Presence and antimicrobial resistance profiles of Escherichia coli, Enterococcusspp. and Salmonellasp. in 12 species of Australian shorebirds and terns.

Antibiotic resistance is an ongoing threat to both human and animal health. Migratory birds are a potential vector for the spread of novel pathogens and antibiotic resistance genes. To date, there has been no comprehensive study investigating the presence of antibiotic resistance (AMR) in the bacteria of Australian shorebirds or terns. In the current study, 1022 individual birds representing 12 species were sampled across three states of Australia (Victoria, South Australia, and Western Australia) and tested for the presence of phenotypically resistant strains of three bacteria with potential to be zoonotic pathogens; Escherichia coli, Enterococcusspp., and Salmonellasp. In total, 206 E. coli, 266 Enterococcusspp., and 20 Salmonellasp. isolates were recovered, with AMR detected in 42% of E. coli, 85% of Enterococcusspp., and 10% of Salmonellasp. Phenotypic resistance was commonly detected to erythromycin (79% of Enterococcusspp.), ciprofloxacin (31% of Enterococcusspp.) and streptomycin (21% of E. coli). Resident birds were more likely to carry AMR bacteria than migratory birds (p ≤ .001). Bacteria isolated from shorebirds and terns are commonly resistant to at least one antibiotic, suggesting that wild bird populations serve as a potential reservoir and vector for AMR bacteria. However, globally emerging phenotypes of multidrug-resistant bacteria were not detected in Australian shorebirds. This study provides baseline data of the carriage of AMR bacteria in Australian shorebirds and terns.

Draft genome sequence of a multidrug-resistant Pseudomonas aeruginosa producing blaSIM metallo-ß-lactamase: London, UK.

OBJECTIVES: We report the draft genome sequence of a multidrug-resistant Pseudomonas aeruginosa isolate (PA3) producing SIM carbapenemase from a patient in the United Kingdom. METHODS: Isolation, identification and antimicrobial susceptibility testing were performed according to local routine microbiology protocols. Whole genomic DNA was sequenced using an Illumina HiSeq platform. The generated reads were de novo assembled using SPAdes version 3.7.1. Annotation was performed by the NCBI Prokaryote Genome Annotation Pipeline version 4.6. Sequence type, antimicrobial resistance and virulence-related genes were predicted from the sequence. RESULTS: P. aeruginosa PA3 was resistant to most antipseudomonal ß-lactams, aminoglycosides and quinolones but susceptible to colistin. The assembly comprised 100 contigs (>1000 bp) with a total length of 7 485 621 bp, and a total of 7190 coding sequences. The isolate belonged to sequence type (ST) 446, serotype O11 and contained blaSIM-1 metallo-ß-lactamase in a class 1 integron structure. CONCLUSION: We report a blaSIM-1 containing multidrug-resistant strain of P. aeruginosa from the UK. Moreover, the isolate was ST 446, a genetic background with potential for greater global dissemination.

Fermentation and the microbial community of Japanese koji and miso: A review.

Miso is a well-known traditional Japanese fermented food, with a characteristic savory flavor and aroma, known predominately as the seasoning in miso soup. Miso production involves a two-stage fermentation, where first a mold, such as Aspergillus oryzae, is inoculated onto a substrate to make koji. A subsequent fermentation, this time by bacteria and yeast, occurs when the koji is added to a salt and soybean mash, with the miso left to ferment for up to 2 years. The microbial community of miso is considered essential to the development of the unique taste, texture, and nutritional profile of miso. Despite the importance of microorganisms in the production of miso, very little research has been undertaken to characterize and describe the microbial process. In this review, we provide an overview of the two-stage fermentation process, describe what is currently known about the microbial communities involved and consider any potential health benefits associated with the consumption of miso, along with food safety concerns. As the popularity of miso continues to expand globally and is produced under new environmental conditions, understanding the microbiological processes involved will assist to ensure that global production of miso is safe as well as delicious.

Draft Genome Sequences of Four Citrobacter Isolates Recovered from Wild Australian Shorebirds.

Citrobacter is a ubiquitous bacterial genus whose members inhabit a variety of niches. Some species are clinically important for both antimicrobial resistance (AMR) carriage and as the cause of nosocomial infections. Surveillance of Citrobacter species in the environment can provide indicators of the spread of AMR genes outside clinical spaces. In this study, we present draft genome sequences of four Citrobacter isolates obtained from three species of wild Australian shorebirds.

Salmonella enterica Serovar Hvittingfoss in Bar-Tailed Godwits (Limosa lapponica) from Roebuck Bay, Northwestern Australia.

