'Omics technologies for the elucidation of the molecular mechanisms related to carbapenem-resistant and extended spectrum β-lactamase-producing Klebsiellapneumoniae.

Klebsiella pneumoniae is a Gram-negative bacterium and a major cause of nosocomial infections such as urinary tract infections (UTIs), pneumonia and meningitis. Although these infections are commonly treated with the β-lactam group of antibiotics and combinations of it, (multi-)drug resistance in K. pneumoniae has steadily increased in the last few decades.

Phylogenomic analysis of a global collection of ST38: evidence of interspecies and environmental transmission?

Extraintestinal pathogenic (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific variants.

Genomic profiling of Pasteurella multocida isolated from feedlot cases of bovine respiratory disease.

Pasteurella multocida causes a range of diseases in many host species throughout the world, including bovine respiratory disease (BRD) which is predominantly seen in feedlot cattle. This study assessed genetic diversity among 139 P. multocida isolates obtained from post-mortem lung swabs of BRD-affected feedlot cattle in four Australian states: New South Wales, Queensland, South Australia, and Victoria during 2014-2019.

Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria.

Even in the setting of optimal resuscitation in high-income countries severe sepsis and septic shock have a mortality of 20-40%, with antibiotic resistance dramatically increasing this mortality risk. To develop a reference dataset enabling the identification of common bacterial targets for therapeutic intervention, we applied a standardized genomic, transcriptomic, proteomic and metabolomic technological framework to multiple clinical isolates of four sepsis-causing pathogens: Escherichia coli, Klebsiella pneumoniae species complex, Staphylococcus aureus and Streptococcus pyogenes. Exposure to human serum generated a sepsis molecular signature containing global increases in fatty acid and lipid biosynthesis and metabolism, consistent with cell envelope remodelling and nutrient adaptation for osmoprotection.

Correction: Alhamami et al. First Emergence of Resistance to Macrolides and Tetracycline Identified in and Isolates from Beef Feedlots in Australia. 2021, , 1322.

The authors wish to make the following corrections to this paper [...

Genomic comparisons of ST131 from Australia.

ST131 is a globally dispersed extraintestinal pathogenic lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 isolates from diverse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed.

First Emergence of Resistance to Macrolides and Tetracycline Identified in and Isolates from Beef Feedlots in Australia.

Bovine respiratory disease (BRD) causes high morbidity and mortality in beef cattle worldwide. Antimicrobial resistance (AMR) monitoring of BRD pathogens is critical to promote appropriate antimicrobial stewardship in veterinary medicine for optimal treatment and control. Here, the susceptibility of and isolates obtained from BRD clinical cases (deep lung swabs at post-mortem) among feedlots in four Australian states (2014-2019) was determined for 19 antimicrobial agents.

ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex.

The 30Rx subclade of ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal.

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

Antibiotic resistance genes (ARGs) including those from the family and that encode resistance to extended spectrum β-lactams and colistin, respectively, have been linked with IncHI2 plasmids isolated from swine production facilities globally but not in IncHI2 plasmids from Australia. Here we describe the first complete sequence of a multiple drug resistance Australian IncHI2-ST4 plasmid, pTZ41_1P, from a commensal from a healthy piglet. pTZ41_1P carries genes conferring resistance to heavy-metals (copper, silver, tellurium and arsenic), β-lactams, aminoglycosides and sulphonamides.

Whole-genome sequence analysis of environmental from the faeces of straw-necked ibis () nesting on inland wetlands.

Wildlife, and birds in particular, play an increasingly recognized role in the evolution and transmission of that pose a threat to humans. To characterize these lineages and their potential threat from an evolutionary perspective, we isolated and performed whole-genome sequencing on 11 sequence types (STs) of recovered from the desiccated faeces of straw-necked ibis () nesting on inland wetlands located in geographically different regions of New South Wales, Australia. Carriage of virulence-associated genes was limited, and no antimicrobial resistance genes were detected, but novel variants of an insertion element that plays an important role in capturing and mobilizing antibiotic resistance genes, IS, were identified and characterized.

Duplication and diversification of a unique chromosomal virulence island hosting the subtilase cytotoxin in ST58.

The AB cytotoxins are important virulence factors in . The most notable members of the AB toxin families include Shiga toxin families 1 (Stx) and 2 (Stx), which are associated with enterohaemorrhagic infections causing haemolytic uraemic syndrome and haemorrhagic colitis. The subAB toxins are the newest and least well understood members of the AB toxin gene family.

