Einführung: Enterobacter (E.) cloacae subsp. cloacae sind wichtige Humanpathogene, insbesondere bei stationär untergebrachten Patienten. Sie sind in der Lage, Medizinprodukte zu kontaminieren, und es wurde über nosokomiale Krankheitsausbrüche in Verbindung mit der Kolonisation von chirurgischen Utensilien berichtet. Es ist daher wichtig, die Wirksamkeit und Effizienz von Desinfektionsmitteln gegenüber dieser Bakterienart zu bestimmen. Ziele: Die aktuelle Studie wurde durchgeführt, um nachzuweisen, ob Peressigsäure, Ethanol, Benzalkoniumchlorid und Natriumhypochlorit, welche weit verbreitet in kommerziellen Desinfektionsmitteln enthalten sind, eine ausreichende Wirksamkeit gegen multiresistente, von Patienten im Krankenhaus isolierte, E. cloacae aufweisen. Material und Methoden: Sechs multiresistente E. cloacae Isolate, die von Patienten in einem klinischen Umfeld gewonnen wurden, wurden getestet und mit dem E. cloacae Typstamm verglichen. Die Studien wurden in vitro mit Peressigsäure, Ethanol, Benzalkoniumchlorid und Natriumhypochlorit nach den Richtlinien der Desinfektionsmittel-Kommission des Verbundes für Angewandte Hygiene e.V. durchgeführt. Die Tests umfassten qualitative und quantitative Suspensionstests zur Bestimmung der bakteriziden Wirkung, den sogenannten Keimträgertest und die Bestimmung der minimalen Hemmkonzentrationen. Ergebnisse: Die Studienergebnisse zeigten, dass multiresistente E. cloacae Stämme genauso empfindlich gegenüber Desinfektionsmitteln waren wie der Typstamm. Organische Belastung interagierte stark mit Natriumhypochlorit und minderte dadurch seine Wirksamkeit, während Peressigsäure und Ethanol nicht durch organische Verunreinigung beeinflusst wurden. Die Kontaktzeit hatte nur einen geringen Einfluss auf die bakterizide Wirkung. Im Gegensatz dazu spielten bei Benzalkoniumchlorid organische Verunreinigung und die Kontaktzeit eine wichtige Rolle. Insgesamt waren die minimalen Hemmkonzentrationen und die bakterizid wirksamen Konzentrationen niedriger als die für kommerzielle Produkte gebräuchlichen Konzentrationen. In den Keimträgertests hatte das Trocknen auf einer glatten Oberfläche einen Einfluss auf das Überleben eines Stammes von E. cloacae. Die Ergebnisse zeigten auch, dass sich die Wirksamkeit der Desinfektionsmittel in den verschiedenen verwendeten Tests deutlich unterscheiden kann. Die Ergebnisse waren schwer mit anderen Studien zu vergleichen, da eine internationale Durchführungsrichtlinie für die Prüfung der Wirksamkeit von Desinfektionsmitteln gegen multiresistente Bakterien fehlt. Fazit: Peressigsäure, Ethanol, Benzalkoniumchlorid und Natriumhypochlorit eignen sich zur Desinfektion von multiresistenten E. cloacae. Die Wirksamkeit von Natriumhypochlorit und Benzalkoniumchlorid wird jedoch stark durch organische Stoffe beeinflusst. Dies unterstreicht die Bedeutung geeigneter Reinigungsmaßnahmen vor der Desinfektion. Wenn dies erfolgt ist, erweisen sich die getesteten Desinfektionsmittel gegen multiresistente E. cloacae genauso effektiv wie gegen den Typstamm.:1. Introduction ............................................................ 1 2. Literature Review ....................................................... 3 2.1 Enterobacteriaceae ..................................................... 4 2.1.1 General properties ................................................... 4 2.1.2 Enterobacter cloacae complex ......................................... 4 2.2 Multidrug-resistant bacteria and disinfectant “resistance” ............. 6 2.3 Disinfectant testing ................................................... 7 2.4 Active substances investigated in this study ........................... 8 2.4.1 Peracetic acid (PAA) ................................................. 8 2.4.2 Ethanol (ETH) ........................................................ 9 2.4.3 Benzalkonium chloride (BKC) .......................................... 9 2.4.4 Sodium hypochlorite (NaOCl) .......................................... 10 3. Materials and Methods ................................................... 11 3.1 Materials .............................................................. 11 3.2 Methods ................................................................ 14 3.2.1 Culture and storage of bacteria ...................................... 14 3.2.2 Preparation of disinfectants and the neutralizing agent .............. 14 3.2.3 Minimum inhibitory concentration (MIC) ............................... 15 3.2.4 Qualitative suspension test .......................................... 15 3.2.5 Quantitative suspension test.......................................... 16 3.2.6 Surface disinfection without mechanical action (germ carrier test) ... 16 3.2.7 Statistical analysis ................................................. 17 4. Results ................................................................. 18 4.1 Minimum inhibitory concentrations ...................................... 18 4.2 Qualitative suspension tests ........................................... 18 4.3 Quantitative suspension tests .......................................... 21 4.4 Surface disinfection without mechanical action (germ carrier test) ..... 24 5. Discussion .............................................................. 