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1.
Int J Food Microbiol ; 340: 109042, 2021 Feb 16.
Artículo en Inglés | MEDLINE | ID: mdl-33461002

RESUMEN

The development of antimicrobial resistance in foodborne pathogens is a growing public health concern. This study was undertaken to determine the antimicrobial susceptibility of Salmonella enterica subspecies enterica isolated from the Australian commercial egg layer industry. S. enterica subspecies enterica (n=307) isolated from Australian commercial layer flock environments (2015-2018) were obtained from reference, research and State Government laboratories from six Australian states. All Salmonella isolates were serotyped. Antimicrobial susceptibility testing (AST) for 16 antimicrobial agents was performed by broth microdilution. Antimicrobial resistance genes and sequence types (STs) were identified in significant isolates by whole genome sequencing (WGS). Three main serotypes were detected, S. Typhimurium (n=61, 19.9%), S. Senftenburg (n=45, 14.7%) and S. Agona (n=37, 12.1%). AST showed 293/307 (95.4%) isolates were susceptible to all tested antimicrobial agents and all isolates were susceptible to amoxicillin-clavulanate, azithromycin, ceftiofur, ceftriaxone, ciprofloxacin, colistin, florfenicol, gentamicin, kanamycin and trimethoprim-sulfamethoxazole. Low levels of non-susceptibility were observed to streptomycin (2.3%, n=7), sulfisoxazole (2.0%, n=6), chloramphenicol (1.3%, n=4) and tetracycline (1.0%, n=3). Very low levels of non-susceptibility were observed to ampicillin (2/307; 0.7%) and cefoxitin (2/307; 0.7%). Two isolates (S. Havana and S. Montevideo), exhibited multidrug-resistant phenotypes to streptomycin, sulfisoxazole and tetracycline and possessed corresponding antimicrobial resistance genes (aadA4, aac(6')-Iaa, sul1, tetB). One S. Typhimurium isolate was resistant to ampicillin and tetracycline, and possessed both tetA and blaTEM-1B. WGS also identified these isolates as belonging to ST4 (S. Montevideo), ST578 (S. Havana) and ST19 (S. Typhimurium). The absence of resistance to highest priority critically important antimicrobials as well as the extremely low level of AMR generally among Australian commercial egg layer Salmonella isolates likely reflect Australia's conservative antimicrobial registration policy in food-producing animals and low rates of antimicrobial use within the industry.

2.
J Glob Antimicrob Resist ; 23: 311-314, 2020 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-33010486

RESUMEN

OBJECTIVES: This report describes the first identification of two Campylobacter isolates harbouring erm(B) in Australia. METHODS: Two erm(B)-positive isolates, Campylobacter coli 18V1065H1 and Campylobacter jejuni 19W1001H1, were isolated from diarrhoeal faecal samples from two travellers who had recently returned from Southeast Asia. Isolates underwent whole-genome sequencing using an Illumina NextSeq system and were analysed with the Nullarbor pipeline. Antimicrobial resistance genes were identified using AMRFinderPlus and sequence types (STs) were determined by multilocus sequence typing and the PubMLST Campylobacter jejuni/coli typing scheme. RESULTS: Besideserm(B), C. jejuni 19W1001H1 possessed six other resistance genes [aad9, aadE, aph(3')-Illa, blaOXA-185, catA13 and tet(O)], the gyrA T86I mutation and the RE-CmeABC multidrug efflux pump variant. Campylobacter coli 18V1065H1 also possessed six resistance genes [aad9, aadE, aph(3')-IIIa, blaOXA-61, sat4 and tet(O)] in addition to erm(B); however, this isolate lacked genetic evidence for resistance to fluoroquinolones (no gyrA mutation). The erm(B) locus differed between isolates and neither was identical to previously identified erm(B) multidrug resistance genomic island (MDRGI) types. Both erm(B)-bearing isolates belonged to novel sequence types: ST9967 (C. jejuni 19W1001H1) and ST10161 (C. coli 18V1065H1). CONCLUSIONS: This study detected the presence oferm(B) in Campylobacter for the first time in Australia. This novel mechanism of macrolide resistance is a major concern both for human and animal health and warrants close surveillance as macrolides are often the drug of choice for treating campylobacteriosis. The erm(B) gene is associated with several MDRGIs and dissemination of this resistance mechanism will likely limit treatment options for Campylobacter infections.