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.IMPORTANCESalmonella 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.

Hypermucoviscous polymyxin-resistant Klebsiella pneumoniae from Kolkata, India: Genomic and phenotypic analysis.

OBJECTIVES: Here we report the draft genome sequence of a colistin-resistant hypermucoviscous Klebsiella pneumoniae isolated from a hospitalised patient with acute kidney injury in Kolkata, India. METHODS: Whole genomic DNA was sequenced using an Illumina HiSeq platform. The generated reads were de novo assembled using SPAdes v.3.7.1. Genome annotation was performed using the NCBI Prokaryote Genome Annotation Pipeline (PGAP) v.4.6. The sequence type (ST), capsular type, antimicrobial resistance and virulence-related genes were predicted from the genome sequence. RESULTS: Klebsiella pneumoniae KP26 belonged to ST147. The assembly comprised 63 contigs (>1000 bp) with a total read length of 5 560 935 bp and a total of 5399 coding sequences. The isolate was resistant to most ß-lactams, aminoglycosides, quinolones, fosfomycin, trimethoprim, sulphonamides and polymyxins. No mcr genes were detected in the genome. CONCLUSION: Isolate KP26 is a hypermucoviscous, multidrug-resistant K. pneumoniae strain that may represent an emerging high-risk clone associated with severe infections in India.

CHROMagar COL-APSE: a selective bacterial culture medium for the isolation and differentiation of colistin-resistant Gram-negative pathogens.

PURPOSE: A selective chromogenic culture medium for the laboratory isolation and differentiation of colistin resistant Acinetobacter, Pseudomonas, Stenotrophomonas and Enterobacteriaceae spp. (CHROMagar COL-APSE) was developed, evaluated and compared to an existing selective bacterial culture medium (SuperPolymyxin). METHODOLOGY: The medium was challenged with 84 isolates, including polymyxin B (POL B)-susceptible and -resistant type strains and colistin (COL)-resistant organisms recovered from human and animal samples. Susceptibility to COL and POL B was determined by agar dilution and broth microtitre dilution. The lower limit for the detection of COL-resistant organisms was also calculated for both CHROMagar COL-APSE and SuperPolymyxin media. The ability to isolate and correctly differentiate COL-resistant organisms within mixed cultures was also assessed and compared using both media. RESULTS: Using CHROMagar COL-APSE, Gram-negative pathogens (n=71) with intrinsic (n=8) or acquired COL (n=63) resistance were recovered with 100 % specificity down to the lower limit of detection of 101 colony-forming units (c.f.u.). The growth on SuperPolymyxin was similar, but notably weaker for COL-resistant non-fermentative bacteria (Acinetobacter, Pseudomonas and Stenotrophomonas). CHROMagar COL-APSE was also more sensitive in supporting the growth of Enterobacteriaceae with COL resistance associated with the carriage of mcr-1. CONCLUSION: CHROMagar COL-APSE is a sensitive and specific medium for the growth of COL-resistant bacterial pathogens. Due to the low limit of detection (101 c.f.u.), it may be useful as a primary isolation medium in the surveillance and recovery of COL-resistant bacteria from complex human, veterinary and environmental samples, especially those with plasmid-mediated MCR-1 or novel mechanisms of polymyxin resistance.

Draft Genome Sequence of a Canine Isolate of Methicillin-Resistant Staphylococcus haemolyticus.

Staphylococcus haemolyticus strain SW007 was isolated from a nasal swab taken from a healthy dog. The isolate is resistant to methicillin, mupirocin, macrolides, and sulfonamides. The SW007 draft genome is 2,325,410 bp and contains 2,277 coding sequences, including 60 tRNAs and nine complete rRNA-coding regions.

Draft Genome Sequence of Staphylococcus cohnii subsp. urealyticus Isolated from a Healthy Dog.

Staphylococcus cohnii subsp. urealyticus strain SW120 was isolated from the ear swab of a healthy dog. The isolate is resistant to methicillin and fusidic acid. The SW120 draft genome is 2,805,064 bp and contains 2,667 coding sequences, including 58 tRNAs and nine complete rRNA coding regions.

Plasmids imparting sulfonamide resistance in Escherichia coli: implications for persistence.