28 6. Summary ................................................................. 31 7. Zusammenfassung ......................................................... 33 8. References .............................................................. 35 9. Appendix ................................................................ 49 Acknowledgments ............................................................ 50 / Introduction: Enterobacter (E.) cloacae subsp. cloacae are important human pathogens, particularly in hospitalized patients. They tend to contaminate various medical devices and nosocomial outbreaks have been reported to be associated with the colonization of surgical equipment. Therefore, it is critical to determine the efficacy and effectiveness of disinfectants against this bacterial species. Objectives: The current study was undertaken to prove whether single active ingredients (i.e. peracetic acid, ethanol, benzalkonium chloride, and sodium hypochlorite) of widely used commercial disinfectants provide proper efficacy against multidrug-resistant human isolates of E. cloacae. Material and Methods: Six multidrug-resistant E. cloacae isolates obtained from patients in a clinical setting were tested and compared to the E. cloacae type strain. The studies were performed in vitro using peracetic acid, ethanol, benzalkonium chloride and sodium hypochlorite following the guidelines specified by the Disinfectants Commission within the Association of Applied Hygiene. Tests included determination of minimum inhibitory concentrations, bactericidal values by qualitative and quantitative suspension tests, and so-called germ carrier tests. The influence of exposure time and organic load on bacteriostatic and bactericidal concentrations was evaluated for each disinfectant using the two-tailed Mann-Whitney U-test. Results: Study results showed that multidrug-resistant E. cloacae strains were equally susceptible to disinfectants as the type strain. Organic matter highly interfered with sodium hypochlorite thereby decreasing its efficacy whereas peracetic acid and ethanol were not influenced by organic soiling. Contact time had only a minor effect on bactericidal values. This was in contrast to benzalkonium chloride where organic soiling and contact time played an important role. On the whole, minimum inhibitory concentrations and bactericidal concentrations were lower than in-use concentrations of commercial products. Drying on smooth surfaces in the carrier tests had an effect on the survival of one E. cloacae strain. Results also showed that efficacious values determined by the different tests used may differ distinctly. Results were difficult to compare with other studies because an international practical standard for testing disinfectant efficacy against multidrug-resistant bacteria is missing. Conclusion: Peracetic acid, ethanol, benzalkonium chloride and sodium hypochlorite are suitable to disinfect multidrug-resistant E. cloacae but the effectiveness of sodium hypochlorite and benzalkonium chloride is strongly influenced by organic matter. This underlines the importance of proper cleaning measures before disinfection. When this is done, the tested disinfectants proved to be as efficient against multidrug-resistant E. cloacae as against the type strain.:1. Introduction ............................................................ 1 2. Literature Review ....................................................... 3 2.1 Enterobacteriaceae ..................................................... 4 2.1.1 General properties ................................................... 4 2.1.2 Enterobacter cloacae complex ......................................... 4 2.2 Multidrug-resistant bacteria and disinfectant “resistance” ............. 6 2.3 Disinfectant testing ................................................... 7 2.4 Active substances investigated in this study ........................... 8 2.4.1 Peracetic acid (PAA) ................................................. 8 2.4.2 Ethanol (ETH) ........................................................ 9 2.4.3 Benzalkonium chloride (BKC) .......................................... 9 2.4.4 Sodium hypochlorite (NaOCl) .......................................... 10 3. Materials and Methods ................................................... 11 3.1 Materials .............................................................. 11 3.2 Methods ................................................................ 14 3.2.1 Culture and storage of bacteria ...................................... 14 3.2.2 Preparation of disinfectants and the neutralizing agent .............. 14 3.2.3 Minimum inhibitory concentration (MIC) ............................... 15 3.2.4 Qualitative suspension test .......................................... 15 3.2.5 Quantitative suspension test.......................................... 16 3.2.6 Surface disinfection without mechanical action (germ carrier test) ... 16 3.2.7 Statistical analysis ................................................. 17 4. Results ................................................................. 18 4.1 Minimum inhibitory concentrations ...................................... 18 4.2 Qualitative suspension tests ........................................... 18 4.3 Quantitative suspension tests .......................................... 21 4.4 Surface disinfection without mechanical action (germ carrier test) ..... 24 5. Discussion .............................................................. 28 6. Summary ................................................................. 31 7. Zusammenfassung ......................................................... 33 8. References .............................................................. 35 9. Appendix ................................................................ 49 Acknowledgments ............................................................ 50

