance is a global concern warning for a one health approach to combat the challenge. Colistin resistant E. coli and their resistance determinants are widely distributed in the environment, and rats could be a potential source of these isolates and resistant determinants to a diverse environmental setting. This study was aimed to determine the presence of colistin resistant E. coli (CREC) in wild rats, their antimicrobial resistance (AMR) phenotypes, and genotypic analysis of mcr-1 CREC through whole genome sequencing (WGS). A total of 39 rats were examined and CREC was isolated from their fecal pellets onto MacConkey agar containing colistin sulfate (1 μg/ mL). AMR of the CREC was determined by disc diffusion and broth microdilution was employed to determine MIC to colistin sulfate. CREC were screened for mcr genes (mcr-1 to mcr-8) and phylogenetic grouping by PCR. Finally, WGS of one mcr-1 CREC was performed to explore its genetic characteristics especially resistomes and virulence determinants. 43.59% of the rats carried CREC with one (2.56%) of them carrying CREC with mcr-1 gene among the mcr genes examined. Examination of seventeen (17) isolates from the CREC positive rats (n = 17) revealed that majority of them belonging to the pathogenic phylogroup D (52.94%) and B2 (11.76%). 58.82% of the CREC were MDR on disc diffusion test. Shockingly, the mcr-1 CREC showed phenotypic resistance to 16 antimicrobials of 8 different classes and carried the ARGs in its genome. The mcr-1 gene was located on a 60 kb IncI2 plasmid. On the other hand, ARGs related to aminoglycosides, phenicols, sulfonamides, tetracyclines and trimethoprims were located on a 288 kb mega-plasmid separately. The mcr-1 CREC carried 58 virulence genes including genes related to adhesion, colonization, biofilm formation, hemolysis and immune-evasion. The isolate belonged to ST224 and closely related to E. coli from different sources including UPEC clinical isolates from human based on cgMLST analysis. The current research indicates that rats might be a possible source of CREC, and the presence of mcr-1 and other ARGs on plasmid increases the risk of ARGs spreading and endangering human health and other environmental components through this infamous pest.

A bioinformatic approach to identify confirmed and probable CRISPR-Cas systems in the Acinetobacter calcoaceticus-Acinetobacter baumannii complex genomes

Introduction

The Acinetobacter calcoaceticus-Acinetobacter baumannii complex, or Acb complex, consists of six species: Acinetobacter baumannii, Acinetobacter calcoaceticus, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii, and Acinetobacter lactucae. A. baumannii is the most clinically significant of these species and is frequently related to healthcare-associated infections (HCAIs). Clustered regularly interspaced short palindromic repeat (CRISPR) arrays and associated genes (cas) constitute bacterial adaptive immune systems and function as variable genetic elements. This study aimed to conduct a genomic analysis of Acb complex genomes available in databases to describe and characterize CRISPR systems and cas genes.

Methods

Acb complex genomes available in the NCBI and BV-BRC databases, the identification and characterization of CRISPR-Cas systems were performed using CRISPRCasFinder, CRISPRminer, and CRISPRDetect. Sequence types (STs) were determined using the Oxford scheme and ribosomal multilocus sequence typing (rMLST). Prophages were identified using PHASTER and Prophage Hunter.

Results

A total of 293 genomes representing six Acb species exhibited CRISPR-related sequences. These genomes originate from various sources, including clinical specimens, animals, medical devices, and environmental samples. Sequence typing identified 145 ribosomal multilocus sequence types (rSTs). CRISPR-Cas systems were confirmed in 26.3% of the genomes, classified as subtypes I-Fa, I-Fb and I-Fv. Probable CRISPR arrays and cas genes associated with CRISPR-Cas subtypes III-A, I-B, and III-B were also detected. Some of the CRISPR-Cas systems are associated with genomic regions related to Cap4 proteins, and toxin-antitoxin systems. Moreover, prophage sequences were prevalent in 68.9% of the genomes. Analysis revealed a connection between these prophages and CRISPR-Cas systems, indicating an ongoing arms race between the bacteria and their bacteriophages. Furthermore, proteins associated with anti-CRISPR systems, such as AcrF11 and AcrF7, were identified in the A. baumannii and A. pittii genomes.

Discussion

This study elucidates CRISPR-Cas systems and defense mechanisms within the Acb complex, highlighting their diverse distribution and interactions with prophages and other genetic elements. This study also provides valuable insights into the evolution and adaptation of these microorganisms in various environments and clinical settings.

Genomic Characterization of a Carbapenem-Resistant Raoultella planticola Strain Co-Harboring blaIMP-4 and blaSHV-12 Genes

Raoultella planticola is an emerging bacterial pathogen responsible for causing infections in both humans and animals. Unfortunately, sporadic reports of carbapenem-resistant R. planticola (CRRP) have been documented worldwide. Here we first reported the complete genome sequence of a CRRP isolate RP_3045 co-carrying blaIMP-4 and blaSHV-12, recovered from a patient in China, and its genetic relatedness to 82 R. planticola strains deposited in the NCBI GenBank database, sourced from humans, animals, and the environment. Whole-genome sequencing was performed using the Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms. Phylogenetic analysis was also performed and visualized using a single nucleotide polymorphism (SNP)-based strategy. The complete genome of R. planticola strain RP_3045 was determined to be 6,312,961 bp in length, comprising five contigs that included one chromosome and four plasmids. RP_3045 was found to be multidrug-resistant and harbored several antimicrobial resistance genes, including both blaIMP-4 and blaSHV-12 genes located on a single plasmid. The most closely related strain was hkcpe63, recovered from humans in Hong Kong, China, in 2014, with 506 SNP differences. R. planticola strains were distributed globally and exhibited strong associations among isolates obtained from different sectors. This study provides evidence for the potential of R. planticola to disseminate carbapenem resistance across different sectors, highlighting the critical need for active and continuous surveillance of CRRP.

Genomic insights into a blaNDM-5-carrying Escherichia coli ST167 isolate recovered from faecal sample of a healthy individual in China

OBJECTIVES

Since its discovery, blaNDM-5 has spread widely amongst Escherichia coli strains in clinical patients, causing carbapenem resistance. Here we report the complete genome sequence of an NDM-5-producing E. coli strain isolated from the faecal sample of a healthy individual in Hangzhou, China.

METHODS

The whole-genome sequence of E. coli CREC8 was obtained utilising both the Nanopore sequencer and the Illumina NovaSeq 6000 platform. Antimicrobial resistance genes, multilocus sequence typing, and plasmid replicons were identified using the BacWGSTdb server. The phylogenetic relationship between CREC8 and other E. coli strains was investigated using the core genome multilocus sequence typing (cgMLST) strategy.

RESULTS

The complete genome sequence of E. coli CREC8 consists of one chromosome and 7 plasmids. CREC8 belongs to ST167 according to the MLST scheme. Seven ARGs were identified, including carbapenem resistance gene blaNDM-5 which was located in an IncFIA/IncFII type plasmid. A total of 164 E. coli ST167 strains related to 25 countries across four continents can be retrieved from the NCBI database, 95 of them carrying the blaNDM gene with blaNDM-5 the most (N = 79). Phylogenetic analysis revealed a worldwide distribution of E. coli ST167 strains, with China having the highest prevalence (37%, 61/165).

CONCLUSION

In summary, we reported a blaNDM-5-carrying E. coli ST167 strain isolated from a healthy individual in China. Such strains are more commonly isolated from hospitalised patients but are rarely isolated from healthy individuals. This indicates a further epidemic of carbapenem-resistant E. coli strains in the healthy population which needs our attention.

Genomic characterization of a carbapenem-resistant Citrobacter freundii clinical isolate from China carrying blaNDM-5 on a novel IncC-IncFIB-IncX3 plasmid

OBJECTIVES

Citrobacter freundii is one of the important pathogens that can cause nosocomial infections. The advent of carbapenem-resistant C. freundii complicates clinical treatment. Here, we reported the genome sequence of a carbapenem-resistant C. freundii strain carrying a novel IncC-IncFIB-IncX3 plasmid in China.

METHODS

The genome sequence of C. freundii CRNMS1 was obtained using the Illumina NovaSeq 6000 platform and the long-read Nanopore sequencer. Multilocus sequence typing was identified using MLST (v.2.23.0). The identification of antimicrobial resistance genes (ARGs) and plasmid replicons was performed using the resfinder and plasmidfinder of ABRicate (v.1.0.1). Circular comparisons of plasmids were performed using the BLAST Ring Image Generator (BRIG).

RESULTS

CRNMS1 belongs to ST116 in the C. freundii MLST scheme. Thirteen ARGs were predicted in all, including blaNDM-5, which was located in a plasmid. The plasmid pblaNDM5-S1, which carried the blaNDM-5 gene, was discovered to be a novel plasmid including three plasmid replicons (IncC, IncFIB, and IncX3) as well as seven ARGs (sul1, sul2, floR, dfrA17, aadA5, qnrA1, and blaNDM-5). A total of 38 blaNDM-5-bearing C. freundii strains can be retrieved from the NCBI database. Phylogenetic analysis revealed a worldwide distribution of C. freundii strains carrying the blaNDM-5 gene, with China having the highest prevalence (39%, 15/38). However, they were distantly related to CRNMS1 with SNP differences >2545.