3.
Antimicrob Agents Chemother ; 64(12)2020 11 17.
Artículo en Inglés | MEDLINE | ID: mdl-33020158

RESUMEN

In Australia, cases of shigellosis usually occur in returned travelers from regions of shigellosis endemicity or in men who have sex with men. Resistance to multiple antibiotics has significantly increased in Shigella sonnei isolates and represents a significant public health concern. We investigate an outbreak of multidrug-resistant S. sonnei in Victoria, Australia. We undertook whole-genome sequencing of 54 extended-spectrum-beta-lactamase (ESBL)-producing S. sonnei isolates received at the Microbiological Diagnostic Unit Public Health Laboratory between January 2019 and March 2020. The population structure and antimicrobial resistance profiles were identified by genomic analyses, with 73 previously characterized Australian S. sonnei isolates providing context. Epidemiological data, including age and sex of the shigellosis cases, were also collected. There was a significant increase in cases of ESBL S. sonnei from July 2019. Most of the ESBL S. sonnei isolates (65%) fell within a single cluster that was predominantly comprised of male cases that were characterized by the presence of the bla CTX-M-27 gene conferring resistance to extended-spectrum cephalosporins. These isolates were also multidrug resistant, including resistance to azithromycin and co-trimoxazole and reduced susceptibility to ciprofloxacin. Our data uncovered a prolonged clonal outbreak of ESBL S. sonnei infection that was likely first introduced by returned travelers and has subsequently been circulating locally in Australia. The emergence of a local outbreak of ESBL S. sonnei with a multidrug-resistant profile, including reduced susceptibility to ciprofloxacin, represents a significant public health threat.

4.
Microb Drug Resist ; 2020 Sep 08.
Artículo en Inglés | MEDLINE | ID: mdl-32898460

RESUMEN

The study investigates the prevalence of antimicrobial resistance in Campylobacter jejuni and Campylobacter coli in gastroenteritis patients in the eight most populous regions in Australia and compares the prevalence of antimicrobial resistance in Europe and North America. A total of 164 Campylobacter isolates were collected from patients with campylobacteriosis and tested for susceptibility to six antimicrobials using ETEST® strips and compared with reports from Europe and the United States. Genomes were sequenced on Illumina NextSeq to identify genetic determinants of resistance. Phenotypically, 1.8%, 14.0%, 14.6%, and 20.1% of isolates were resistant to erythromycin (ERY), ampicillin, tetracycline (TET), and ciprofloxacin (CIP), respectively. Comparing published phenotypic results of antimicrobial resistance in several European countries and the United States with these Australian isolates reveals that rates observed in Australia are among the lowest observed for ERY, CIP, and TET for both C. coli and C. jejuni. For each antimicrobial tested, concordance between resistance phenotype and genotype ranged from 66.6% to 100.0%. This study highlights that, among industrialized countries, Portugal and Spain have very high levels of antimicrobial resistance in C. jejuni and C. coli, especially when compared with the United Kingdom, United States, and Australia.

