Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids

Extraintestinal pathogenic Escherichia coli (ExPEC) are the most frequent cause of urinary tract infections (UTIs) globally. Most studies of clinical E. coli isolates are selected based on their antimicrobial resistance (AMR) phenotypes; however, this selection bias may not provide an accurate portrayal of which sequence types (STs) cause the most disease. Here, whole genome sequencing (WGS) was performed on 320 E. coli isolates from urine samples sourced from a regional hospital in Australia in 2006. Most isolates (91%) were sourced from patients with UTIs and were not selected based on any AMR phenotypes. No significant differences were observed in AMR and virulence genes profiles across age sex, and uro-clinical syndromes. While 88 STs were identified, ST73, ST95, ST127 and ST131 dominated. F virulence plasmids carrying senB-cjrABC (126/231; 55%) virulence genes were a feature of this collection. These senB-cjrABC+ plasmids were split into two categories: pUTI89-like (F29:A- :B10 and/or >95% identity to pUTI89) (n=73) and non-pUTI89-like (n=53). Compared to all other plasmid replicons, isolates with pUTI89-like plasmids carried fewer antibiotic resistance genes (ARGs), whilst isolates with senB-cjrABC+/non-pUTI89 plasmids had a significantly higher load of ARGs and class 1 integrons. F plasmids were not detected in 89 genomes, predominantly ST73. Our phylogenomic analyses identified closely related isolates from the same patient associated with different pathologies and evidence of strain-sharing events involving isolates sourced from companion and wild animals.Dmitriy Li, Paarthiphan Elankumaran, Timothy Kudinha, Amanda K. Kidsley, Darren J. Trott, Veronica Maria Jarocki, and Steven Philip Djordjevi

Genomic comparisons of Escherichia coli ST131 from Australia.

Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli 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 E. coli 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. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH41, 2 fimH89, 1 fimH141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron-integrase intI1, 128 (45 %) isolates harboured a truncated intI1 (462-1014 bp), highlighting the ongoing evolution of this element. The module intI1-dfrA17-aadA5-qacEΔ1-sul1-ORF-chrA-padR-IS1600-mphR-mrx-mphA, conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27. Notably, dual parC-1aAB and gyrA-1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries diverse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across diverse reservoirs

Prevalence of coagulase-negative staphylococci in bovine mastitis in Zimbabwe

This study was carried out to determine the prevalence of coagulase-negative staphylococci in clinical and subclinical mastitis in commercial and small-scale farms in Zimbabwe. Thirty five quarter milk samples from clinical mastitis cases and 371 quarter milk samples from cows with subclinical mastitis were cultured for bacterial pathogens. The most frequent pathogens isolated in clinical mastitis were the enteric bacteria (31.4 %), followed by coagulase negative staphylococci (22.9 %) and then Staphylococcus aureus (17.1 %), whereas in subclinical mastitis S. aureus (34.2 %) and coagulase-negative staphylococci were (33.2 %) the most common. Bacillus species were only isolated in milk samples from subclinical mastitis. Coagulase-negative staphylococci were observed in mixed infections with other bacteria in only 2.2 % of the 406 milk samples from clinical and subclinical mastitis where they were isolated together with Bacillus species in 6 of the 9 mixed infection cases. About 95 % of the milk samples from which 131 coagulase-negative staphylococci were isolated had correspondingly high somatic cell counts. The coagulase-negative staphylococci isolated most frequently were S. chromogenes (7.9 %), S. epidermidis (7.4 %) and S. hominis (5.9 %). They were all associated with high somatic cell counts. All the coagulase-negative staphylococci isolates were susceptible to cloxacillin and erythromycin, and more than 90 %of the isolates were susceptible to neomycin, penicillin and streptomycin. The highest resistance was to tetracycline (17.6 %), followed by lincomycin (13.7 %). About 8 % of the isolates were resistant to both penicillin and streptomycin

Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections.

Urinary tract infections (UTIs) are the most common bacterial infections requiring medical attention and a leading justification for antibiotic prescription. Trimethoprim is prescribed empirically for uncomplicated cases. UTIs are primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) and ExPEC strains play a central role in disseminating antimicrobial-resistance genes worldwide. Here, we describe the whole-genome sequences of trimethoprim-resistant ExPEC and/or ExPEC from recurrent UTIs (67 in total) from patients attending a regional Australian hospital from 2006 to 2008. Twenty-three sequence types (STs) were observed, with ST131 predominating (28 %), then ST69 and ST73 (both 7 %). Co-occurrence of trimethoprim-resistance genes with genes conferring resistance to extended-spectrum β-lactams, heavy metals and quaternary ammonium ions was a feature of the ExPEC described here. Seven trimethoprim-resistance genes were identified, most commonly dfrA17 (38 %) and dfrA12 (18 %). An uncommon dfrB4 variant was also observed. Two blaCTX-M variants were identified - blaCTX-M-15 (16 %) and blaCTX-M-14 (10 %). The former was always associated with dfrA12, the latter with dfrA17, and all blaCTX-M genes co-occurred with chromate-resistance gene chrA. Eighteen class 1 integron structures were characterized, and chrA featured in eight structures; dfrA genes featured in seventeen. ST131 H30Rx isolates possessed distinct antimicrobial gene profiles comprising aac(3)-IIa, aac(6)-Ib-cr, aph(3')-Ia, aadA2, blaCTX-M-15, blaOXA-1 and dfrA12. The most common virulence-associated genes (VAGs) were fimH, fyuA, irp2 and sitA (all 91 %). Virulence profile clustering showed ST131 H30 isolates carried similar VAGs to ST73, ST405, ST550 and ST1193 isolates. The sole ST131 H27 isolate carried molecular predictors of enteroaggregative E. coli/ExPEC hybrid strains (aatA, aggR, fyuA). Seven isolates (10 %) carried VAGs suggesting ColV plasmid carriage. Finally, SNP analysis of serial UTI patients experiencing worsening sequelae demonstrated a high proportion of point mutations in virulence factors