CONCLUSION

In summary, we reported a novel IncC-IncFIB-IncX3 plasmid carrying blaNDM-5 in a carbapenem-resistant C. freundii strain in China. The development of such hybrid plasmids facilitates the transmission of ARGs.

Genomic and epidemiological characterization of a blaCTX-M-27-carrying ST34 Salmonella enterica serotype Typhimurium in China

OBJECTIVES

Consuming contaminated food and water is a leading cause of food poisoning, with Salmonella being one of the primary culprits. The aim of this study is to elucidate the genomic characteristics of a blaCTX-M-27-carrying S. enterica strain recovered from a patient with diarrhoea in China.

METHODS

Antimicrobial susceptibility of S. enterica strain 123 was determined by microdilution broth assay. Whole-genome sequencing was performed using both long-read MinION and short-read Illumina platforms to fully characterize the genetic structure of the blaCTX-M-27-carrying plasmid of the S. enterica 123. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and genomic epidemiological analysis of 69 Salmonella strains carrying the blaCTX-M-27 gene stored in NCBI GenBank were further analysed by BacWGSTdb 2.0 server.

RESULTS

The isolate was resistant to ampicillin, ampicillin/sulbactam, ceftazidime, ceftriaxone, cefepime, aztreonam, azithromycin, but still susceptible to ciprofloxacin, levofloxacin, imipenem, amikacin, trimethoprim-sulfamethoxazole and gentamicin. The complete genome sequence of Salmonella 123 is made up of one chromosome and three plasmids, which could be assigned as sequence type (ST)34. The blaCTX-M-27 gene was found in the 65 644 bp IncFII-type plasmid with IS26 and IS5 exist upstream of blaCTX-M-27 gene, and IS26 and IS1B are located downstream as a truncated fragment. The closest relative of Salmonella 123 was Salmonella strain La89, another ST34 strain recovered in 2011, which differed by only 52 SNPs.

CONCLUSION

This study reports the complete genome of a blaCTX-M-27-carrying S. enterica that can be used for gaining insights into the antimicrobial resistance mechanisms and dissemination patterns of the emerging pandemic lineage ST34.

Nosocomial outbreak of colistin-resistant, carbapenemase-producing Klebsiella pneumoniae ST11 in a medical intensive care unit

OBJECTIVES

Klebsiella pneumoniae is an important opportunistic Gram-negative pathogen. This study describes an outbreak due to colistin-resistant and carbapenem-resistant Klebsiella pneumoniae (ColR-CRKP) in a tertiary hospital related to six patients successively admitted to the department of medical intensive care unit (MICU) between March 11 and April 29, 2021.

METHODS

Phenotypic characterization was conducted on 16 ColR-CRKP strains obtained from six infected patients and five ColR-CRKP strains isolated from 48 environmental samples, followed by whole-genome sequencing (WGS) and polymerase chain reaction (PCR) analysis.

RESULTS

All ColR-CRKP strains showed resistance to commonly used antibiotics. Whole-genome sequencing revealed a variety of resistance genes such as blaKPC-2, blaCTX-M-65, and blaTEM-4 present in all strains, which is consistent with their antimicrobial resistance profile. All isolates were identified as the high-risk sequence type 11 (ST11) clonal lineage by multilocus sequencing typing (MLST) and subsequently clustered into a single clonal type by core genome MLST (cgMLST). IS5-like element ISKpn26 family transposase insertion mutations at positions 74 nucleotides in the mgrB gene were the main cause of colistin resistance in these ColR-CRKP. The variations of genes were verified by PCR. SCOTTI analysis demonstrated the transmission pathway of the ColR-CRKP between the patients.

CONCLUSION

Our study highlights the importance of coordinated efforts between clinical microbiologists and infection control teams to implement aggressive surveillance cultures and proper bacterial genotyping to diagnose nosocomial infections and take control measures. Routine surveillance and the use of advanced sequencing technologies should be implemented to enhance nosocomial infection control and prevention measures.

Characteristics of a Carbapenem-Resistant Acinetobacter baumannii Strain Causing Community-Acquired Pneumonia in a Young Healthy Women

Background

Multidrug-resistant Acinetobacter baumannii rarely causes community-acquired pneumonia. Here, we report the clinical and genomic characteristics of a multidrug-resistant A. baumannii strain responsible for community-acquired pneumonia in a 31-year-old healthy young women.

Methods

A. baumannii strain W2LL was recovered from the alveolar lavage fluid sample of a hospitalized patient with pulmonary infection. Growth rate studies were conducted under various conditions, and virulence assessments were performed using Galleria Mellonella larvae. Whole Genome Sequencing (WGS) was carried out using Oxford Nanopore MinIon and Illumina HiSeq. In silico multilocus sequence typing (MLST), plasmid replicons, antimicrobial resistance genes, and virulence genes were determined using the BacWGSTdb webserver. Phylogenetic analysis between strain W2LL and other closely related A. baumannii genomes retrieved from NCBI database was performed.

Results

WGS identified strain W2LL as a rare sporadic lineage sequence type (ST) 1431. In addition to the detection of the β-lactamase gene (blaOXA-98) on the chromosome, blaOXA-58 was found on a 92,034 bp plasmid. Antimicrobial susceptibility testing revealed this strain was resistant to cephalosporins and carbapenems, with initial treatment using cefoxitin proving ineffective. Subsequent treatment with piperacillin-sulbactam combined with levofloxacin led to gradual improvement. Compared to A. baumannii ATCC 17978, W2LL exhibited similar growth rates at 37°C and 42°C, as well as in the presence of zinc. However, strain W2LL exhibited higher virulence phenotype compared to ATCC 17978 in G. mellonella model. The closest relative of A. baumannii W2LL was CAM180_1, another isolate recovered from Cambodia, which differed by 191 SNPs.

Conclusion

W2LL is a rare ST1431 carbapenem-resistant A. baumannii strain recovered from a patient with no prior hospitalization or typical risk factors. This underscores the growing menace posed by carbapenem-resistant A. baumannii, no longer limited to hospitalized patients, potentially impacting the broader, younger population.

MIST: A microbial identification and source tracking system for next-generation sequencing data

The Professional Committee of Microbiology of the National Pharmacopoeia Commission organized the drafting of the Technical Guidelines for Microbial Whole Genome Sequencing (WGS), aiming to standardize the method process and technical indicators of microbial WGS and ensure the accuracy of sequencing and identification. On the basis of the Guidelines, we developed an integrated microbial identification and source tracking (MIST) system, which could meet the needs of microbial identification and contamination investigation in food and drug quality control. MIST integrates three analysis pipelines: 16S/18S/internal transcribed spacer amplicon-based microbial identification, WGS-based microbial identification, and single-nucleotide polymorphism-based microbial source tracking. MIST can analyze sequence data in a variety of formats, such as Fasta, base call file, and FASTQ. It can be connected to a high-throughput sequencing instrument to acquire sequencing data directly. We also developed a publicly accessible web server for MIST (http://syj.i-sanger.cn).

Global emergence of carbapenem-resistant Klebsiella pneumoniae co-carrying multiple carbapenemases

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) co-carrying multiple carbapenemases is complicating clinical treatment. This study aimed to investigate the global dissemination trends of CRKP strains that co-carry multiple carbapenemases. The CRKP isolate KP424 co-carrying bla_NDM-1 and bla_KPC-2, recovered from a stool specimen, was identified by the NG-Test Carba 5 test, and the genome sequence was further determined by using Nanopore MinION and Illumina NovaSeq 6000 technologies. The genome sequences of the CRKP strains carrying multiple carbapenemase genes were further retrieved from the NCBI GenBank database. Thirteen antimicrobial resistance genes, including bla_NDM-1 and bla_KPC-2, have been identified in KP424, with bla_NDM-1 and bla_KPC-2 located on different plasmids. In total, 832 genome sequences of CRKP strains co-carrying two carbapenemase genes were retrieved from the NCBI database. Strains carrying both bla_NDM and bla_OXA-48-like accounted for 665 (79.9 %) of the total strains, ranking first, and those carrying both bla_KPC and bla_NDM accounted for 103 (12.4 %), ranking second. The prevalence of CRKP strains co-carrying two carbapenemase genes increased significantly over time, from 0.40 % in 2010 to 9.67 % in 2021. The proportion of strains carrying both bla_KPC and bla_NDM has also increased, from 0.00 % in 2010 to 4.40 % in 2021. The strains carrying both bla_KPC and bla_NDM had the highest prevalence (66.7 %, 52/78) in China, while those carrying both bla_NDM and bla_OXA-48-like had the highest prevalence worldwide. Multiple-carbapenemase producers pose a great threat to public health; further research on the mechanisms underlying multiple carbapenemase gene occurrence is required to prevent their global dissemination.