Sulfonamide resistance remains prevalent among clinical isolates of Escherichia coli in the United Kingdom, despite a dramatic (>97%) national decline in the rate of prescription of sulfonamides in the 1990s. To investigate potential mechanisms accounting for this persistence, we characterized plasmids carrying sul2, the most prevalent determinant of sulfonamide resistance. Among 33 conjugative and 5 nonconjugative plasmids carrying sul2, resistance to other antimicrobial agents was common, but the spectrum of resistance profiles was diverse: 82%, 74%, and 45% carried resistance to ampicillin, streptomycin, and trimethoprim, respectively. Resistance to mercury was carried by 33% of the plasmids, but none conferred significant resistance to silver or to any of three disinfectants tested. The potential virulence genes iutA (aerobactin system) and traT (serum survival) were carried by 21% and 36% of the plasmids, respectively. The 33 conjugative plasmids belonged to five different incompatibility groups, FIB, B/O, I1, K/B, and P (42%, 33%, 9%, 3% and 3%, respectively), with 3 plasmids being unassigned, and to 19 similarity groups on the basis of their restriction profiles. The sequences flanking sul2 were diverse and suggested more than one mechanism of genetic mobility. The five nonconjugative plasmids were all related to p9123 (pBP1), which was previously found to confer a fitness advantage on its host. We propose that the persistence of sul2, despite the reduced rate of prescription of sulfonamides, is due to a combination of coselection by antibiotics still in common use, a lack of a selective disadvantage in sul2 carriage, and the genetic mobility of sul2.

Antimicrobial resistance in community and nosocomial Escherichia coli urinary tract isolates, London 2005-2006.

BACKGROUND: Escherichia coli is the commonest cause of community and nosocomial urinary tract infection (UTI). Antibiotic treatment is usually empirical relying on susceptibility data from local surveillance studies. We therefore set out to determine levels of resistance to 8 commonly used antimicrobial agents amongst all urinary isolates obtained over a 12 month period. METHODS: Antimicrobial susceptibility to ampicillin, amoxicillin/clavulanate, cefalexin, ciprofloxacin, gentamicin, nitrofurantoin, trimethoprim and cefpodoxime was determined for 11,865 E. coli urinary isolates obtained from community and hospitalised patients in East London. RESULTS: Nitrofurantoin was the most active agent (94% susceptible), followed by gentamicin and cefpodoxime. High rates of resistance to ampicillin (55%) and trimethoprim (40%), often in combination were observed in both sets of isolates. Although isolates exhibiting resistance to multiple drug classes were rare, resistance to cefpodoxime, indicative of Extended spectrum beta-lactamase production, was observed in 5.7% of community and 21.6% of nosocomial isolates. CONCLUSION: With the exception of nitrofurantoin, resistance to agents commonly used as empirical oral treatments for UTI was extremely high. Levels of resistance to trimethoprim and ampicillin render them unsuitable for empirical use. Continued surveillance and investigation of other oral agents for treatment of UTI in the community is required.

Evaluation of the BD ProbeTec ET system for direct detection of Mycobacterium bovis in veterinary specimens.

We describe the application of the BD ProbeTec ET direct tuberculosis system for the detection of Mycobacterium bovis in bovine and cervine lymph node tissues. Compared to traditional culture, the overall sensitivity, specificity, and positive and negative predictive values of the BD ProbeTec were 87, 100, 100, and 87%, respectively.

Investigations into the in vitro antimicrobial activity and mode of action of the phenazine antibiotic D-alanylgriseoluteic acid.

D-Alanylgriseoluteic acid (AGA) is a potent antimicrobial phenazine compound produced by Pantoea agglomerans (Erwinia herbicola) Eh1087. Susceptibility tests against a range of microbes indicated that AGA had a broad spectrum of antimicrobial activity and was particularly active against Gram-positive pathogens. Comparison of the in vitro efficacy of AGA with eight other antibiotics against 119 clinical isolates of Streptococcus pneumoniae demonstrated that all were inhibited by low concentrations of AGA (minimal inhibitory concentration range

In-vitro activity of polymyxin B in combination with imipenem, rifampicin and azithromycin versus multidrug resistant strains of Acinetobacter baumannii producing OXA-23 carbapenemases.