Master of Science / Food Science Institute / Daniel Y.C. Fung / ECA Check® Easygel® Plus (ECA) is a pectin-based gelling system that reacts with calcium ions bound to a pre-treated Petri dish, eliminating autoclaving prior to use. It can chromogenically and/or fluorogenically distinguish three organisms: Escherichia coli, Salmonella spp., and coliforms. This study compared the recovery of these organisms to conventional media using stock culture, inoculated, and non-inoculated ground beef and ground turkey. ECA was compared to Violet Red Bile Agar (VRB), Violet Red Bile Agar with 4-methylumbelliferyl-β-D-glucuronide (VRB-MUG), Xylose Lysine Desoxycholate Agar (XLD), Escherichia coli/Coliform (ECC) Count Plate Petrifilm™, and Tryptic Soy Agar (TSA). The stock culture recovery of Salmonella Typhimurium for ECA, TSA, and XLD were 8.62, 8.69, and 6.82 log CFU/ml, respectively. There was very little difference between the media in the recovery of Escherichia coli and Cronobacter spp., formerly referred to as Enterobacter sakazakii. Mean counts of presumptive E. coli in ground beef were 7.24 and 7.41 logs for ECA and VRB-MUG. Total coliform mean counts were 7.43, 7.63, and 7.37 logs for ECA, Petrifilm™, and VRB. Presumptive Salmonella means were 6.68 and 6.21 logs on ECA and XLD, while total aerobic counts were 7.84 and 6.51 logs on ECA and TSA. At 6.72 logs, ECA recovered considerably more Salmonella than XLD (5.71 logs) from the inoculated ground turkey; ECA recovered 7.62 logs total aerobic count which was significantly more than TSA at 6.89 logs. Total counts for both non-inoculated ground meats resulted in significant differences between TSA recovery and all other media. ECA also recovered significantly more than Petrifilm™ from both non-inoculated foods. The randomly selected organisms recovered from ECA were identified using BBL™ Crystal™ Enteric/Nonfermenter ID or Gram-Positive kits, and correlated precisely to the chromogenic reaction of the colonies. ECA Check® Easygel® was efficient, less labor-intensive, comparable to, and, in some instances, better than conventional media at recovering target organisms.

Thesis (Msc Food Sc (Food Science))--University of Stellenbosch, 2005. / It is estimated by the World Health Organisation (WHO) that thousands of millions of cases of foodborne diseases occur world–wide every year. Enterobacter sakazakii is a member of the family Enterobacteriaceae and has been identified as an occasional contaminant of powdered infant formula milk (IFM). Enterobacter sakazakii is an opportunistic emerging pathogen and has the ability to cause a severe form of neonatal meningitis. This organism was referred to as “yellow pigmented Enterobacter cloacae” until 1980 after which it was renamed as E. sakazakii. The current method for the detection of E. sakazakii is very time consuming and includes pre–enrichment, enrichment in Enterobacteriaceae enrichment broth, subsequent plating on violet red bile glucose agar and subculturing on tryptone soy agar. In this study a polymerase chain reaction (PCR) method was developed for the identification of the presence of E. sakazakii in infant food products. A part of the 16S ribosomal RNA (rRNA) gene from E. sakazakii was amplified using the primer pair Esak2 and Esak3. An internal amplification control (IAC) was constructed as part of the PCR detection method. The 850 base pair (bp) E. sakazakii PCR product was digested with AluI and the two fragments containing the primer binding sites were ligated, resulting in a 240 bp IAC. During this study a positive band for both the target DNA (850 bp) and the IAC (240 bp) was simultaneously observed when the IAC was added to the PCR mixture at a concentration of 0.72 pg.ml-1. Four of 22 South African food products tested positive for the presence of E. sakazakii, using both the PCR and recommended culturing methods. The PCR method was used successfully for the detection of E. sakazakii within three days and thus provides a possible alternative and improvement on the recommended current culturing methods. Other microorganisms present in the products tested included Escherichia coli, Klebsiella pneumoniae, Raoultella terrigena (“Klebsiella terrigena”) and Chryseomonas luteola. Since E. sakazakii is usually present in low numbers in food products, it is possible that these few cells are unevenly distributed in the products, making it important to take multiple samples when evaluating IFM and thereby ensuring that even low numbers of this pathogen are detected.