Genomic Characteristics of Extended Spectrum β-Lactamase Producing Escherichia coli Isolates Recovered from a District Hospital in China

Purpose

The isolation rate of extended spectrum β-lactamase (ESBL)-producing Escherichia coli is increasing, posing a challenge to clinical anti-infective therapy. This study aims to provide new insight into the genomic characteristics and antimicrobial resistance mechanisms of extended spectrum β-lactamase producing E. coli isolates recovered from a district hospital in China.

Methods

A total of 36 ESBL-producing E. coli isolates were collected from body fluid samples from a Chinese district hospital. All isolates were subjected to whole genome sequencing to identify their antimicrobial resistance genes, virulence genes, serotypes, sequence types, and phylogenetic relationships by BacWGSTdb 2.0 webserver.

Results

Among these isolates, all were resistant to cefazolin, cefotaxime, ceftriaxone, ampicillin, 24 (66.7%) were resistant to aztreonam, 16 (44.4%) were resistant to cefepime, and 15 were resistant (41.7%) to ceftazidime. The bla_CTX-M gene was detected in all ESBL-producing E. coli isolates. Two isolates carrying two different types of bla_CTX-M genes simultaneously. The carbapenem resistance gene bla_KPC-2 was detected in one (2.8%) isolate. A total of 17 sequence types (STs) were found, with ST131 accounting for the majority (n =13; 36.1%). The most common serotype was O16:H5 associated with seven ST131 strains, followed by O25:H4/ST131 (n = 5) and O75:H5/ST1193 (n = 5). Evaluation of clonal relatedness revealed that all bla_CTX-M gene-carrying E. coli had a difference of SNPs range from 7 to 79,198, which could be divided into four clusters. Only 7 SNPs could be found between EC266 and EC622, indicating that they are variants of the same clonal lineage.

Conclusion

This study investigated the genomic characteristics of ESBL-producing E. coli isolates recovered from a district hospital in China. Continuous surveillance of ESBL-producing E. coli infections is imperative to create efficient strategies for controlling the transmission of these multi-drug resistant bacteria in clinical and community settings.

Genomic Characteristics of a Multidrug-Resistant ST648 Escherichia coli Isolate Co-Carrying blaKPC-2 and blaCTX-M-15 Genes Recovered from a Respiratory Infection in China

Background

The transmission of carbapenem-resistant Enterobacterales pose a significant threat to global public health, which weakens the effectiveness of most antimicrobial agents. The aim of this study is to present the genomic characteristics of a multidrug-resistant Escherichia coli, which contains both bla_KPC-2 and bla_CTX-M-15 genes, discovered from a respiratory infection in China.

Methods

The antimicrobial susceptibility of E. coli isolate 488 was measured by using the broth microdilution method. The Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms were applied to determine the whole-genome sequence of this isolate. De novo assembly of short Illumina reads and long MinION reads were performed by Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicon types were determined using the genome sequencing data. Additionally, a pairwise core genome single nucleotide polymorphism (cgSNP) comparison between E. coli 488 and all ST648 E. coli strains retrieved from NCBI GenBank database were conducted using the BacWGSTdb 2.0 server.

Results

E. coli 488 was resistant to aztreonam, levofloxacin, cefepime, fosfomycin, amikacin, imipenem, cefotaxime, and meropenem. The complete genome sequence of E. coli 488 (belong to ST648) is made up of eleven contigs totaling 5,573,915 bp, including one chromosome and ten plasmids. Eight antimicrobial resistance genes were identified, including bla_KPC-2 located in a 46,161 bp IncI1-type plasmid and the bla_CTX-M-15 gene situated in the chromosome. Other two E. coli S617-2 and R616-1 isolates, recovered from China in 2018, are the closest relatives of E. coli 488, with only 52 SNPs difference. The genome also contains at least 57 genomic islands and several IS elements.

Conclusion

Our study reveals the first ST648 E. coli isolate containing both bla_KPC-2 and bla_CTX-M-15 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant Enterobacterales in clinical settings.

Genomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying blaCTX-M-55 gene and Tn6777 isolated from a paediatric patient in China

OBJECTIVES

Here we report a complete genome sequence of a multidrug-resistant Salmonella Rissen, carrying blaCTX-M-55 and Tn6777, isolated from a Chinese paediatric patient.

METHODS

Whole genome of S. Rissen S1905 was sequenced using the Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Unicycler was used to perform a de novo assembly of Illumina and Nanopore reads. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. In silico multilocus sequence typing, plasmid replicons, antimicrobial resistance genes and virulence factors were identified from the genome sequence by multiple bioinformatics tools. Core genome multilocus sequence typing analysis between S. Rissen S1905 and all retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server.

RESULTS

Six contigs totaling 5 056 896 bp make up the complete genome sequence of S. Rissen S1905, which includes 1 chromosome and 5 plasmids. The blaCTX-M-55 was embedded in the ISEcp1-blaCTX-M-55-wbuC transposition unit located in an 85 991-bp IncI1 plasmid. However, the pco-sil operon and other eight antimicrobial resistance genes were carried by Tn6777 in the chromosome. There are 162 virulence genes in S1905. S. Rissen S1905 belongs to ST469; the closest relative was another isolate originating from a human faecal specimen in Shanghai, China, which differed by 60 core genome multilocus sequence type alleles.

CONCLUSION

These data on the multidrug-resistant S. Rissen carrying blaCTX-M-55 and Tn6777 can provide a foundation for further studies on the molecular epidemiological characteristics, pathogenicity, antimicrobial resistance mechanisms, and dissemination mechanism of Salmonella.

A parallel and silent emerging pandemic: Antimicrobial resistance (AMR) amid COVID-19 pandemic

World is in the middle of the pandemic (COVID-19), caused by SARS-COV-2 virus, which is a significant global health crisis after Spanish influenza in the beginning of 20th century. Progressive drastic steps have been enforced to minimize the transmission of the disease. Likewise, in the current years, antimicrobial resistance (AMR) has been referred as one of the potential perils to the global economy and health; however, it is now veiled under the present pandemic. During the current pandemic, AMR to available frontline antibiotics may prove fatal and life threatening to bacterial and fungal infections during routine procedures like elective surgery, C-sections, etc. Currently, a swift elevation in multidrug-resistant organisms (MDROs), like carbapenem-resistant New Delhi metallo-β-lactamase (NDM)-producing Acinetobacter baumannii, Enterobacterales, extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae, methicillin-resistant Staphylococcus aureus (MRSA), multi-triazole-resistant Aspergillus fumigatus and pan-echinocandin-resistant Candida glabrata has been seen. Thereupon, the global outbreak of COVID-19 also offers some important ramification for developing antimicrobial drug resistance. This article aims to highlights episodes and aspects of AMR prevalence, impact of management and mismanagement of COVID-19 crisis, hospital settings, community, environment, and travel on the AMR during the current pandemic.

Genomic Characterization of Salmonella enterica serovar Weltevreden Associated with Human Diarrhea

Salmonella Weltevreden is an emerging pathogen associated with human diarrhea, and knowledge of the genomics and epidemiology of this serovar is still limited. In this study, we performed whole-genome sequencing of 96 S. Weltevreden isolates recovered from diarrheal patients and 62 isolates from food animals in China between 2006 and 2017. Together, with an additional 199 genome sequences of S. Weltevreden published in NCBI, we performed an analysis on all 357 S. Weltevreden genome sequences. Our results demonstrated that the majority of S. Weltevreden from diarrheal patients from China (97.92%, 94/96) and the other regions in the world (94.97%, 189/199) identified in this study were sequence type (ST) 365. The remaining types were ST3771 (n = 3), ST22 (n = 1), ST155 (n = 1), and ST684 (n = 1). In addition, ST365 was also widely recovered from animals, food, and environmental samples in different regions of the world. Phylogenetic analysis and pulsed-field gel electrophoresis (PFGE) revealed that S. Weltevreden from diarrheal patients was closely related to those recovered from food and environmental specimens. We also showed that S. Weltevreden did not exhibit severe antimicrobial resistance profiles, suggesting administering antibiotics is still effective for controlling the agent. Interestingly, we found that S. Weltevreden strains carried a number of virulence factor genes, and a 100.03-kb IncFII(S) type plasmid was widely distributed in S. Weltevreden strains. Elimination of this plasmid decreased the bacterial capacity to infect both Caco-2 cells and C57BL/6 mice, suggesting the importance of this plasmid for bacterial virulence. Our results contribute to the understanding of the epidemiology and virulence of S. Weltevreden. IMPORTANCE Salmonella Weltevreden is a pathogen associated with human diarrheal diseases found across the globe. However, knowledge of the genomics and epidemiology of this pathogen is still limited. In this study, we found S. Weltevreden sequence type (ST) 365 is commonly recovered from diarrheal patients in China and many other regions of the world, and there is no major difference between the Chinese isolates and the global isolates at the phylogenetic level. We also demonstrated that ST365 was widely recovered from animal, food, and environmental samples collected in different, global regions. Importantly, we discovered an IncFII(S) type plasmid commonly carried by S. Weltevreden strains of human, animal, and food origins, and this plasmid is likely to contribute to the bacterial pathogenesis. These findings enhance our understanding of the emergence of S. Weltevreden involved in diarrheal outbreaks and the global spread of S. Weltevreden strains.