5.
Appl Environ Microbiol ; 86(19)2020 09 17.
Artículo en Inglés | MEDLINE | ID: mdl-32737126

RESUMEN

Salmonella enterica serovar Hvittingfoss is an important foodborne serotype of Salmonella, being detected in many countries where surveillance is conducted. Outbreaks can occur, and there was a recent multistate foodborne outbreak in Australia. S Hvittingfoss can be found in animal populations, though a definitive animal host has not been established. Six species of birds were sampled at Roebuck Bay, a designated Ramsar site in northwestern Australia, resulting in 326 cloacal swabs for bacterial culture. Among a single flock of 63 bar-tailed godwits (Limosa lapponica menzbieri) caught at Wader Spit, Roebuck Bay, in 2018, 17 (27%) were culture positive for Salmonella All other birds were negative for Salmonella The isolates were identified as Salmonella enterica serovar Hvittingfoss. Phylogenetic analysis revealed a close relationship between isolates collected from godwits and the S Hvittingfoss strain responsible for a 2016 multistate foodborne outbreak originating from tainted cantaloupes (rock melons) in Australia. While it is not possible to determine how this strain of S Hvittingfoss was introduced into the bar-tailed godwits, these findings show that wild Australian birds are capable of carrying Salmonella strains of public health importance.IMPORTANCE Salmonella is a zoonotic pathogen that causes gastroenteritis and other disease presentations in both humans and animals. Serovars of S. enterica commonly cause foodborne disease in Australia and globally. In 2016-2017, S Hvittingfoss was responsible for an outbreak that resulted in 110 clinically confirmed human cases throughout Australia. The origin of the contamination that led to the outbreak was never definitively established. Here, we identify a migratory shorebird, the bar-tailed godwit, as an animal reservoir of S Hvittingfoss. These birds were sampled in northwestern Australia during their nonbreeding period. The presence of a genetically similar S Hvittingfoss strain circulating in a wild bird population, 2 years after the 2016-2017 outbreak and ∼1,500 km from the suspected source of the outbreak, demonstrates a potentially unidentified environmental reservoir of S Hvittingfoss. While the birds cannot be implicated in the outbreak that occurred 2 years prior, this study does demonstrate the potential role for wild birds in the transmission of this important foodborne pathogen.


Asunto(s)
Enfermedades de las Aves/epidemiología , Charadriiformes , Salmonelosis Animal/epidemiología , Salmonella enterica/aislamiento & purificación , Animales , Enfermedades de las Aves/microbiología , Femenino , Incidencia , Masculino , Prevalencia , Salmonelosis Animal/microbiología , Serogrupo , Australia Occidental/epidemiología
6.
PLoS One ; 15(7): e0236889, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32730330

RESUMEN

Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.


Asunto(s)
Antibacterianos/farmacología , Infecciones por Campylobacter/microbiología , Campylobacter coli/genética , Campylobacter jejuni/genética , Farmacorresistencia Bacteriana/genética , Carne/análisis , Animales , Infecciones por Campylobacter/tratamiento farmacológico , Infecciones por Campylobacter/genética , Campylobacter coli/efectos de los fármacos , Campylobacter coli/aislamiento & purificación , Campylobacter jejuni/efectos de los fármacos , Campylobacter jejuni/aislamiento & purificación , Bovinos , Pollos , ADN Bacteriano/genética , Microbiología de Alimentos , Pruebas de Sensibilidad Microbiana , Carne Roja , Ovinos , Porcinos , Secuenciación Completa del Genoma
7.
Nat Commun ; 10(1): 4828, 2019 10 23.
Artículo en Inglés | MEDLINE | ID: mdl-31645551

RESUMEN

Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance.


Asunto(s)
Farmacorresistencia Bacteriana/genética , Disentería Bacilar/microbiología , Fluoroquinolonas , Genoma Bacteriano/genética , Shigella sonnei/genética , Antibacterianos/uso terapéutico , Asia Sudoriental/epidemiología , Asia Occidental/epidemiología , Teorema de Bayes , Ciprofloxacino/uso terapéutico , Girasa de ADN/genética , Topoisomerasa de ADN IV/genética , Evolución Molecular Dirigida , Disentería Bacilar/tratamiento farmacológico , Disentería Bacilar/epidemiología , Europa (Continente)/epidemiología , Evolución Molecular , Humanos , Epidemiología Molecular , Mutación , Filogenia , Polimorfismo de Nucleótido Simple , Shigella sonnei/fisiología
8.
Microb Genom ; 5(5)2019 05.
Artículo en Inglés | MEDLINE | ID: mdl-31107203

RESUMEN

Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype. Strong concordance between in silico and phenotypic serotyping was observed, along with concordance between in silico and conventional detection of stx genes. These data represent the most comprehensive STEC analysis from the Southern Hemisphere, and provide a framework for future national genomics-based surveillance of STEC in Australia.