MSc (Chemistry) / Department of Chemistry

Among abiotic stresses, salinity is considered the main limiting stress that negatively affects plant growth and reduces productivity worldwide. To overcome this challenge, a sustainable solution such as plant growth-promoting bacteria (PGPB) can be used to meet the increasing demand for food. The desert microbe Enterobacter sp SA187, an endophytic PGPB, induces salt tolerance in both model plant and crops. The interaction between SA187 and the host plant triggers the sulfur pathway in the bacteria which then provides multiple sulfur-containing compounds to its host plant. However, the molecular sensor of these compounds in the host plant is not known. Here, we show that SA187 activates the plant target of rapamycin (TOR) pathway. The beneficial effect of SA187 was lost in TOR mutants like raptor, and by the application of TOR inhibitor AZD8055. Next, we show that SA187 modulates the one- carbon (1C) metabolism of the host plant consisting of methionine and folate cycles. The beneficial effect of SA187 was compromised by using chemical inhibitors of folate cycle like Methotrexate (MTX) and Sulfadiazine (SDZ). The intermediates of the 1C metabolism like Homocysteine and S-adenosyl methionine (SAM) showed similar beneficial effects as SA187 colonized plants. Finally, we showed that SA187 enhances 1C metabolism activity by increasing methylation index (SAM/SAH ratio) in the plants. Taken together, we could show that host TOR-1C axis is essential for plant salt tolerance by SA187.

Thesis (MSc)--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: The World Health Organisation (WHO) estimates that at least 75% of infants receive infant formula milk (IFM) either entirely or in conjunction with breast milk during the first four months after birth. The presence of the emerging pathogen Enterobacter sakazakii in IFM has been associated with rare but fatal cases of neonatal infections and deaths. There is thus a need for accurate methods for the rapid detection of E. sakazakii in foods. At present, the methods used to detect and identify this micro-organism are inadequate, controversial and contradictory. The aim of this study was to determine the most suitable method for E. sakazakii detection after evaluation of the currently available methods. A further aim was to optimise a polymerase chain reaction (PCR) method for the detection of only viable E. sakazakii cells utilising the DNA-intercalating dyes ethidium monoazide (EMA) and propidium monoazide (PMA). The Food and Drug Administration (FDA) method for E. sakazakii detection was utilised to select 50 isolates from IFM and 14 from the environment, regardless of colony appearance. These isolates were identified by sequencing a 1.5 kilobase (kb) fragment of the 16S ribosomal DNA (rDNA) and by using the National Centre for Biotechnological Information (NCBI) database to confirm the closet known relatives. Seven of the 50 (14%) IFM isolates and six of the 14 (43%) environmental isolates were identified as E. sakazakii. The methods that were evaluated for accuracy in detecting and identifying these E. sakazakii isolates included yellow pigment production on tryptone soy agar (TSA), chromogenic Druggan-Forsythe-Iversen (DFI) and Enterobacter sakazakii (ES) agars and PCR using six different species-specific primer pairs described in the literature. The suitability of the FDA method was lowered by the low sensitivity, specificity and accuracy (87%, 71% and 74%, respectively) of using yellow pigment production for E. sakazakii identification. DFI and ES agars were shown to be sensitive, specific and accurate (100%, 98% and 98%, respectively) for the detection of E. sakazakii. The specificity of the PCR amplifications was found to vary between 8% and 92%, with Esakf and Esakr being the most accurate of the primer pairs evaluated. The current FDA method for E. sakazakii detection requires revision in the light of the availability of more sensitive, specific and accurate detection methods. Based on the results obtained in this study, a new method is proposed for the detection of E. sakazakii in food and environmental samples. This proposed method replaces the culturing steps on violet red bile glucose agar (VRBGA) and TSA with culturing on