Molecular epidemiology and genomic insights into the transmission of carbapenem-resistant NDM-producing Escherichia coli

Escherichia coli is a leading cause of nosocomial infections. Carbapenem-resistant E. coli (CREC), which has been frequently isolated in recent years because of the widespread use of carbapenems, poses a significant challenge to clinical anti-infection treatment. In this study, a total of 27 CREC strains were identified from a set of 795 E. coli isolates collected over a two-year period from a tertiary hospital in China. Whole-genome sequencing revealed that 17 strains carried the bla _NDM-5 gene, 5 strains carried the bla _NDM-1 gene, 1 strain carried the bla _NDM-7 gene, and the remaining 4 strains carried the bla _KPC-2 gene. All 23 NDM-producing E. coli strains were resistant to all antibiotics except tigecycline, colistin, and cefiderocol. Nine different sequence types (STs) were identified, with ST410 and ST167 being the most prevalent. All of the bla _NDM genes were located on conjugatable plasmids. We identified five different plasmid replicon types ranging in size from 20 kb to 200 kb, with the IncX3-type plasmid, 46 kb in size, being a key factor in facilitating the horizontal transmission of the bla _NDM gene in E. coli. The structure surrounding the bla _NDM gene was relatively conserved and mainly contained the following structures: IS3000-ISAbal25-IS5-bla _NDM-ble _MBL-trpF-dsbC-IS26. However, the plasmid backbone structure was highly variable, which indicates that the bla _NDM gene has already spread horizontally among different types of plasmids. In addition, we discovered two copies of the bla _NDM-5 gene in a single plasmid (pEC29-NDM-5), with an identical structure around the gene and the complete sequence of the class 1 integron. Our findings detail the prevalence of CREC in a tertiary hospital in China, and the emergence of multiple copies of the bla _NDM-5 gene on a single plasmid needs our attention.

The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum

Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.

Pathogenome comparison and global phylogeny of Escherichia coli ST1485 strains

Escherichia coli ST1485 strains belong to the clinically important phylogroup F and have disseminated worldwide in humans, animals, and the environment. Here, we elucidated the pathogenome of a global collection of E. coli ST1485 isolates from diverse sources retrieved from public databases and a high-quality sequenced complete genome of colistin-resistant E. coli strain CFSAN061771 isolated from raw milk cheese which designated as a reference strain. CFSAN061771 belongs to O83:H42-ST1485 pathotype and carries a conjugative ColV plasmid, pCFSAN061771_01, combining extraintestinal virulence genes (ompt, sitA, iroN, etsC, traT, cvaC, hylF, iss, tsh, mchf, iucC, iutA) with a multidrug resistance island (bla_TEM-1, aph(6)-Id, aph(3″)-Ib, sul2, dfrA14). Comparative genomic analysis revealed a high frequency of pCFSAN061771_01-like plasmids in E. coli ST1485. A notable evolutionary genetic event in E. coli ST1485 strains is the acquisition of a pCFSAN061771_02-like plasmid, which confers resistance to several antimicrobials, tellurium, and quaternary ammonium compounds. The identical virulence and antibiotic resistance profiles identified in some human and animal strains are worrisome. This is the first study to emphasize the significance of E. coli ST1485 as a global high-risk virulent and multidrug-resistant clone with zoonotic potential.

Genomic Characterization of a Multidrug-Resistant Escherichia coli Isolate Co-Carrying blaNDM-5 and blaCTX-M-14 Genes Recovered from a Pediatric Patient in China

Background

Public health is seriously threatened by the rise of carbapenem-resistant Enterobacterales (CRE). However, the genomic characteristics of CRE detected in pediatric patients are largely unknown. Here, we reported the genomic characteristics of a multidrug-resistant Escherichia coli strain containing the plasmid-borne bla_NDM-5 and bla_CTX-M-14 genes recovered from a Chinese pediatric patient.

Methods

The genome sequence of E. coli strain B379 was determined using Illumina NovaSeq 6000 and Oxford Nanopore MinION. Multiple bioinformatics tools were used to annotate the genome sequence, identify antimicrobial resistance genes and plasmid replicons and perform the in silico multilocus sequence typing (MLST) analysis. Using BacWGSTdb 2.0 server, a core genome MLST (cgMLST) comparison was made between E. coli B379 and all ST746 E. coli strains downloaded from the public database.

Results

The E. coli B379 genome sequence is comprised of six contigs totaling 5,152,502 bp, including one chromosome and five plasmids. Nineteen antimicrobial resistance genes were predicted. The bla_NDM-5, which is located on a 46,161 bp IncX3 plasmid and the bla_CTX-M-14 gene which is located on a 147,204 bp IncFII/IncFIA/IncFIB plasmid are two examples of these 19 genes. E. coli B379 was resistant to ampicillin, ampicillin/sulbactam, ceftriaxone, ceftazidime, imipenem, cefepime, ciprofloxacin, ertapenem, trimethoprim-sulfamethoxazole. This isolate belonged to ST746 and the closest relative was another one originating from a human material specimen in Denmark, which differed by 273 cgMLST alleles.

Conclusion

Our study reports the emergence of a multidrug-resistant E. coli strain co-carrying bla_NDM-5 and bla_CTX-M-14 recovered from a pediatric patient in China. These data would help us better understand the prevalence, genetic characteristics, and mechanisms of antimicrobial resistance of this recently identified multidrug-resistant bacteria in children.

Genomic Insights into the Colistin Resistant mcr-Carrying Escherichia coli Strains in a Tertiary Hospital in China

Colistin is an important antimicrobial agent in the treatment of infections caused by multidrug resistant (MDR) Gram-negative bacteria. The horizontal transfer of mobile colistin resistance gene (mcr) poses a major threat to the public health worldwide. In this study, a total of thirteen mcr-carrying Escherichia coli (MCREC) strains were recovered from a tertiary hospital in Zhejiang, China, between 2016 and 2019. The minimum inhibitory concentration (MIC) of antimicrobial agents, epidemiological characteristics, and transmission dynamics of mcr-carrying isolates were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and southern blotting analysis. All strains were discovered to be resistant to colistin, and the majority displayed MDR phenotype. However, none of the 13 MCREC strains were resistant to carbapenems. The 13 MCREC isolates were divided into 10 different STs, including ST744, ST156, ST453, ST410, ST57, ST131, ST7034, ST2599, ST457, and ST13239, in which ST13239 was discovered for the first time. Based on core genome single nucleotide polymorphism (cgSNP) analysis, no clear epidemiological link was discovered in these strains with the exception of EC2118 and EC3807, which differ by just one SNP. A total of 35 antimicrobial resistance genes which can be divided into 14 classes were identified from the 13 MCREC isolates. According to S1-PFGE and southern blotting analyses, all 13 MCREC strains had plasmid-mediated mcr-1, and nine of them carried conjugative plasmids. In conclusion, our study revealed the emergence and dissemination of colistin-resistant E. coli isolates carrying mcr-1 in a Chinese hospital, which poses a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in China.

Genomic Characterization of a Clinical Listeria monocytogenes ST1 Isolate Recovered from the Blood Sample of a Woman with Third Trimester Stillbirth

Background

Listeria monocytogenes is a foodborne gram-positive bacterium which causes adverse pregnancy outcomes. Here, the genomic and phylogenetic characteristics of a L. monocytogenes isolate obtained from blood sample of a third trimester pregnant woman with stillbirth are investigated.

Methods

Whole genome DNA of L. monocytogenes ST1 was sequenced with HiSeq X Ten platform. The NCBI Prokaryotic Genome Annotation Pipeline was used to annotate the genome sequence. The sequence type (ST) and antimicrobial resistance genes were then identified. The core genome multilocus sequence typing (cgMLST) analysis with other closely related L. monocytogenes stored in the NCBI GenBank database was performed using BacWGSTdb 2.0.

Results

The complete genome sequence of L. monocytogenes ST1 is made up of 20 contigs totaling 2,914,725 bp, with 2886 protein-coding sequences and a GC content of 37.9%. Fosfomycin [fosX], Lincosamide antibiotic [lin] and peptide antibiotic [mprF] were discovered as antimicrobial resistance genes. In silico serogroup typing prediction revealed that L. monocytogenes ST1 belonged to serotype IVb. The closest relative of L. monocytogenes ST1, obtained from Poland in 2015, differs by only 15 cgMLST alleles.