Asunto(s)
Infecciones por Escherichia coli/microbiología , Genoma Bacteriano , Epidemiología Molecular , Toxina Shiga/genética , Escherichia coli Shiga-Toxigénica/genética , Escherichia coli Shiga-Toxigénica/aislamiento & purificación , Australia/epidemiología , Simulación por Computador , Farmacorresistencia Bacteriana/genética , Infecciones por Escherichia coli/epidemiología , Escherichia coli O157/genética , Proteínas de Escherichia coli/genética , Evolución Molecular , Humanos , Tipificación de Secuencias Multilocus , Mutación , Fenotipo , Filogenia , Salud Pública , Serotipificación , Escherichia coli Shiga-Toxigénica/clasificación , Secuenciación Completa del Genoma
9.
Clin Infect Dis ; 69(9): 1535-1544, 2019 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-30615105

RESUMEN

BACKGROUND: In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages. METHODS: A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews. RESULTS: Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates. CONCLUSIONS: Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.


Asunto(s)
Homosexualidad Masculina/estadística & datos numéricos , Shigella/patogenicidad , Adolescente , Adulto , Antibacterianos/uso terapéutico , Azitromicina/uso terapéutico , Niño , Ciprofloxacino/uso terapéutico , Biología Computacional , Farmacorresistencia Bacteriana/genética , Femenino , Humanos , Masculino , Pruebas de Sensibilidad Microbiana , Mutación/genética , Plásmidos/genética , Factores de Riesgo , Enfermedades de Transmisión Sexual/microbiología , Enfermedades de Transmisión Sexual/prevención & control , Combinación Trimetoprim y Sulfametoxazol/uso terapéutico , Victoria , Secuenciación Completa del Genoma , Adulto Joven
10.
Infect Genet Evol ; 64: 52-56, 2018 10.
Artículo en Inglés | MEDLINE | ID: mdl-29906636

RESUMEN

Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2-4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns.


Asunto(s)
Antiinfecciosos/farmacología , Disentería Bacilar/epidemiología , Disentería Bacilar/microbiología , Shigella/efectos de los fármacos , Shigella/genética , Genes Bacterianos , Humanos , Pruebas de Sensibilidad Microbiana , Oceanía/epidemiología , Shigella/patogenicidad , Virulencia , Factores de Virulencia/genética
11.
Foodborne Pathog Dis ; 15(5): 285-292, 2018 05.
Artículo en Inglés | MEDLINE | ID: mdl-29638170

RESUMEN

Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated between November 2015 and March 2016. We identified a common egg grading facility in five of the outbreaks. While no Salmonella Typhimurium was detected at the grading facility and eggs could not be traced back to a particular farm, whole genome sequencing (WGS) of isolates from cases from all seven outbreaks indicated a common source. WGS was able to provide higher discriminatory power than MLVA and will likely link more Salmonella Typhimurium cases between states and territories in the future. National harmonization of Salmonella surveillance is important for effective implementation of WGS for Salmonella outbreak investigations.


Asunto(s)
Brotes de Enfermedades , Huevos/microbiología , Intoxicación Alimentaria por Salmonella/epidemiología , Salmonella typhimurium/genética , Australia/epidemiología , Genoma Bacteriano , Humanos , Repeticiones de Minisatélite , Secuenciación Completa del Genoma
12.
Foodborne Pathog Dis ; 15(3): 161-167, 2018 03.
Artículo en Inglés | MEDLINE | ID: mdl-29336594

RESUMEN

In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses. Epidemiological evidence was integrated with WGS-derived data to identify related isolates and sources of infection, and we compared WGS data for surveillance with findings from MLVA typing. We found that WGS data combined with epidemiological data linked an additional 9% of isolates to at least one other isolate in the study in contrast to MLVA and epidemiological data, and 19% more isolates than epidemiological data alone. Analysis of risk factors showed that in one WGS-defined cluster, human cases had higher odds of purchasing a single egg brand. While WGS was more sensitive and specific than conventional typing methods, we identified barriers to uptake of genomic surveillance around complexity of reporting of WGS results, timeliness, acceptability, and stability. In conclusion, WGS offers higher resolution of Salmonella Typhimurium laboratory surveillance than existing methods and can provide further evidence on sources of infection in case and outbreak investigations for public health action. However, there are several challenges that need to be addressed for effective implementation of genomic surveillance in Australia.