chromogenic DFI or ES agar. For identification and confirmation of presumptive E. sakazakii isolates, the oxidase test, yellow pigment production and API biochemical profiling is replaced by DNA sequencing and/or species-specific PCR with the most accurate primer pair (Esakf and Esakr). The amendments to the current FDA method will reduce the time to detect E. sakazakii from approximately 7 days to 4 days and should prove to be more sensitive, specific and accurate for E. sakazakii detection. In this study, a novel PCR-based method was developed which was shown to be capable of discriminating between viable and dead E. sakazakii cells. This was achieved utilising the irreversible binding of bacterial DNA to photo-activated PMA or EMA in order to prevent PCR amplification from the dead cells. At concentrations of 50 and 100 μg.ml-1, PMA completely inhibited PCR amplification from dead cells, while causing no significant inhibition of the PCR amplification from viable cells. EMA was equally effective in preventing PCR amplification from dead cells, however, it also inhibited PCR amplification from viable cells. PMA-PCR in particular, will be useful for assessing the efficacy of processing techniques, as well as for monitoring the resistance, survival strategies and stress responses of E. sakazakii. This will be an important step in the efforts to eliminate E. sakazakii from food and food production environments. / AFRIKAANSE OPSOMMING: Die Wêreld Gesondheidsorganisasie (WGO) beraam dat ten minste 75% van alle babas net baba formule melk (BFM) of BFM in kombinasie met moedersmelk in die eerste vier maande na geboorte kry. Die teenwoordigheid van die voortkomende patogeen Enterobacter sakazakii in BFM is al geassosieer met skaars maar noodlottige gevalle van neonatale infeksies en sterftes. Akkurate metodes word dus benodig vir die vinnige deteksie van E. sakazakii in voedsel. Die metodes wat huidiglik gebruik word vir die deteksie en identifikasie van hierdie mikroörganisme is onvoldoende, kontroversieël en teenstrydig. Die doel van hierdie studie was om die beste metode vir die deteksie van E. sakazakii te bepaal, na 'n evaluasie van die metodes wat huidiglik beskikbaar is. 'n Verdere doel was om 'n polimerase ketting reaksie (PKR) metode vir die deteksie van slegs lewensvatbare E. sakazakii selle te optimiseer deur gebruik te maak van die DNSbindende kleurstowwe, etidium mono-asied (EMA) en propidium mono-asied (PMA). Die Voedsel en Medisyne Administrasie (VMA) se metode vir E. sakazakii deteksie is gebruik om, ongeag van die kolonie kleur, 50 isolate vanuit BFM en 14 isolate vanuit die omgewing te kies. Hierdie isolate is geïdentifiseer deur die DNS volgorde van 'n 1.5 kilo-basis (kb) fragment van die 16S ribosomale DNS (rDNS) te bepaal en die Nationale Sentrum vir Biotegnologiese Informasie (NSBI) databasis te gebruik om die mees verwante spesie te bevestig. Sewe van die 50 (14%) BFM isolate en ses van die 14 (43%) omgewings isolate is geïdentifiseer as E. sakazakii. Die metodes wat geëvalueer is in terme van akkuraatheid vir deteksie en identifikasie van hierdie E. sakazakii isolate het PKR met ses verskillende spesie-spesifieke peiler pare soos beskryf in die literatuur, geel-pigment produksie op triptoon soja agar (TSA) en chromogeniese Druggan-Forsythe-Iversen (DFI) en Enterobacter sakazakii (ES) agars ingesluit. Die geskiktheid van die VMA metode is verlaag deur die lae sensitiwiteit, spesifisiteit en akkuraatheid (87%, 71% en 74% onderskeidelik) van geel pigment produksie vir E. sakazakii identifikasie. Chromogeniese DFI en ES agars was sensitief, spesifiek en akkuraat (100%, 98% en 98% onderskeidelik) vir die identifikasie van E. sakazakii. Die spesifisiteit van die PKR produkte het gewissel tussen 8% en 92%, en Esakf en Esakr is as die akkuraatste geëvalueerde peiler paar geidentifiseer. Die huidige VMA metode vir E. sakazakii deteksie vereis hersiening aangesien meer sensitiewe, spesifieke en akkurate deteksiemetodes voortdurend beskikbaar word. 