Conclusion

We identified a L. monocytogenes ST1 strain from blood sample of a woman with third trimester stillbirth in China. These discoveries would aid in our understanding of the genomic characteristics, mechanisms of antimicrobial resistance, and epidemiological features of this pathogen.

Molecular and clinical characterization of hypervirulent Klebsiella pneumoniae isolates from individuals with urinary tract infections

Despite being a significant public health concern, hypervirulent Klebsiella pneumoniae (hvKP) has rarely been investigated in urinary tract infections (UTIs). To investigate the molecular and clinical characterization of hvKP in UTIs, we collected K. pneumoniae strains and clinical data from patients with UTIs. HvKP was confirmed by virulence-related genes and the Galleria mellonella model and sequenced by next-generation sequencing. Our data showed that 30/121 isolates were hvKP [17 carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP), 12 hvKP, and 1 extended-spectrum β-lactamase-producing hvKP]; these had higher resistance to most antimicrobials and were more likely to cause complicated UTIs (cUTIs). Notably, the mucoid phenotype-regulating genes _prmpA and _prmpA2 were truncated in 3 and 19 hvKP, respectively. Eight serotypes were detected and divided into three groups: K64 (n = 17), K1/K2 (n = 6), and others (n = 7). Furthermore, 16/17 K64 hvKP isolates were CR-hvKP but with a lower mortality rate of G. mellonella as the truncated _prmpA/_prmpA2 incurred high fitness cost to the isolates. In addition, all K64 isolates belonged to ST11 with the same cluster, and in two of these strains (KP88 and KP92) bla_KPC-2 gene was successfully transferred to EC600. Genetic environment analysis showed that IS26–tnpR–ISKpn27–bla_KPC−2–ISKpn6 may be the core structure in the horizontal transfer of bla_KPC-2. The highest mortality rate among the infected G. mellonella was observed in the K1/K2 group. In conclusion, hvKP had a higher resistance rate and was more likely to lead to cUTIs. Convergence of hypervirulence and carbapenem resistance in a transmissible ST11 clone of K64 K. pneumoniae was mediated by a plasmid in UTIs. Therefore, surveillance of hvKP in UTIs should be strengthened.

Genomic and phylogenetic analysis of a multidrug-resistant Klebsiella pneumoniae ST15 strain co-carrying blaOXA-232 and blaCTX-M-15 recovered from a gallbladder infection in China

OBJECTIVES

The occurrence of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) has been increasing in China during the last five years. The bla_OXA-232-carrying CRKP strain's clonal propagation can readily lead to nosocomial epidemics. Here, we report the genome sequence of OXA-232 and CTX-M-15 co-producing K. pneumoniae strain isolated from a gallbladder infection in China.

METHODS

The genome sequence of K. pneumoniae S105 was determined using the Illumina NovaSeq 6000 platform. Antimicrobial resistance genes (ARGs), multilocus sequence typing (MLST) and plasmid replicons were identified using the BacWGSTdb server. The phylogenetic relationship between S105 and other K. pneumoniae strains was analysed using the core genome multilocus sequence typing (cgMLST) strategy.

RESULTS

The genomic sequence of K. pneumoniae S105 is made up of 111 contigs with a total length of 5,748,752 bp. According to the Pasteur MLST scheme, S105 belongs to sequence type (ST) 15. Fifteen ARGs were discovered in the genome, including the beta-lactam resistance genes bla_OXA-232 and bla_CTX-M-15. The bla_OXA-232 gene was located in a ColKP3 plasmid. KL112 was anticipated to be the capsule and lipopolysaccharide serotype. A total of 73 phylogenetically related strains were found from 19 nations across four continents; 22 of them were from China, with 21 strains harboring the bla_OXA-232 gene, and the majority of them diverged by just 6-37 cgMLST alleles.

CONCLUSIONS

In summary, we reported the genomic sequencing of a K. pneumoniae ST15 clinical strain that co-carrying the bla_OXA-232 and bla_CTX-M-15 genes. The clonal dissemination of OXA-232-producing K. pneumoniae ST15 strains in China needs our attention.

Invasive Infection With emm3/ST15 Streptococcus pyogenes: The First Case Report From China and Complete Genome Analysis

Streptococcus pyogenes (GAS) may cause severe invasive disease with a high fatality rate, especially M3-type strains, which are less common in China. Here, we report the first emm3/ST15 invasive GAS infection case in China. The patient was diagnosed with severe skin and soft tissue infection (SSTI) and septicaemia caused by one GAS strain. Antibiotic susceptibility tests showed that the isolate was susceptible to all tested drugs. Antimicrobial therapy was then applied, and the patient fully recovered and was discharged from the hospital on Day 43. Whole-genome sequencing was carried out using the Illumina and Oxford Nanopore platforms and revealed this to be the first emm3/ST15-type GAS invasive infection in China. The closely related emm3/ST15-type GAS strains are MGAS315 from the United States and M3-b from Japan. Our finding is a warning that we should pay attention to invasive M3-type GAS infections in China and indicates the global spread of the highly virulent emm3/ST15 GAS strain.

Emergence of a Multidrug-Resistant Escherichia coli Co-Carrying a New mcr-1.33 Variant and blaNDM-5 Genes Recovered from a Urinary Tract Infection

Background

Carbapenem-resistant Enterobacterales (CRE) are a significant threat to worldwide public health, resulting in increased morbidity, death, hospitalization time and healthcare expenses. Here, the genomic and phylogenetic characteristics of a multidrug-resistant Escherichia coli isolate carrying both the new mcr-1.33 variant and bla_NDM-5 gene obtained from a urinary tract infection in China are investigated.

Methods

Antimicrobial susceptibility of E. coli 779 was evaluated by using the broth microdilution method. Short-read Illumina NovaSeq 6000 and long-read Oxford Nanopore MinION platforms were applied to sequence the bacterial whole genomic DNA and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, and antibiotic resistance genes. BacWGSTdb 2.0 was used to perform the core genome multilocus sequence typing (cgMLST) analysis with other closely related E. coli isolates deposited in the public database.

Results

E. coli 779 was resistant to aztreonam, levofloxacin, fosfomycin, cefoxitin, cefepime, cefotaxime, imipenem, meropenem, polymyxin, and tigecycline. The complete genome sequence of E. coli 779 is made up of nine contigs totaling 5,667,876 bp, including one chromosome and eight plasmids. The isolate was assigned to ST101, serotype O-:H31, and phylogroup B1. The colistin resistance gene mcr-1.33 (located in a 242,460 bp IncHI2/IncHI2A plasmid) and the β-lactam resistance gene bla_NDM-5 (located in a 46,161 bp IncX3 plasmid) were among the 27 antimicrobial resistance genes discovered. The closest relative of E. coli 779, another ST101 strain (E. coli 443) obtained from a sewage sample in Shandong, China in 2015, differs by only 24 cgMLST alleles.

Conclusion

We discovered the first multidrug-resistant ST101 E. coli strain with plasmid-mediated mcr-1.33 variant and bla_NDM-5 gene in China. These findings would help us to better understanding the genomic traits, antimicrobial resistance mechanisms and epidemiological aspects of this bacterial pathogen.

Emergence of polymyxin B-heteroresistant hypervirulent Klebsiella pneumoniae from an individual in the community with asymptomatic bacteriuria

Background

The heteroresistance of polymyxin B, a last-resort antibiotic used to treat many serious bacterial infections, may lead to antibiotic treatment failure. However, polymyxin B-heteroresistant isolates are rare in individuals living in the community. We report a polymyxin B-heteroresistant hypervirulent Klebsiella pneumoniae (hvKP) isolate from an individual in the community with asymptomatic bacteriuria.

Results

The NYTJ35 isolate had multiple virulence genes that encoded a mucoid phenotype regulator (rmpA), aerobactin (iucABCD-iutA), salmochelin (iroBCDN), yersiniabactin (irp1–2 and ybtAEPQSTUX), and a truncated rmpA2. Infection of galleria mellonella larvae indicated the isolate was hypervirulent. Antimicrobial susceptibility testing showed it was susceptible to all tested antibiotics except polymyxin B. The proportion of surviving bacteria was 1.2 × 10^− 7 based on the population analysis profile (PAP) method, suggesting the presence of polymyxin B heteroresistance. The isolate was not hypermucoviscous, but it was a strong biofilm producer. It had capsular serotype K1 and belonged to sequence type 23 (ST23). The isolate also had the D150G substitution in phoQ, which is known to confer polymyxin B resistance.

Conclusions

We identified the co-occurrence of hypervirulence and polymyxin B heteroresistance in a K. pneumoniae isolate from an individual with asymptomatic bacteriuria. We suggest the use of increased screening for hvKP in individuals living in the community.