Asunto(s)
Brotes de Enfermedades , Genoma Bacteriano/genética , Infecciones por Salmonella/epidemiología , Salmonella typhimurium/genética , Australia/epidemiología , Técnicas de Tipificación Bacteriana , ADN Bacteriano/química , ADN Bacteriano/genética , Humanos , Repeticiones de Minisatélite/genética , Estudios Prospectivos , Salud Pública , Infecciones por Salmonella/microbiología , Salmonella typhimurium/aislamiento & purificación , Secuenciación Completa del Genoma
13.
Artículo en Inglés | MEDLINE | ID: mdl-29180525

RESUMEN

Australia has high and increasing rates of salmonellosis. To date, the serovar distribution and associated antimicrobial resistance (AMR) patterns of nontyphoidal Salmonella enterica (NTS) in Australia have not been assessed. Such information provides critical knowledge about AMR in the food chain and informs decisions about public health. We reviewed longitudinal data on NTS in two Australian states over a 37-year period, between 1979 and 2015, and antimicrobial resistance since 1984. Overall, 17% of isolates were nonsusceptible to at least one antimicrobial, 4.9% were nonsusceptible to ciprofloxacin, and 0.6% were nonsusceptible to cefotaxime. In total, 2.5% of isolates were from invasive infections, with no significant difference in AMR profiles between invasive and noninvasive isolates. Most isolates with clinically relevant AMR profiles were associated with travel, particularly to Southeast Asia, with multiple "incursions" of virulent and resistant clones into Australia. Our findings represent the largest longitudinal surveillance system for NTS in Australia and provide valuable public health knowledge on the trends and distribution of AMR in NTS. Ongoing surveillance is critical to identify local emergence of resistant isolates.


Asunto(s)
Antibacterianos/uso terapéutico , Farmacorresistencia Bacteriana/efectos de los fármacos , Infecciones por Salmonella/tratamiento farmacológico , Infecciones por Salmonella/epidemiología , Salmonella enterica/efectos de los fármacos , Australia/epidemiología , Cefotaxima/uso terapéutico , Ciprofloxacino/uso terapéutico , Humanos , Pruebas de Sensibilidad Microbiana/métodos , Serogrupo
15.
Int J Antimicrob Agents ; 50(1): 101-105, 2017 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-28476613

RESUMEN

Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-generation cephalosporins (3GCs) a particular concern. The aim of this study was to use whole-genome sequencing (WGS) to characterise recently identified human and non-human isolates of 3GC-resistant Salmonella enterica subsp. enterica serovar Typhimurium from Australia. The Illumina NextSeq sequencing platform was used to determine the genome sequences of 78 S. Typhimurium definitive type 44 isolated in Australia between 1992 and 2016, including 31 3GC-resistant isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools. We report the emergence of 3GC resistance in locally-acquired Australian S. Typhimurium for the first time. Phenotypically resistant isolates of human and animal origin were geographically restricted and were found by WGS all to be closely related and to carry blaCTX-M-9. Dairy cattle were the suspected source based on geographical clustering of animal isolates, which were predominantly bovine in origin. In conclusion, locally-acquired human cases of S. Typhimurium carrying blaCTX-M-9 were identified that appear to be of bovine origin, raising concerns regarding the human impact of off-label use of ceftiofur in cattle.


Asunto(s)
Antibacterianos/farmacología , Cefalosporinas/farmacología , Farmacorresistencia Bacteriana Múltiple , Proteínas de Escherichia coli/metabolismo , Salmonelosis Animal/microbiología , Infecciones por Salmonella/microbiología , Salmonella typhimurium/efectos de los fármacos , beta-Lactamasas/metabolismo , Animales , Australia , Bovinos , Biología Computacional , Humanos , Epidemiología Molecular , Filogenia , Infecciones por Salmonella/epidemiología , Salmonelosis Animal/epidemiología , Salmonella typhimurium/clasificación , Salmonella typhimurium/enzimología , Salmonella typhimurium/genética , Secuenciación Completa del Genoma
16.
Avian Pathol ; 46(3): 319-331, 2017 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-28000500

RESUMEN

Consumption of poultry products contaminated with Salmonella is one of the major causes of foodborne diseases worldwide and therefore detection and differentiation of Salmonella spp. in poultry is important. In this study, oligonucleotide primers were designed from hemD gene and a PCR followed by high-resolution melt (HRM) curve analysis was developed for rapid differentiation of Salmonella isolates. Amplicons of 228 bp were generated from 16 different Salmonella reference strains and from 65 clinical field isolates mainly from poultry farms. HRM curve analysis of the amplicons differentiated Salmonella isolates and analysis of the nucleotide sequence of the amplicons from selected isolates revealed that each melting curve profile was related to a unique DNA sequence. The relationship between reference strains and tested specimens was also evaluated using a mathematical model without visual interpretation of HRM curves. In addition, the potential of the PCR-HRM curve analysis was evaluated for genotyping of additional Salmonella isolates from different avian species. The findings indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Salmonella isolates to determine the serovar/serotype.