National antimicrobial stewardship and fluoroquinolone-resistant Clostridium difficile in China

Meng Xiao,1,* Jing-Wei Cheng,1,2,* Timothy Kudinha,3 Fanrong Kong,4 Ying-Chun Xu1,21Department of Clinical Laboratory, Peking Union Medical College Hospital, 2Faculty of Clinical Laboratory Diagnostics, Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China; 3School of Biomedical Sciences, The Charles Sturt University, Leeds Parade, Orange, 4Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR–Pathology West, Westmead Hospital, University of Sydney, Westmead, NSW, Australia*These authors contributed equally to this workIn a recent report, Dingle et al showed that national intervention programs aimed at judicious antimicrobial usage, especially restrictions to fluoroquinolones, contributed to a significant decrease in Clostridium difficile infection (CDI) in England.1 This is considered an outstanding achievement in combating antimicrobial resistance worldwide

Escherichia coli sequence type 131 (ST131) as a prominent cause of antibiotic resistance among clinical and fecal Escherichia coli isolates from reproductive-age women

The recent emergence of multidrug-resistantEscherichia colisequence type 131 (ST131) has coincided with an increase in general antibiotic resistance ofE. coli, suggesting that ST131 has a contributing role in resistance. However, there is little information about the contribution of ST131 to different clinical syndromes or the basis for its impressive emergence and epidemic spread. To investigate this, we studied 953E. coliisolates from women of reproductive age in the central west region of New South Wales, Australia, including 623 urinary isolates from patients with cystitis (cystitis isolates) (n 322) or pyelonephritis (pyelonephritis isolates) (n 301) and 330 fecal isolates from healthy controls. The characteristics studied included ST131 clonal group status, resistance to different antibiotics, presence of virulence factor (VF) genes, and biofilm production. As expected, fecal isolates differed significantly from urinary (cystitis and pyelonephritis) isolates in most of the studied characteristics. Antibiotic resistance was significantly more common in ST131 than in non-ST131 isolates. Both antibiotic resistance and ST131 were more common in pyelonephritis than cystitis isolates and least so among fecal isolates. Within each source group, individual VF genes were more prevalent and VF scores were higher for ST131 than for non-ST131 isolates. For ST131 only, the prevalences of most individual VF genes and VF scores were the lowest in the fecal isolates, higher in the cystitis isolates, and highest in the pyelonephritis isolates. Biofilm production was strongly associated with ST131 status and antibiotic resistance. These results clarify the distribution of the ST131 clonal group and its epidemiological associations in our region and suggest that it exhibits both enhanced virulence and increased antibiotic resistance compared with those of other urinary tract infection (UTI) and fecalE. coliisolates from women of reproductive ageOffice of Research and Development, Medical Research Service, Department of Veterans Affairs, grant no. 1 I01 CX000192 01 (to J.R.J.)

Distribution of phylogenetic groups, sequence type ST131, and virulence-associated traits among Escherichia coli isolates from men with pyelonephritis or cystitis and healthy controls

AbstractUrinary tract infections (UTI), which are mostly caused by Escherichia coli, are an important public health problem worldwide. Although men experience diverse UTI syndromes, there have been relatively few molecular-epidemiological studies of UTI pathogenesis in men. We studied the distribution of 22 E. coli virulence factor (VF) genes, major phylogenetic groups, sequence type ST131, and UTI-associated O antigens among 101 pyelonephritis, 153 cystitis and 135 fecal healthy control E. coli isolates from men aged 30–70 years in a regional area of NSW, Australia. Overall, the studied traits exhibited a prevalence gradient across these groups, highest in pyelonephritis, intermediate in cystitis, and lowest among fecal isolates. Differences in virulence gene prevalence between cystitis and pyelonephritis isolates were limited to eight genes. The UTI-associated O antigens were also distributed widely, but types O6, O25 and O75 were significantly associated with pyelonephritis. The ST131 clonal group, which accounted for 13% of isolates overall (22% of group B2 isolates), likewise exhibited a significant descending prevalence gradient from pyelonephritis (36%), through cystitis (8%), to fecal (0%) isolates. These findings contribute to better understanding of the pathogenesis of UTIs in men and identify specific VF genes and O types, and a prominent clonal group (ST131), as being important in UTI pathogenesis in this population