Toward accurate diagnosis and surveillance of bacterial infections using enhanced strain-level metagenomic next-generation sequencing of infected body fluids

Metagenomic next-generation sequencing (mNGS) enables comprehensive pathogen detection and has become increasingly popular in clinical diagnosis. The distinct pathogenic traits between strains require mNGS to achieve a strain-level resolution, but an equivocal concept of 'strain' as well as the low pathogen loads in most clinical specimens hinders such strain awareness. Here we introduce a metagenomic intra-species typing (MIST) tool (https://github.com/pandafengye/MIST), which hierarchically organizes reference genomes based on average nucleotide identity (ANI) and performs maximum likelihood estimation to infer the strain-level compositional abundance. In silico analysis using synthetic datasets showed that MIST accurately predicted the strain composition at a 99.9% average nucleotide identity (ANI) resolution with a merely 0.001× sequencing depth. When applying MIST on 359 culture-positive and 359 culture-negative real-world specimens of infected body fluids, we found the presence of multiple-strain reached considerable frequencies (30.39%-93.22%), which were otherwise underestimated by current diagnostic techniques due to their limited resolution. Several high-risk clones were identified to be prevalent across samples, including Acinetobacter baumannii sequence type (ST)208/ST195, Staphylococcus aureus ST22/ST398 and Klebsiella pneumoniae ST11/ST15, indicating potential outbreak events occurring in the clinical settings. Interestingly, contaminations caused by the engineered Escherichia coli strain K-12 and BL21 throughout the mNGS datasets were also identified by MIST instead of the statistical decontamination approach. Our study systemically characterized the infected body fluids at the strain level for the first time. Extension of mNGS testing to the strain level can greatly benefit clinical diagnosis of bacterial infections, including the identification of multi-strain infection, decontamination and infection control surveillance.

Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study

We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the bla_OXA-181, bla_OXA-48, bla_OXA-484, bla_NDM-1, and bla_GES-5 genes. Multiple species/clones carried bla_OXA-48 and bla_NDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.

First Outbreak of NDM-1-Producing Klebsiella pneumoniae ST11 in a Portuguese Hospital Centre during the COVID-19 Pandemic

New Delhi metallo-β-lactamase (NDM) carbapenemase has been considered a global threat due to its worldwide widespread in recent years. In Portugal, a very low number of infections with NDM-producing Enterobacterales has been reported. A total of 52 strains from 40 patients and 1 environmental sample isolated during COVID-19 pandemic were included in this study. Wholegenome sequencing (WGS) was performed on 20 carbapenemase-producing strains, including 17 NDM-1-producing Klebsiella pneumoniae ST11-KL105 lineage strains, one NDM-1-producing Escherichia coli ST58 strain and one KPC-3-producing K. pneumoniae ST147 strain, recovered from a total of 19 patients. Of interest, also one NDM-1-producing K. pneumoniae ST11-KL105 was collected from the hospital environment. Genome-wide phylogenetic analysis revealed an ongoing dissemination of NDM-1-producing K. pneumoniae ST11 strains (n = 18) with the same genetic features seen across multiple wards. Furthermore, the ST58 E. coli strain, collected from a patient rectal swab that was also colonised with a K. pneumoniae strain, also showed the IncFIA plasmid replicon and the bla_NDM-1 gene (preceded by IS30 and followed by genes ble_MBL, trpF, dsbC, cutA, groES and groEL). The bla_NDM-1 is part of Tn125-like identical to those reported in Poland, Italy and India. The bla_KPC-3 K. pneumoniae ST147-KL64 strain has the genetic environment Tn4401d isoform. In conclusion, herein we report the molecular epidemiology, resistome, virulome and mobilome of the first NDM-1 carbapenemase outbreak caused by K. pneumoniae ST11-KL105 lineage during the COVID-19 pandemic in Portugal. Moreover, the outbreak strains characterised included seventeen different patients (infected and colonised) and one environmental sample which also emphasises the role of commensal and hospital environment strains in the dissemination of the outbreak.

Distribution, characterization, and antibiotic resistance of hypervirulent Klebsiella pneumoniae isolates in a Chinese population with asymptomatic bacteriuria

Background

Asymptomatic bacteriuria (ASB) frequently occurs among all ages and may develop into urinary tract infections (UTIs). Hypervirulent Klebsiella pneumoniae (hvKP) has become a new threat to human health. In our study, we aimed to investigate the epidemiological characteristics of hvKP in population with ASB.

Results

A total of 61 K. pneumoniae isolates were collected from 7530 urine samples between October and December 2020. The strains were sensitive to most of the antimicrobial agents tested, but a polymyxin resistant strain was found (MIC>16 μg/mL). Three serotypes were detected, including K1 (16.4%, 10/61), K5 (1.6%, 1/61) and K57 (3.2%, 2/61). Four strains (KPNY9, KPNY31, KPNY40, and KPNY42) carried a combination of two or more hypervirulent markers (peg-344, iroB, iucA, _prmpA, and _prmpA2), and their survival rates after Galleria mellonella infection were lower than those of the other strains (40.0 vs. 70.0%), suggesting that they were hvKP. These hvKP strains with lower biofilm forming ability than classical K. pneumoniae (0.2625 ± 0.0579 vs. 0.6686 ± 0.0661, P = 0.033) were identified as belonging to K2-ST65, K2-ST86, K57-ST592, and K2-ST5559 (a new ST type). KPNY31 (ST5559) shared a close genetic relationship with KPNY42 (ST86) and other ST86 isolates, which have been detected in both nosocomial and community-acquired infections.

Conclusions

The hvKP with relatively weak biofilm formation was detected in a population with ASB, which was more likely to cause bacteremia and serious consequences. A novel sequence type (ST5559) hvKP derived from ST86 was found. Therefore, hvKP should be monitored in the population with ASB.

Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr-10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East

Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (n = 350) and subclinical (n = 95) bovine mastitis, and raw unpasteurized milk (n = 125). Klebsiella pneumoniae, Aeromonas hydrophila, Enterobacter cloacae (100% each), Escherichia coli (87.78%), and Proteus mirabilis (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in P. mirabilis (30.30%) and E. coli (3.33%) isolates. Ten isolates (four E. coli, three Klebsiella species and three P. mirabilis) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced E. coli isolates. Three E. coli isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas E. coli ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin mcr-10 and fosfomycin fosA5 resistance genes in a K. pneumoniae (K1) isolate from bovine milk. Sequence analysis of the reconstructed mcr-10 plasmid from WGS of K1 isolate, showed that mcr-10 gene was bracketed by xerC and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including mcr-10-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of K. pneumoniae co-harboring mcr-10 and fosA5 genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.

Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China

Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.

Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants

Gut dysbiosis may precede neonatal sepsis, but the association is still not well-understood. The goal of this study is to investigate the association between gut microbiota and neonatal sepsis, and to seek the evidence of colonization of pathogenic bacteria in the gut before evolving into an invasive infection. A prospective cohort study examined fecal microbiota composition in preterm infants with and without sepsis. Thirty-two very-low-birth-weight (VLBW) preterm infants and 10 healthy term infants as controls were enrolled. The fecal samples collected from the participants at the first, fourth, and seventh weeks of life underwent 16S rRNA amplicon sequencing for measurement of the diversity and composition of the microbiota. The bacterial isolates causing neonatal sepsis were genome sequenced. PCR was performed to confirm the translocation of the bacteria from the gut to the blood. The results showed that VLBW preterm infants with sepsis had lower microbial diversity in the gut at birth compared to preterm infants without sepsis and term infants. The composition of gut microbiome in preterm infants was similar to healthy terms at birth but evolved toward dysbiosis with increasing Proteobacteria and decreasing Firmicutes weeks later. The strain-specific PCR confirmed the presence of causative pathogens in the gut in 4 (40%) out of 10 VLBW preterms with sepsis before or at onset of sepsis, and persistence of the colonization for weeks after antibiotic treatment. The same bacterial strain could horizontally spread to cause infection in other infants. Prolonged antibiotic exposure significantly reduced beneficial Bifidobacterium and Lactobacillus in the gut. In conclusion, preterm infants with gut dysbiosis are at risk for neonatal sepsis, and the causative pathogens may be from the gut and persist to spread horizontally. The association of increased Proteobacteria abundance and decrease in microbiome diversity suggests the need for interventions targeting the gut microbiome to prevent dysbiosis and sepsis in VLBW preterm infants.

