Clonal diversity of Escherichia coli isolates from marketed beef in East Malaysia

Escherichia coli, including Shiga-like toxin producing E. coli (STEC), serogroup O157:H7 and E. coli O157, were isolated from raw beef marketed in Sarawak and Sabah, East Malaysia. Molecular subtyping by pulsed-field gel electrophoresis (PFGE) was performed on 51 confirmed E. coli isolates. Of the 51 isolates, five were E. coli O157:H7, four E. coli O157, two non-O157 STEC and 40 other E. coli isolates (non-STEC). Digestion of chromosomal DNA from these E. coli isolates with restriction endonuclease XbaI (5′-TCTAGA-3′), followed by PFGE, produced 45 restriction endonuclease digestion profiles (REDPs) of 10–18 bands. E. coli O157:H7 isolates from one beef sample were found to have identical PFGE profiles. In contrast, E. coli serogroup O157 from different beef samples displayed considerable differences in their PFGE profiles. These suggested that E. coli isolates of both serogroups were not closely related. A large variety of PFGE patterns among non-STEC isolates were observed, demonstrating a high clonal diversity of E. coli in the beef marketed in East Malaysia. The distance matrix values (D), calculated showed that none of the pathogenic E. coli strains displayed close genetic relationship with the non-STEC strains. Based on the PFGE profiles, a dendrogram was generated and the isolates were grouped into five PFGE clusters (A–E). From the dendrogram, the most related isolates were E. coli O157:H7, grouped within cluster B. The STEC O157:H7 beef isolates were more closely related to the clinical E. coli O157:H7 isolate than the E. coli O157:H7 reference culture, EDL933. Cluster A, comprising many of other E. coli isolates was shown to be the most heterogeneous. PFGE was shown to possess high discriminatory power in typing pathogenic and non-pathogenic E. coli strains, and useful in studying possible clonal relationship among strains

Identification of Methane-producing Bacteria from Palm Oil Mill Sludge (POMS) with Solid Cud from Ruminant Stomach

Biological generation in anaerobic environments such as enteric fermentation and anaerobic waste treatment from agriculture sector are the major contributor of methane gas which has the potential as biogas. The aimed of this study was to identify methane-producing bacteria in anaerobic vessel which contained a mixture of Palm Oil Mill Sludge (POMS) and solid cud taken from the first compartment of cow’s stomach (1:2 and 2:1 ratio) as co-mixture. The comixture was incubated at 50 °C in a 2 L vessel with initial starter of 400 ml and sampling was conducted every 4 weeks interval during 12 weeks of incubation. For specific detection of methanogens, 16S rRNA-cloning analysis was carried out. Methanobrevibacter sp. and Methanosaeta sp. were confirmed to be presence within the 2:1 ratio of co-mixture while only Methanobrevibacter sp. was found in 1:2 ratio of co-mixture on both Week 0 and Week 4. No methanogens were detected for both co-mixtures on Week 8 and Week 1

Molecular confirmation and characterization of Vibrio parahaemolyticus from retailed fish

The present study was conducted to assess the rapid molecular identification and characterization of 45 Vibrio parahaemolyticus isolates from 15 samples of 3 different types of fish (Kembung, Bawal and Sangeh) in the Kuching-Samarahan district. Polymerase chain reaction (PCR) based confirmation was done targeting the 450 bp fragment of the thermolabile (tl) gene, while DNA fingerprinting was performed using Randomly Amplified Polymorphic DNA (RAPD) PCR with the primer GEN15008. All the 45 V. parahaemolyticus isolates were positive for the tl gene, however, only 34 were typable via RAPD-PCR with bands sizes ranging from slightly over 250 bp to 2.5 kbp. The degree of diversity was then determined via the Simpson Index which showed a value of 0.891, indicating high diversity among the isolates. Data from the RAPD-PCR fingerprints were later used to construct a dendrogram for clustal analysis. From the dendrogram, the 34 isolates were grouped into 2 major clusters containing 26 and 8 isolates, respectively. Further analyses of the dendrogram also indicated that the 34 isolated were clustered according to the period of sampling. This is an interesting observation as it shows the high discriminatory capability of RAPD-PCR to be used as molecular epidemiological tool to study the temporal distribution of V. parahaemolyticus

Antimicrobial Susceptibilities of Escherichia coli Isolates from Food Animals and Wildlife Animals in Sarawak, East Malaysia.