Escherichia coli sequence type 131 (ST131) as a prominent cause of antibiotic resistance among clinical and fecal Escherichia coli isolates from reproductive-age women

The recent emergence of multidrug-resistantEscherichia colisequence type 131 (ST131) has coincided with an increase in general antibiotic resistance ofE. coli, suggesting that ST131 has a contributing role in resistance. However, there is little information about the contribution of ST131 to different clinical syndromes or the basis for its impressive emergence and epidemic spread. To investigate this, we studied 953E. coliisolates from women of reproductive age in the central west region of New South Wales, Australia, including 623 urinary isolates from patients with cystitis (cystitis isolates) (n 322) or pyelonephritis (pyelonephritis isolates) (n 301) and 330 fecal isolates from healthy controls. The characteristics studied included ST131 clonal group status, resistance to different antibiotics, presence of virulence factor (VF) genes, and biofilm production. As expected, fecal isolates differed significantly from urinary (cystitis and pyelonephritis) isolates in most of the studied characteristics. Antibiotic resistance was significantly more common in ST131 than in non-ST131 isolates. Both antibiotic resistance and ST131 were more common in pyelonephritis than cystitis isolates and least so among fecal isolates. Within each source group, individual VF genes were more prevalent and VF scores were higher for ST131 than for non-ST131 isolates. For ST131 only, the prevalences of most individual VF genes and VF scores were the lowest in the fecal isolates, higher in the cystitis isolates, and highest in the pyelonephritis isolates. Biofilm production was strongly associated with ST131 status and antibiotic resistance. These results clarify the distribution of the ST131 clonal group and its epidemiological associations in our region and suggest that it exhibits both enhanced virulence and increased antibiotic resistance compared with those of other urinary tract infection (UTI) and fecalE. coliisolates from women of reproductive ageOffice of Research and Development, Medical Research Service, Department of Veterans Affairs, grant no. 1 I01 CX000192 01 (to J.R.J.)

Molecular epidemiology of Clostridium difficile in two tertiary care hospitals in Shandong Province, China

Ying Luo,1,2 Wen Zhang,2 Jing-Wei Cheng,3 Meng Xiao,3 Gui-Rong Sun,1 Cheng-Jie Guo,2 Ming-Jun Liu,1 Pei-Shan Cong,1 Timothy Kudinha4,5 1Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, China; 2Department of Clinical Laboratory, Zibo Central Hospital, Zibo, China; 3Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China; 4Charles Sturt University, Orange, NSW, Australia; 5Central West Pathology Laboratory, Orange, NSW, Australia Purpose: The incidence and severity of Clostridium difficile infection (CDI) have markedly increased over the past decade. However, there is very limited epidemiological data on CDI in China so far, specifically no data in Shandong Province. The aim of this study was to evaluate diagnostic algorithm for CDI and to gain data on molecular epidemiology of CDI in the Shandong Province of China.Materials and methods: Nonrepetitive unformed fecal specimens (n=504) were investigated by the glutamate dehydrogenase (GDH), C. difficile toxin A&B (CDAB) tests and toxigenic culture. Furthermore, 85 isolates were characterized by toxin gene detection, multilocus sequence typing, ribotyping and antimicrobial susceptibility testing.Results: The algorithm of combining GDH and CDAB tests could define diagnosis of 54.2% CDI cases and excluded 90% of non-CDI. Further adding the toxigenic culture to the algorithm enhanced the detection sensitivity to 100%. Toxigenic strains comprised 84.7% of isolates, including A+B+CDT− (71.8%, 61/85), A–B+CDT– (11.8%, 10/85) and A+B+CDT+ (1.2%, 1/85) isolates. RT046/ST35 (13.9%, 10/72), RT014/ST2 (12.5%, 9/72) and RT017/ST37 (12.5%, 9/72) were the more common genotypes among toxigenic C. difficile strains. The clinical severity score of A–B+CDT– toxin genes genotype (3.50±0.85) was significantly higher than the A+B+CDT– type (2.59±0.93) (P<0.05). RT046/ST35 isolates were highly prevalent and had high clinical severity scores (3.80±0.92). Variations in resistance from different sequence types (STs) were observed. Toxigenic strains showed higher resistance rates to erythromycin, clindamycin and ciprofloxacin compared to nontoxigenic strains (P<0.05). Conclusion: The epidemiology of C. difficile in Shandong Province differed from other regions in China. Comprehensive optimized diagnosis strategy and continuous surveillance should be established and applied in order to curb the spread of toxigenic C. difficile strains, especially for hospitalized patients.Keywords: Clostridium difficile, genotype, antimicrobial resistance, severity score, Shandong Province, China&nbsp