'n Nuwe metode, gebaseer op die resultate van hierdie studie, word voorgestel vir die deteksie van E. sakazakii in voedsel- en omgewingsmonsters. Die voorgestelde metode vervang die kwekingsstap op violet rooi gal glukose agar (VRGGA) en TSA deur kweking op chromogeniese DFI of ES agars. Verder word die oksidase toets, geel pigment produksie en API biochemiese profiele van vermoeidelike E. sakazakii isolate vervang deur DNS volgorde bepaling en/of spesie-spesifieke PKR met die mees spesifieke peiler paar (Esakf and Esakf) vir die identifikasie en bevestiging van E. sakazakii. Die voorgestelde wysigings van die VMA metode sal die tydsduur van E. sakazakii identifikasie van 7 dae na 4 dae verminder, en behoort ook meer sensitief, spesifiek en akkuraat te wees vir die deteksie van E. sakazakii. 'n Nuwe PKR-gebaseerde metode wat tussen lewensvatbare en dooie E. sakazakii selle kan onderskei is in hierdie studie ontwikkel. Dit is bereik deur die onomkeerbare binding van bakteriële DNS aan lig-geaktiveerde EMA of PMA om die PKR amplifisering van dooie selle te voorkom. Konsentrasies van 50 en 100 μg.ml-1 PMA het PKR amplifikasie heeltemal geïnhibeer, terwyl geen inhibisie van lewensvatbare selle bespeur kon word nie. EMA was ook suksesvol in die voorkoming van die PKR amplifikasie van dooie selle, alhoewel daar ook 'n mate van DNS inhibisie was tydens die amplifikasie van lewensvatbare selle. PMA-PKR kan ook van nut wees vir die assessering van die doeltreffendheid van prosesseringstegnieke, en ook vir die waarneming van die weerstandigheid, oorlewingsstrategieë en stresresponse van E. sakazakii. Dit sal 'n belangrike stap wees in pogings om E. sakazakii van voedsel en voedsel produksieomgewings te elimineer.

Thesis (MSc Food Sc)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: The genus Cronobacter (Enterobacter sakazakii) contains opportunistic pathogens that can cause a severe form of neonatal meningitis, necrotising enterocolitis and septicaemia. Cronobacter infections have been reported in all age groups, however, immunocompromised infants are more susceptible to these infections. Furthermore, Cronobacter strains have been reported to show differences in sensitivity to antibiotics and virulence. These differences led to the reclassification of Cronobacter and currently the genus contains five distinct species, namely Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter dublinensis and Cronobacter muytjensii. As this reclassification was only accepted recently, there are not many typing methods optimised for differentiation between the five Cronobacter species. Typing of Cronobacter strains are important as the species may be diverse regarding their virulence. Cronobacter strains have been isolated from infant formula milk (IFM), the environment of an IFM processing facility and fresh produce in South Africa. However, little is known about the phylogeny and prevalence of these strains. The aim of this study was to classify 24 South African Cronobacter strains (previously identified as E. sakazakii) and to evaluate the phylogeny of the isolates based on the 16S ribosomal RNA (rRNA) and rpoA genes. All 24 South African strains were identified as Cr. sakazakii despite a wide variety of isolation sources. Other studies have also found that irrespective of the isolation source, the majority of Cronobacter strains are identified as Cr. sakazakii. The South African strains were found to be phylogenetically closely related. However, two distinct clusters separated at a 93 % confidence level were observed in the Cr. sakazakii group based on the 16S rRNA gene analysis. Strains of Cr. sakazakii, Cr. dublinensis, Cr. turicensis and Cr. muytjensii were differentiated from each other with sequence data of the 16S rRNA and rpoA genes, but it was not possible to differentiate between Cr. sakazakii and Cr. malonaticus. The phylogram based on the rpoA gene sequences did separate Cr. malonaticus and Cr. sakazakii strains, however, the clusters were separated with a low bootstrap value of 70 %. Phylogenetic analysis based on the rpoA and 16S rRNA genes were, therefore, not sufficient to distinguish between all the Cronobacter species. The sequence data of these two genes can be used to differentiate between the Cronobacter strains when used in combination with malonate utilisation analysis. A PCR-RFLP method was subsequently developed to facilitate the simultaneous differentiation between all five Cronobacter species. The PCR-RFLP assay was based on the amplification of the rpoB gene followed by the