Asunto(s)
Enfermedades de las Aves de Corral/microbiología , Salmonelosis Animal/microbiología , Salmonella/aislamiento & purificación , Animales , Proteínas Bacterianas/genética , Técnicas de Tipificación Bacteriana/veterinaria , Cartilla de ADN/genética , Genotipo , Reacción en Cadena de la Polimerasa/veterinaria , Aves de Corral , Salmonella/genética , Especificidad de la Especie , Temperatura de Transición
17.
Aust N Z J Public Health ; 40(6): 588-591, 2016 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-27774718

RESUMEN

OBJECTIVE: To review the national case definition for shigellosis following the introduction of culture independent diagnostic testing by clinical laboratories and provide evidence to reform jurisdictional public health practices for the management shigellosis., . METHODS: A review of all Australian jurisdictional public health guidelines for shigellosis was conducted. Victorian 2014 shigellosis data were analysed: demographics and risk factors for cases identified by conventional culture or culture-independent diagnostic methods were described. RESULTS: There was considerable variation in reporting of cases to the National Notifiable Disease Surveillance System (NNDSS) by the eight Australian jurisdictions, with an array of classifications based on diagnostic testing methodologies. Analysis of Victorian 2014 shigellosis data found that culture positive cases were more likely to have reported men who have sex with men (MSM) as a risk factor than PCR positive only cases (p<0.0001) and less likely to have reported overseas travel during their incubation period (p<0.0001). Over a 10-year period (2005 to 2014), only two of 86 cases who were employed in high-risk occupations had ongoing positive faecal cultures after appropriate treatment. CONCLUSIONS: The national surveillance case definition for shigellosis should be reviewed to facilitate standardised reporting across Australia. All jurisdictions must consider the public health significance of PCR positive only results in their surveillance risk assessments to inform management of shigellosis cases.


Asunto(s)
Pruebas Diagnósticas de Rutina , Disentería Bacilar/diagnóstico , Vigilancia de la Población , Administración en Salud Pública , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Australia , Niño , Preescolar , Femenino , Humanos , Lactante , Entrevistas como Asunto , Masculino , Persona de Mediana Edad , Investigación Cualitativa , Adulto Joven
18.
PLoS Med ; 13(8): e1002055, 2016 08.
Artículo en Inglés | MEDLINE | ID: mdl-27483136

RESUMEN

BACKGROUND: Antimicrobial resistance is a major issue in the Shigellae, particularly as a specific multidrug-resistant (MDR) lineage of Shigella sonnei (lineage III) is becoming globally dominant. Ciprofloxacin is a recommended treatment for Shigella infections. However, ciprofloxacin-resistant S. sonnei are being increasingly isolated in Asia and sporadically reported on other continents. We hypothesized that Asia is a primary hub for the recent international spread of ciprofloxacin-resistant S. sonnei. METHODS AND FINDINGS: We performed whole-genome sequencing on a collection of 60 contemporaneous ciprofloxacin-resistant S. sonnei isolated in four countries within Asia (Vietnam, n = 11; Bhutan, n = 12; Thailand, n = 1; Cambodia, n = 1) and two outside of Asia (Australia, n = 19; Ireland, n = 16). We reconstructed the recent evolutionary history of these organisms and combined these data with their geographical location of isolation. Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S. sonnei formed a single clade within a Central Asian expansion of lineage III. Furthermore, our data show that resistance to ciprofloxacin within S. sonnei may be globally attributed to a single clonal emergence event, encompassing sequential gyrA-S83L, parC-S80I, and gyrA-D87G mutations. Geographical data predict that South Asia is the likely primary source of these organisms, which are being regularly exported across Asia and intercontinentally into Australia, the United States and Europe. Our analysis was limited by the number of S. sonnei sequences available from diverse geographical areas and time periods, and we cannot discount the potential existence of other unsampled reservoir populations of antimicrobial-resistant S. sonnei. CONCLUSIONS: This study suggests that a single clone, which is widespread in South Asia, is likely driving the current intercontinental surge of ciprofloxacin-resistant S. sonnei and is capable of establishing endemic transmission in new locations. Despite being limited in geographical scope, our work has major implications for understanding the international transfer of antimicrobial-resistant pathogens, with S. sonnei acting as a tractable model for studying how antimicrobial-resistant Gram-negative bacteria spread globally.