Transmission Dynamics of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 Strains Carrying Capsular Loci KL64 and rmpA/rmpA2 Genes

The presence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates recovered from two fetal outbreaks of nosocomial infections. Between April 2016 and March 2018, a total of 70 isolates of K. pneumoniae were collected from sterile samples in a tertiary hospital in Hangzhou, China. The minimal inhibitory concentrations (MICs) of 21 antimicrobial agents were determined using the broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was performed on 47 CRKP isolates, and 16 clonally related isolates were further characterized by Illumina sequencing. In addition, the complete genome sequences of three representative isolates (KP12, KP36, and KP37) were determined by Oxford Nanopore sequencing. The K. pneumoniae isolates were recovered from patients diagnosed with pulmonary infection, cancer, or encephalopathy. For all CRKP isolates, PFGE separated three clusters among all strains. The most predominant PFGE cluster contained 16 isolates collected from patients who shared close hospital units and represented a potential outbreak. All 16 isolates showed an extremely high resistance level (≥87.5%) to 18 antimicrobials tested but remain susceptible to colistin (CST). Multiple antimicrobial resistance and virulence determinants, such as the carbapenem resistance gene bla_KPC-2, and genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype (rmpA and rmpA2), were observed in the 16 CRKP isolates. These isolates belonged to sequence type 11 (ST11) and capsular serotype KL64. A core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis indicated that the 16 CRKP isolates could be partitioned into two separate clades (≤15 SNPs), suggesting the two independent transmission scenarios co-occurred. Moreover, a high prevalence of IncFIB/IncHI1B type virulence plasmid with the iroBCDN locus deleted, and an IncFII/IncR type bla_KPC-2-bearing plasmid was co-harbored in ST11-KL64 CRKP isolates. In conclusion, our data indicated that the nosocomial dissemination of ST11-KL64 CRKP clone is a potential threat to anti-infective therapy. The development of novel strategies for surveillance, diagnosis, and treatment of this high-risk CRKP clone is urgently needed.

The global dissemination of bacterial infections necessitates the study of reverse genomic epidemiology

Whole genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. Traditional genomic epidemiology often uses WGS as a verification tool, namely, when a common source or epidemiological link is suspected, the collected isolates are sequenced for the determination of clonal relationships. However, increasingly frequent international travel and food transportation, and the associated potential for the cross-border transmission of bacterial pathogens, often lead to an absence of information on bacterial transmission routes. Here we introduce the concept of 'reverse genomic epidemiology', i.e. when isolates are inspected by genome comparisons to be sufficiently similar to one another, they are assumed to be a consequence of infection from a common source. Through BacWGSTdb (http://bacdb.org/BacWGSTdb/), a database we have developed for bacterial genome typing and source tracking, we have found that almost the entire analyzed 20 bacterial species exhibit the phenomenon of cross-border clonal dissemination. Five networks were further identified in which isolates sharing nearly identical genomes were collected from at least five different countries. Three of these have been documented as real infectious disease outbreaks, therefore demonstrating the feasibility and authority of reverse genomic epidemiology. Our survey and proposed strategy would be of potential value in establishing a global surveillance system for tracing bacterial transmissions and outbreaks; the related database and techniques require urgent standardization.

Genomic surveillance reveals international circulation and local transmission of Salmonella enterica serovars Typhi and Paratyphi A in Taiwan

BACKGROUND/PURPOSE

Morbidity and mortality from typhoid and paratyphoid fever remain an important problem for public health authorities in developing countries. In countries with lower incidences, most cases occur in travelers who visit regions in which typhoid and paratyphoid fever are highly endemic. The aim was to evaluate the source and transmission dynamics of typhoid and paratyphoid fever in Taiwan by using genomic analysis.

METHODS

During 2012-2019, 15 clinical isolates of Salmonella Typhi and S. Paratyphi A were collected. Demographic and clinical information of the infections were analyzed. We performed whole genome sequencing and evolutionary analysis on these isolates.

RESULTS

Clinical and microbiological data from 7 S. Typhi and 8 S. Paratyphi A isolates in Taiwan showed epidemiological and bacterial genomic link to the infection in South and Southeast Asia. The Taiwanese typhoidal isolates also share highly similar genomes with those collected from UK, indicating global circulation of the typhoidal clones. Local transmission of the imported but indigenized international clones was observed. Mutations occurring at gyrA 83 aa, including S83Y and S83F, were identified in the ciprofloxacin-resistant strains.

CONCLUSION

Due to the advance of global transportation and communication, the transmission mode of infectious disease has been modified. Domestic typhoid and paratyphoid fever caused by international resistant clones can occur in low-incidence countries. Genome analysis showed that the indigenous clone originally imported from other countries has been circulating in Taiwan for over a decade.

The global emergence of a novel Streptococcus suis clade associated with human infections

Streptococcus suis, a ubiquitous bacterial colonizer in pigs, has recently extended host range to humans, leading to a global surge of deadly human infections and three large outbreaks since 1998. To better understand the mechanisms for the emergence of cross-species transmission and virulence in human, we have sequenced 366 S. suis human and pig isolates from 2005 to 2016 and performed a large-scale phylogenomic analysis on 1,634 isolates from 14 countries over 36 years. We show the formation of a novel human-associated clade (HAC) diversified from swine S. suis isolates. Phylogeographic analysis identified Europe as the origin of HAC, coinciding with the exportation of European swine breeds between 1960s and 1970s. HAC is composed of three sub-lineages and contains several healthy-pig isolates that display high virulence in experimental infections, suggesting healthy-pig carriers as a potential source for human infection. New HAC-specific genes are identified as promising markers for pathogen detection and surveillance. Our discovery of a human-associated S. suis clade provides insights into the evolution of this emerging human pathogen and extend our understanding of S. suis epidemics worldwide.

In vivo Emergence of Colistin Resistance in Carbapenem-Resistant Klebsiella pneumoniae Mediated by Premature Termination of the mgrB Gene Regulator

Multidrug-resistant (MDR) Klebsiella pneumoniae is a severe threat to public health worldwide. Worryingly, colistin resistance, one of the last-line antibiotics for the treatment of MDR K. pneumoniae infection, has been increasingly reported. This study aims to investigate the emergence of evolved colistin resistance in a carbapenem-resistant K. pneumoniae isolate during colistin treatment. In this study, a pair of sequential carbapenem-resistant K. pneumoniae isolates were recovered from the same patient before and after colistin treatment, named KP1-1 and KP1-2, respectively. Antibiotic susceptibility testing was performed by the microdilution broth method. Whole genome sequencing was performed, and putative gene variations were analyzed in comparison of the genome sequence of both isolates. The bacterial whole genome sequence typing and source tracking analysis were performed by BacWGSTdb 2.0 server. Validation of the role of these variations in colistin resistance was examined by complementation experiments. The association between colistin resistance and the expression level of PhoP/PhoQ signaling system and its regulated genes was evaluated by quantitative real-time PCR (qRT-PCR) assay. Our study indicated that KP1-1 displayed extensively antibiotic resistant trait, but only susceptible to colistin. KP1-2 showed additional resistance to colistin. Both isolates belonged to Sequence Type 11 (ST11). The whole genome sequence analysis uncovered multiple resistance genes and virulence genes in both isolates. No plasmid-mediated mcr genes were found, but genetic variations in five chromosomal genes, especially the Gln30^∗ alteration in MgrB, were detected in colistin-resistant isolate KP1-2. Moreover, only complementation with wild-type mgrB gene restored colistin susceptibility, with colistin MIC decreased from 32 to 1 mg/L. Expression assays revealed an overexpression of the phoP, phoQ, and pmrD genes in the mgrB-mutated isolate KP1-2 compared to the wild-type isolate KP1-1, confirming the MgrB alterations was responsible for increased expression levels of those genes. This study provides direct in vivo evidence that Gln30^∗ alteration of MgrB is a critical region responsible for colistin resistance in K. pneumoniae clinical strains.

Coexistence of two blaCTX-M-14 genes in a blaNDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China

OBJECTIVES

The emergence of carbapenem-resistant Enterobacteriaceae has become a serious public-health threat. Here we report the complete genome sequence of a multidrug-resistant (MDR) Escherichia coli carrying bla_NDM-5 and two copies of bla_CTX-M-14 recovered from a bloodstream infection in China.

METHODS

Whole-genome sequencing of E. coli strain 2D was performed both using Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicons were identified from the genome sequence. Core genome MLST (cgMLST) analysis between E. coli 2D and all ST354 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server.

RESULTS

The complete genome sequence of E. coli 2D consists of six contigs comprising 5 363 300 bp, including one chromosome and five plasmids, and was assigned to ST354. Six antimicrobial resistance genes were identified, including bla_NDM-5 located in a 46 161-bp IncX3 plasmid and two copies of the bla_CTX-M-14 gene located both in the chromosome and in a 96 499-bp IncB plasmid. The closest relative of E. coli 2D was another isolate recovered from Lebanon, which differed by 162 cgMLST loci.

CONCLUSION

This study reports the first genome sequence of a MDR E. coli carrying bla_NDM-5 and two copies of bla_CTX-M-14 in China. These data may help to understand the antimicrobial resistance mechanisms and transmission dynamics of carbapenem-resistant Enterobacteriaceae in clinical settings.