combined digestion with restriction endonucleases Csp6I and HinP1I. Unique profiles for each of the five Cronobacter species were obtained and it was also possible to differentiate between Enterobacteriaceae and Cronobacter strains. Furthermore, two strains which were identified as Cr. sakazakii with sequencing based on the 16S rRNA and rpoA genes had PCR-RFLP profiles identical to that of Cr. malonaticus. Sequencing based on the rpoB gene and additional biochemical analysis with malonate broth confirmed the identities of these two strains as Cr. malonaticus. This PCR-RFLP assay is, therefore, an accurate typing method that ensures rapid differentiation between the five species of Cronobacter. / AFRIKAANSE OPSOMMING: Die Cronobacter genus (Enterobacter sakazakii) bevat opportunistiese patogene wat 'n ernstige vorm van neonatale meningitis, enterokolitis en septisemie kan veroorsaak. Cronobacter infeksies is al in alle ouderdomsgroepe aangemeld, maar immuungekompromitteerde babas is die meeste vatbaar vir hierdie infeksies. Verder toon Cronobacter spesies verskille in virulensie en sensitiwiteit vir antibiotika. Hierdie verskille het gelei tot die herklassifikasie van Cronobacter en tans bestaan die genus uit vyf afsonderlike spesies, naamlik Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter dublinensis en Cronobacter muytjensii. Aangesien hierdie herklassifikasie slegs onlangs aanvaar is, is daar nie baie metodes wat geskik is vir onderskeiding tussen die vyf Cronobacter spesies nie. Onderskeiding tussen Cronobacter spesies is belangrik omdat die spesies verskillend kan wees met betrekking tot hulle virulensie. Cronobacter is geisoleer uit baba formule melk (BFM), die omgewing van 'n BFM fabriek en vars produkte in Suid-Afrika. Daar is egter nie baie bekend oor die filogenie en voorkoms van hierdie isolate nie. Die doel van hierdie studie was om 24 Suid-Afrikaanse Cronobacter stamme (voorheen geïdentifiseer as E. sakazakii) te klassifiseer en die filogenie van die isolate te evalueer gebaseer op die 16S ribosomale RNS (rRNS) en rpoA gene. Al 24 Suid-Afrikaanse stamme is geïdentifiseer as Cr. sakazakii ten spyte van 'n wye verskeidenheid isolasie bronne. Ander studies het ook gevind dat, ongeag die isolasie bron, die meerderheid van Cronobacter stamme as Cr. sakazakii geïdentifiseer word. In hierdie studie is gevind dat die Suid-Afrikaanse stamme filogeneties nou verwant is. Op grond van die 16S rRNA geen analise is die Cr. sakazakii stamme egter in twee afsonderlike groepe gedeel met 'n 93% vertrouens vlak. Dit was moontlik om stamme van Cr. sakazakii, Cr. dublinensis, Cr. turicensis en Cr. muytjensii van mekaar te onderskei met die DNS volgorde data van die 16S rRNA en rpoA gene, maar geen onderskeid tussen Cr. sakazakii en Cr. malonaticus stamme was moontlik nie. Die filogram gebaseer op die rpoA DNS volgorde data het aparte takke vir Cr. malonaticus en Cr. sakazakii stamme getoon, maar die twee takke is met ‘n lae vertrouens waarde van slegs 70 % geskei. Filogenetiese analise gebaseer op die rpoA en 16S rRNA gene is dus nie voldoende om te onderskei tussen al die Cronobacter spesies nie. Die DNS volgorde data van hierdie twee gene sou egter gebruik kon word om te onderskei tussen die Cronobacter spesies wanneer dit gebruik word in kombinasie met malonaatbenutting-analises. 'n Polimerase ketting reaksie (PKR) beperkings fragment lengte polimorfisme (BFLP) metode is ontwikkel om die gelyktydige onderskeiding tussen al vyf Cronobacter spesies te fasiliteer. Die PKR-BFLP metode is gebaseer op die vermeerdering van die rpoB geen gevolg deur die gesamentlike vertering met die beperkingsensieme, Csp6I en HinP1I. Unieke profiele vir elk van die vyf Cronobacter spesies is verkry en dit was ook moontlik om tussen Enterobacteriaceae en Cronobacter spesies te onderskei. Verder het twee stamme wat as Cr. sakazakii geïdentifiseer is met DNS volgordebepaling van die 16S rRNA en rpoA gene, PKR-BFLP profiele identies aan dié van Cr. malonaticus getoon. DNS volgordebepaling van die rpoB geen en ‘n addisionele biochemiese toets met malonaat sop het die identiteit van hierdie twee stamme as Cr. malonaticus bevestig. Hierdie PKR-BFLP is dus 'n akkurate metode wat vinnige onderskeid tussen die vyf spesies van Cronobacter kan verseker.