Genomic profiling of isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital.

This study sought to assess the genetic variability of isolated from bloodstream infections (BSIs) presenting at Concord Hospital, Sydney during 2013-2016. Whole-genome sequencing was used to characterize 81 isolates sourced from community-onset (CO) and hospital-onset (HO) BSIs. The cohort comprised 64 CO and 17 HO isolates, including 35 multidrug-resistant (MDR) isolates exhibiting phenotypic resistance to three or more antibiotic classes.

Molecular Analysis of an IncF ColV-Like Plasmid Lineage That Carries a Complex Resistance Locus with a Trackable Genetic Signature.

IncF ColV plasmids are important plasmid incompatibility group that are currently restricted to the Enterobacteriaceae. These plasmids carry an important repertoire of virulence-associated genes (VAGs) that contribute to the ability of avian pathogenic to cause disease in poultry. VAGs found on ColV plasmids have also been linked to urosepsis and meningitis in humans but the mechanisms that elicit these disease conditions are not well understood.

Osteoarticular Infection in Three Young Thoroughbred Horses Caused by a Novel Gram Negative Cocco-Bacillus.

We describe three cases of osteoarticular infection (OAI) in young thoroughbred horses in which the causative organism was identified by MALDI-TOF as . The pattern of OAI resembled that reported with infection in humans. Analysis by 16S rRNA PCR enabled construction of a phylogenetic tree that placed the isolates closer to and , rather than .

Genomic Island 1B Variant Found in a Sequence Type 117 Avian Pathogenic Escherichia coli Isolate.

genomic island 1 (SGI1) is an integrative genetic island first described in serovars Typhimurium DT104 and Agona in 2000. Variants of it have since been described in multiple serovars of , as well as in , , , and several other genera. The island typically confers resistance to older, first-generation antimicrobials; however, some variants carry , , and genes that encode resistance to frontline, clinically important antibiotics, including third-generation cephalosporins.

Identification of a novel lineage of plasmids within phylogenetically diverse subclades of IncHI2-ST1 plasmids.

IncHI2-ST1 plasmids play an important role in co-mobilizing genes conferring resistance to critically important antibiotics and heavy metals. Here we present the identification and analysis of IncHI2-ST1 plasmid pSPRC-Echo1, isolated from an Enterobacter hormaechei strain from a Sydney hospital, which predates other multi-drug resistant IncHI2-ST1 plasmids reported from Australia. Our time-resolved phylogeny analysis indicates pSPRC-Echo1 represents a new lineage of IncHI2-ST1 plasmids and show how their diversification relates to the era of antibiotics.

High contiguity genome sequence of a multidrug-resistant hospital isolate of .

Background: is an important emerging pathogen and a key member of the highly diverse complex. strains can persist and spread in nosocomial environments, and often exhibit resistance to multiple clinically important antibiotics. However, the genomic regions that harbour resistance determinants are typically highly repetitive and impossible to resolve with standard short-read sequencing technologies.

Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene.

Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains.

Multidrug Resistant Uropathogenic ST405 With a Novel, Composite IS Transposon in a Unique Chromosomal Location.

ST405 is an emerging urosepsis pathogen, noted for carriage of , , and a repertoire of virulence genes comparable with O25b:H4-ST131. Extraintestinal and multidrug resistant ST405 are poorly studied in Australia. Here we determined the genome sequence of a uropathogenic, multiple drug resistant ST405 (strain 2009-27) from the mid-stream urine of a hospital patient in Sydney, Australia, using a combination of Illumina and SMRT sequencing.

Genomic analysis of multidrug-resistant Escherichia coli ST58 causing urosepsis.

Sequence type 58 (ST58) phylogroup B1 Escherichia coli have been isolated from a wide variety of mammalian and avian hosts but are not noted for their ability to cause serious disease in humans or animals. Here we determined the genome sequences of two multidrug-resistant E. coli ST58 strains from urine and blood of one patient using a combination of Illumina and Single Molecule, Real-Time (SMRT) sequencing.

Corrigendum: , an Evolutionary Dead-End Pathogen.

[This corrects the article on p. 1054 in vol. 8, PMID: 28649238.

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26.

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E.