BACKGROUND: Acinetobacter baumannii has emerged as a major nosocomial pathogen worldwide. Many of the circulating strains exhibit multi-drug resistance remaining consistently susceptible only to polymyxins. In-vitro studies have reported that polymyxins combined with carbapenems, rifampicin or azithromycin are synergistic against these strains despite in-vitro resistance to these agents alone. The use of antimicrobial combinations have therefore been advocated for the treatment of severe A. baumannii infection in man. In order to determine whether such combinations are synergistic against the prevalent clones of multi-drug resistant A. baumannii causing infection in the UK, we performed synergy testing against representative isolates using two rapid Etest methods. METHODS: The activity of polymyxin in combination with imipenem, azithromycin or rifampicin was assessed against five strains of multi-drug resistant A. baumannii encoding OXA-23 carbapenemases. Synergy studies were performed by Etest-agar dilution and a combined Etest strip method. Synergy was defined as a FICI of < or = 0.5. RESULTS: All strains were resistant to beta-lactams, carbapenems, quinolones and aminoglycosides but susceptible to polymyxins. Marked synergy was not seen with polymyxin in combination with imipenem, rifampicin or azithromycin against any of the strains. Borderline synergy (FICI = 0.5) was seen against one strain belonging to OXA-23 clonal group 2, using the Etest-agar dilution method only. CONCLUSION: In-vitro synergy with polymxyin in combination with imipenem, rifampicin or azithromycin is highly strain and method dependent. As reliable synergy could not be demonstrated against the prevalent UK multi-drug resistant strains, use of such combinations should not be used for empirical treatment of these infections in the UK. The optimal treatment for serious multi-drug A. baumannii infection and the role of combination therapy should be addressed in a prospective clinical trial.

Resistance among Escherichia coli to sulphonamides and other antimicrobials now little used in man.

OBJECTIVES: We investigated whether sulphonamide resistance in Escherichia coli remained prevalent in 2004, 9 years since the formal introduction of a UK prescribing restriction on co-trimoxazole. Resistance to other agents no longer in common use was also examined. METHODS: Consecutive urinary E. coli isolates were obtained at the diagnostic microbiology laboratory of the Royal London Hospital from January to March 2004. The presence of the sulphonamide resistance genes, sul1, sul2 and sul3, and the class I integrase gene, int1, were determined by PCR. RESULTS: Of the 391 E. coli isolates recovered in 2004, 45.5% were sulphonamide-resistant compared with 46.0% in 1999 and 39.7% in 1991. The sul2 gene remained the most prevalent sulphonamide resistance determinant, present in 81% of resistant isolates in 2004 compared with 79% and 67% in 1999 and 1991, respectively; 28% of resistant isolates carried both sul1 and sul2 genes; sul3 was not found. Resistance to streptomycin also remained common, whereas resistance to chloramphenicol and kanamycin had decreased since 1999. CONCLUSION: Sulphonamide resistance in E. coli persists undiminished despite the prolonged withdrawal of this antibiotic in the UK; resistance to streptomycin also seems stable whilst that to chloramphenicol and kanamycin is declining.

Characterization of major clones of antibiotic-resistant Streptococcus pneumoniae in New Zealand by multilocus sequence typing.

OBJECTIVES: To determine the relationship between New Zealand isolates of antibiotic-resistant Streptococcus pneumoniae and internationally widespread resistant clones. METHODS: Fifty-nine isolates representing both invasive and non-invasive pneumococci from multiple locations, serotypes and years were analysed by multilocus sequence typing. RESULTS: Major international clones, including Spain(23F)-1, France(9V)-3 and Taiwan(19F)-14, were found to be present in New Zealand. A one-allele variant of the Taiwan(19F)-14 clone (aroE 15-->4, ST 271) was particularly prominent. CONCLUSIONS: Antibiotic-resistant pneumococci have not evolved de novo in New Zealand, but were introduced to the country during the early 1990s.

Molecular characterization of penicillin non-susceptible Streptococcus pneumoniae in Christchurch, New Zealand.

OBJECTIVES: To determine the epidemiological relationship between non-invasive penicillin non-susceptible Streptococcus pneumoniae isolates collected in the Christchurch community between 1997 and 2001. METHODS: One hundred and ninety-seven pneumococcal isolates were examined by macrorestriction profile analysis of SmaI-digested genomic DNA separated by PFGE and restriction fragment length polymorphism analysis of penicillin binding protein genes. RESULTS: Four major clonal lineages were identified, the largest and most homogeneous containing 95 (48.2%) of the isolates, the bulk of which (93.7%), had identical macrorestriction patterns. Members of this clonal group were multidrug-resistant and exhibited high resistance to third-generation cephalosporins, with MICs > or =8.0 mg/L not uncommon (23.1%). Two of the clonal groups, each containing 24 (12.2%) isolates, appeared indistinguishable from the globally widespread Spain23F-1 and France9V-3 strains, respectively. The fourth (12.7% of isolates) multidrug-resistant clone possessed intermediate penicillin susceptibility (MIC 0.12 mg/L). CONCLUSIONS: This study shows that several distinct penicillin-resistant pneumococcal clones are present in the Christchurch community, most of which appear to have been imported into New Zealand.