Cracking the Challenge of Antimicrobial Drug Resistance with CRISPR/Cas9, Nanotechnology and Other Strategies in ESKAPE Pathogens

Antimicrobial resistance is mushrooming as a silent pandemic. It is considered among the most common priority areas identified by both national and international agencies. The global development of multidrug-resistant strains now threatens public health care improvement by introducing antibiotics against infectious agents. These strains are the product of both continuous evolution and unchecked antimicrobial usage (AMU). The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are the leading cause of nosocomial infections throughout the world. Most of them are now multidrug-resistant, which pose significant challenges in clinical practice. Understanding these bacteria’s resistance mechanisms is crucial for developing novel antimicrobial agents or other alternative tools to fight against these pathogens. A mechanistic understanding of resistance in these pathogens would also help predict underlying or even unknown mechanisms of resistance of other emerging multidrug-resistant pathogens. Research and development to find better antibacterial drugs and research on tools like CRISPER-Cas9, vaccines, and nanoparticles for treatment of infections that can be further explored in the clinical practice health sector have recognized these alternatives as essential and highly effective tools to mitigate antimicrobial resistance. This review summarizes the known antimicrobial resistance mechanisms of ESKAPE pathogens and strategies for overcoming this resistance with an extensive overview of efforts made in this research area.

MDR Salmonella enterica serovar Typhimurium ST34 carrying mcr-1 isolated from cases of bloodstream and intestinal infection in children in China

OBJECTIVES

Children are vulnerable to Salmonella infection due to their immature immune system. Cases of infection with mcr-1-harbouring Salmonella in child inpatients have not been reported in China before.

METHODS

Salmonella isolates from gastroenteritis and bacteraemia were screened using primers targeting mcr-1. Complete genome sequences of mcr-1-harbouring isolates were determined using the PacBio RS II platform. The transferability of mcr-1-harbouring plasmids was verified by conjugation.

RESULTS

We investigated two mcr-1-carrying polymyxin-resistant Salmonella enterica serovar Typhimurium ST34 isolates, S61394 and S44712, from bloodstream and intestinal Salmonella infection of two child inpatients, respectively. Both isolates were non-susceptible to commonly used antibiotics for children that compromised the success of clinical treatment and infection control. The mcr-1-harbouring plasmids pLS61394-MCR and pLS44712-MCR (from S61394 and S44712, respectively) were both conjugative pHNSHP45-2-like IncHI2-type epidemic plasmids carrying multiple resistance genes. Compared with pHNSHP45-2, a ∼33 kb insertion region encoding Tn7 transposition protein and heavy metal resistance proteins was identified in pLS61394-MCR, which might enhance adaptation of bacteria carrying this plasmid to various ecological niches. The phylogenetic tree of worldwide mcr-harbouring Salmonella indicated a host preference of mcr and a worldwide and cross-sectoral prevalence of the mcr-positive Salmonella ST34 clone.

CONCLUSIONS

To our knowledge, for the first time we report completed whole genomes of mcr-1-positive MDR Salmonella Typhimurium ST34 isolated from infected children in China, suggesting that improved surveillance is imperative for tackling the dissemination of mcr-harbouring MDR Salmonella Typhimurium ST34.

Combining Functional Genomics and Whole-Genome Sequencing to Detect Antibiotic Resistance Genes in Bacterial Strains Co-Occurring Simultaneously in a Brazilian Hospital

(1) Background: The rise of multi-antibiotic resistant bacteria represents an emergent threat to human health. Here, we investigate antibiotic resistance mechanisms in bacteria of several species isolated from an intensive care unit in Brazil. (2) Methods: We used whole-genome analysis to identify antibiotic resistance genes (ARGs) and plasmids in 34 strains of Gram-negative and Gram-positive bacteria, providing the first genomic description of Morganella morganii and Ralstonia mannitolilytica clinical isolates from South America. (3) Results: We identified a high abundance of beta-lactamase genes in resistant organisms, including seven extended-spectrum beta-lactamases (OXA-1, OXA-10, CTX-M-1, KPC, TEM, HYDRO, BLP) shared between organisms from different species. Additionally, we identified several ARG-carrying plasmids indicating the potential for a fast transmission of resistance mechanism between bacterial strains. Furthermore, we uncovered two pairs of (near) identical plasmids exhibiting multi-drug resistance. Finally, since many highly resistant strains carry several different ARGs, we used functional genomics to investigate which of them were indeed functional. In this sense, for three bacterial strains (Escherichia coli, Klebsiella pneumoniae, and M. morganii), we identified six beta-lactamase genes out of 15 predicted in silico as those mainly responsible for the resistance mechanisms observed, corroborating the existence of redundant resistance mechanisms in these organisms. (4) Conclusions: Systematic studies similar to the one presented here should help to prevent outbreaks of novel multidrug-resistant bacteria in healthcare facilities.

Genomic and phylogenetic analysis of multidrug-resistant Achromobacter xylosoxidans ST273 strain MTYH1 co-carrying blaOXA-114g and blaCARB-2 recovered from a wound infection in China

OBJECTIVES

Achromobacter xylosoxidans is widely distributed in the environment and is increasingly recognised as a significant nosocomial pathogen in healthcare settings. However, the genomic and phylogenetic characteristics of this pathogen are not fully understood. Here we report the first genome sequence of a multidrug-resistant A. xylosoxidans ST273 strain (MTYH1) isolated from a wound infection in China.

METHODS

Whole-genome sequencing of the strain was performed using an Illumina NovaSeq 6000 platform. Generated short reads were de novo assembled into contigs using SPAdes v.3.13.0. Antimicrobial resistance genes (ARGs) were identified using ResFinder 4.0. Phylogenetic analysis was conducted using NJ/UPGMA phylogeny (MAFFT v.7) based on core genome single nucleotide polymorphism data.

RESULTS

The draft genome sequence of A. xylosoxidans ST273 strain MTYH1 consists of 45 contigs comprising 6 643 045 bp with a GC content of 67.5%. According to the Achromobacter spp. multilocus sequence typing (MLST) scheme, MTYH1 belongs to ST273. MTYH1 is resistant to aminoglycosides, ciprofloxacin, aztreonam and cephalosporins. Five ARGs belonging to three different classes were identified in the genome, namely aac(6')-IIa, ant(2'')-Ia, bla_CARB-2, bla_OXA-114g and sul1. Phylogenetic analysis showed that MTYH1 was not epidemiologically related to any of the strains retrieved from the NCBI GenBank database.

CONCLUSION

We unravelled the genome sequence of multidrug-resistant A. xylosoxidans ST273 clinical strain MTYH1 recovered from a wound infection in China. Our data may help to understand the antimicrobial resistance mechanisms, genomic features and phylogenetic characteristic of this bacterial pathogen.

The Plasmid-Borne tet(A) Gene Is an Important Factor Causing Tigecycline Resistance in ST11 Carbapenem-Resistant Klebsiella pneumoniae Under Selective Pressure

The emergence and prevalence of tigecycline-resistant Klebsiella pneumoniae have seriously compromised the effectiveness of antimicrobial agents in the treatment of infections. To explore the role of the plasmid-borne tet(A) gene in tigecycline resistance in carbapenem-resistant K. pneumoniae (CRKP), a total of 63 CRKP isolates were collected from a tertiary hospital in Hangzhou, China. The minimum inhibitory concentration (MIC) of tigecycline, mutation rate of tet(A) gene, genetic surroundings of tet(A)-carrying transmissible plasmid and the contribution of tet(A) mutation to tigecycline resistance were analyzed using antimicrobial susceptibility test, whole-genome sequencing, tigecycline resistance evolution experiment, and plasmid conjugation experiment. Our results showed that 52.4% (33 isolates) of the test isolates carried the tet(A) gene; among them, 75.8% (25 isolates) exhibited a tigecycline non-susceptible phenotype (MIC = 4 mg/L). Three clonal groups (cluster I, cluster II, and cluster III) were identified in these tet(A)-bearing isolates. All 17 isolates belonged to serotype KL21 (cluster I), which differed by only 13 SNPs, suggesting a clonal spread of tet(A)-positive ST11 K. pneumoniae with serotype KL21 occurred in the sampling hospital. The induction of tigecycline resistance experiments showed that 71.4% of strains evolved tet(A) mutations and developed a high-level tigecycline resistance. Eight amino acid substitutions were identified in these mutants. The most common amino acid substitution was A370V, followed by S251A and G300E. Twelve isolates carrying tet(A) mutants succeeded in the filter mating experiment with a conjugation efficiency of 10^-3-10^-8. Tigecycline MICs in E. coli EC600 transconjugants with a mutated tet(A) were 2 to 8-fold higher than those in E. coli EC600 transconjugants with a wild-type tet(A). One ColRNAI/IncFII type and two IncFII type tet(A)-bearing conjugative plasmids were identified in this study, including a class 1 integron containing multiple antibiotic resistance genes, i.e., tet(A), qnrS1, bla _{LAP- 2}, catA2, sul2, and dfrA14. Our study revealed the wide-spread situation of plasmid-borne tet(A) gene in clinical CRKP, and mutation of tet(A) is a potential driven force that lead to tigecycline resistance.