Asunto(s)
Antibacterianos/uso terapéutico , Ciprofloxacino/uso terapéutico , Disentería Bacilar/tratamiento farmacológico , Shigella sonnei/efectos de los fármacos , Australia/epidemiología , Bután/epidemiología , Cambodia/epidemiología , Preescolar , Estudios Transversales , Farmacorresistencia Bacteriana/genética , Farmacorresistencia Bacteriana Múltiple/genética , Disentería Bacilar/epidemiología , Disentería Bacilar/microbiología , Genoma Bacteriano/genética , Humanos , Irlanda/epidemiología , Filogenia , Shigella sonnei/genética , Tailandia/epidemiología , Vietnam/epidemiología
19.
Microb Genom ; 2(7): e000064, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-28348859

RESUMEN

The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli 'strain space' may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.


Asunto(s)
Proteínas de Escherichia coli/genética , Escherichia coli/genética , Escherichia coli/patogenicidad , Variación Genética , Serogrupo , Animales , Antígenos Bacterianos/genética , Simulación por Computador , Escherichia coli/clasificación , Antígenos O/genética , Filogenia , Análisis de Secuencia de ADN , Serotipificación
20.
Clin Infect Dis ; 62(6): 722-729, 2016 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-26679624

RESUMEN

BACKGROUND: Knowledge of relationships between antibiotic susceptibility of Shigella isolates and travel destination or other risk factors can assist clinicians in determining appropriate antibiotic therapy prior to susceptibility testing. We describe relationships between resistance patterns and risk factors for acquisition in Shigella isolates using routinely collected data for notified cases of shigellosis between 2008 and 2012 in Victoria, Australia. METHODS: We included all shigellosis patients notified during the study period, where Shigella isolates were tested for antimicrobial sensitivity using Clinical and Laboratory Standards Institute breakpoints. Cases were interviewed to collect data on risk factors, including recent travel. Data were analyzed using Stata 13.1 to examine associations between risk factors and resistant strains. RESULTS: Of the 500 cases of shigellosis, 249 were associated with overseas travel and 210 were locally acquired. Forty-six of 51 isolates of Indian origin displayed decreased susceptibility or resistance to ciprofloxacin. All isolates of Indonesian origin were susceptible to ciprofloxacin. Twenty-six travel-related isolates were resistant to all tested oral antimicrobials. Male-to-male sexual contact was the primary risk factor for 80% (120/150) of locally acquired infections among adult males, characterized by distinct periodic Shigella sonnei outbreaks. CONCLUSIONS: Clinicians should consider travel destination as a marker for resistance to common antimicrobials in returning travelers, where severe disease requires empirical treatment prior to receipt of individual sensitivity testing results. Repeated outbreaks of locally acquired shigellosis among men who have sex with men highlight the importance of prevention and control measures in this high-risk group.


Asunto(s)
Antibacterianos/uso terapéutico , Farmacorresistencia Bacteriana Múltiple , Disentería Bacilar/microbiología , Conducta Sexual , Shigella/efectos de los fármacos , Viaje , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Antiinfecciosos/uso terapéutico , Niño , Preescolar , Ciprofloxacino/uso terapéutico , Brotes de Enfermedades , Disentería Bacilar/tratamiento farmacológico , Disentería Bacilar/prevención & control , Femenino , Humanos , Indonesia/epidemiología , Lactante , Recién Nacido , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Factores de Riesgo , Minorías Sexuales y de Género , Shigella/genética , Shigella/aislamiento & purificación , Shigella sonnei/efectos de los fármacos , Shigella sonnei/aislamiento & purificación , Medicina del Viajero/métodos , Victoria/epidemiología , Adulto Joven
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