Introduction: La pneumonie associée à la ventilation mécanique (VM) est fréquente chez les patients ventilés. L’étirement cyclique (EC) induit par la VM pourrait amorcer le poumon vers une réponse inflammatoire en cas d'exposition à des bactéries. Les Toll-like Receptors (TLR) reconnaissent les bactéries et déclenchent l'immunité. La VM pourrait moduler l'expression des TLR et leur réactivité aux agonistes. Le décubitus ventral (DV) réduit l’étirement du poumon. Méthodes: Les niveaux de TLR2 et la réponse à ses agonistes ont été mesures dans des cellules pulmonaires soumises à un EC, et dans un modèle de lapin ventilé. Une stimulation ex vivo du sang total prélevé sur lapins ventilés a été réalisée. Une pneumonie a été induite chez des lapins soumis à VM et maintenus en décubitus dorsal ou tournés en DV. Résultats: L’EC des cellules ainsi que des poumons de lapins augmente les niveaux de TLR2 et la réponse inflammatoire à ses agonistes. La VM et l’exposition du poumon à des agonistes TLR2 induisent synergiquement des lésions. Chez des lapins avec pneumonie sous VM la clairance bactérienne pulmonaire est réduite, la probabilité de bactériémie et le taux des cytokines circulantes augmentés. Le sang total provenant d'animaux sous VM libère de grandes quantités de cytokines après stimulation. Le DV est associe à des niveaux plus faibles de concentrations bactériennes et d'inflammation. Conclusions: La VM sensibilise le poumon aux ligands bactériens de TLR2, modifie la clairance bactérienne pulmonaire, favorise les lésions pulmonaires et de l'inflammation. La surexpression de TLR2 induite par l’EC pourrait expliquer ces différences. Le DV pourrait avoir un effet protecteur. / Introduction: Ventilator-associated pneumonia is common in patients subjected to mechanical ventilation (MV). Cyclic stretch subsequent to MV could prime the lung toward an inflammatory response if exposed to bacteria. Toll-like receptors (TLRs) recognize pathogens thus triggering immunity. MV could modulate TLRs expression and responsiveness to agonists. The prone position (PP) reduces lung stretch.Methods:TLR2 levels and response to the TLR2 ligands were measured in human pulmonary cells submitted to cyclic stretch, and either spontaneously breathing (SB) or MV rabbits. Ex vivo stimulation of whole blood taken from SB or MV rabbits was performed.Enterobacter aerogenes pneumonia was induced in rabbits subjected to MV and kept supine or turned to the PP. Results: Cyclic stretch of human cells as well as rabbitsÕ lung increased both TLR2 levels and inflammatory response to its agonist. MV and airways exposure to TLR2 ligands acted synergistically in causing lung injury.A decrease of lung bacterial clearance and a greater likelihood of bacteremia were observed in MV rabbits with S. aureus pneumonia. Circulating cytokines rose significantly only in these animals. MV induced TLR2 spleen overexpression. Whole blood obtained from MV animals released larger amounts of cytokines after stimulation. PP was associated with lower levels of bacterial concentrations and inflammation. Conclusions: MV sensitizes the lung to bacterial TLR2 ligands, alters lung bacterial clearance, promotes lung injury and inflammation. Both pulmonary and peripheral blood stretch-induced TLR2 overexpression could account at least in part for such differences. The PP could be protective.

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