A total of 133 E. coli strains isolated from different food animals and wildlife sources in Sarawak, Malaysia were screened to determine their antibiotic resistance pattern using the disk diffusion methods

Impacts of pig farming on the water quality of Serin River , Sarawak

In Sarawak, pig farm operators are required to treat the wastewater containing pig waste and spilt food in oxidation ponds before discharge. However, information on the impact of this industry on surface water quality is lacking. Therefore, the objective of this study is to determine the impact of pig farm effluent on the water quality of Serin River and its tributaries. Results of analysis show that the tributary that received pond effluent has significantly higher mean of total suspended solids (TSS), biochemical oxygen demand (BOD5) chemical oxygen demand (COD), ammonia-nitrogen (NH3 -N), reactive phosphorus (SRP) and Escherichia coli (E. coli) concentrations when compared to those of the tributary that did not receive pond effluent. Comparisons between the stations upstream and downstream of the discharge point indicated that BOD5 and COD were significantly higher at the downstream station that received pond effluent. Dissolved oxygen (DO) was the lowest at the tributary receiving effluent from pig farms with a mean of 2.40 mg/l. According to the Interim Water Quality Standard of the Department of Environment, water quality at the tributary that received pig farm effluent falls into Class III whereas that of the other stations falls into Class II. It is recommended that further studies be conducted on the management of waste to explore the possibility of turning the waste into a resource so that water quality of rivers can remain pristine for drinking and recreation

Detection of Cryptosporidium and Cyclospora Oocysts from Environmental Water for Drinking and Recreational Activities in Sarawak, Malaysia

Cryptosporidiosis and cyclosporiasis are caused by waterborne coccidian protozoan parasites of the genera Cryptosporidium and Cyclospora, respectively. This study was conducted to detect Cryptosporidium and Cyclospora oocysts from environmental water abstracted by drinking water treatment plants and recreational activities in Sarawak, Malaysia. Water samples (12 each) were collected from Sungai Sarawak Kanan in Bau and Sungai Sarawak Kiri in Batu Kitang, respectively. In addition, 6 water samples each were collected from Ranchan Recreational Park and UNIMAS Lake at Universiti Malaysia Sarawak, Kota Samarahan, respectively. Water physicochemical parameters were also recorded. All samples were concentrated by the iron sulfate flocculation method followed by the sucrose floatation technique. Cryptosporidium and Cyclospora were detected by modified Ziehl-Neelsen technique. Correlation of the parasites distribution with water physicochemical parameters was analysed using bivariate Pearson correlation. Based on the 24 total samples of environmental water abstracted by drinking water treatment plants, all the samples (24/24; 100%) were positive with Cryptosporidium, and only 2 samples (2/24; 8.33%) were positive with Cyclospora. Based on the 12 total samples of water for recreational activities, 4 samples (4/12; 33%) were positive with Cryptosporidium, while 2 samples (2/12; 17%) were positive with Cyclospora. Cryptosporidium oocysts were negatively correlated with dissolved oxygen (DO)

Identification of Methane-producing Bacteria from Palm Oil Mill Sludge (POMS) with Solid Cud from Ruminant Stomach

Biological generation in anaerobic environments such as enteric fermentation and anaerobic waste treatment from agriculture sector are the major contributor of methane gas which has the potential as biogas. The aimed of this study was to identify methane-producing bacteria in anaerobic vessel which contained a mixture of Palm Oil Mill Sludge (POMS) and solid cud taken from the first compartment of cow’s stomach (1:2 and 2:1 ratio) as co-mixture. The comixture was incubated at 50 °C in a 2 L vessel with initial starter of 400 ml and sampling was conducted every 4 weeks interval during 12 weeks of incubation. For specific detection of methanogens, 16S rRNA-cloning analysis was carried out. Methanobrevibacter sp. and Methanosaeta sp. were confirmed to be presence within the 2:1 ratio of co-mixture while only Methanobrevibacter sp. was found in 1:2 ratio of co-mixture on both Week 0 and Week 4. No methanogens were detected for both co-mixtures on Week 8 and Week 12