Microbial and Physiochemical Analysis of Water From Semenggok Inland Fishery Centre, Kuching, Sarawak

Water quality is emphasized by the aquaculture sector as it affects the health and growth performance of aquaculture species. However, due to the outbreak of COVID-19 pandemic in Malaysia, various sectors including aquaculture sector, have been instructed to shut down as a lockdown alternative to control the spread of the disease. The total lockdown has made impossible to give proper management to the aquaculture ponds and indirectly led to the high mortality of aquaculture organisms. High mortality has led to rapid microbial growth, which affected the water quality and the balance in the aquaculture system. The objective of this project was to examine the water quality of selected ponds at Semenggok Inland Fishery Centre via physiochemical and microbial analysis. This project also aimed to determine and identify the bacteria population in examined water samples. Lastly, this project sought to determine the antimicrobial susceptibility patterns of identified isolates. In this study, the characteristics of aquaculture environmental samples were determined. Water and soil samples were collected from three randomly selected ponds in the Semenggok Inland Fishery Centre, Kuching, Sarawak and the physiochemical and biological parameters were analysed. Bacteria were isolated from both water and soil samples and then characterised. Boiling-centrifugation method with modifications were used for DNA extraction of the bacteria [1,2]. (GTG)5-PCR was utilized to screen for clonal diversity among the isolates. A dendrogram was constructed using GelJ 1.0 software from the banding profile of (GTG)5-PCR products[3]. Out of all the isolates analysed, 11 representative isolates were selected for 16S rRNA sequencing based on the grouping from the dendrogram. The 11 isolates were identified as Brevundimonas sp., Staphylococcus sp., Pseudomonas sp., Escherichia sp., Ralstonia sp., and Exiguobacterium sp.The isolates were tested for antibiotic resistance using the disc diffusion method. Most of the isolates tested were resistant to ampicillin (10 μg), penicillin (10 μg), and streptomycin (10 μg). The MAR index of isolates were calculated, ranged from 0.143 to 0.714, indicating high possibility of culturing fish in the contaminated water. This study revealed the risk of presence of multiple antibiotic resistance (MAR) bacteria in the fishery centre. Therefore, the fishery centre should improve the aquaculture system by constantly monitoring and also provide a proper management to the wastewater to minimise the distribution of MAR bacteria

Emerg Infect Dis

201627648951PMC5038415826

The overlap of accessory virulence factors and multidrug resistance among clinical and surveillance Klebsiella pneumoniae isolates from a neonatal intensive care unit in Nepal: a single-centre experience in a resource-limited setting

Background: There is a lack of data on the characteristics of overlap between acquired antimicrobial resistance and virulence factors in Klebsiella pneumoniae in high-risk settings, especially with the inclusion of surveillance isolates along with the clinical. We investigated K. pneumoniae isolates, from a neonatal intensive care unit (NICU) in Nepal, for the presence of both accessory virulence factors and acquired antimicrobial resistance. Methods: Thirty-eight clinical and nineteen surveillance K. pneumoniae isolates obtained between January 2017 and August 2022 in the NICU of Siddhi Memorial Hospital, Bhaktapur, Nepal were investigated with antimicrobial susceptibility testing, PCR-based detection of β-lactamases and virulence factors, and genetic similarity by ERIC–PCR. Results: K. pneumoniae was found positive in 37/85 (43.5%) blood culture-positive neonatal bloodstream infections, 34/954 (3.6%) patient surveillance cultures, and 15/451 (3.3%) environmental surveillance samples. Among 57 isolates analyzed in this study, we detected multidrug resistance in 37/57 (64.9%), which was combined with at least one accessory virulence factor in 21/37 (56.8%). This overlap was mostly among β-lactamase producing isolates with accessory mechanisms of iron acquisition. These isolates displayed heterogenous ERIC–PCR patterns suggesting genetic diversity. Conclusions: The clinical significance of this overlap between acquired antimicrobial resistance and accessory virulence genes in K. pneumoniae needs further investigation. Better resource allocation is necessary to strengthen infection prevention and control interventions in resource-limited settings

Clones de alto risco de Klebsiella pneumoniae produtores de ESBL colonizando pacientes de UTI em Natal, Nordeste do Brasil

Background and objectives: colonization by extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae in Intensive Care Unit (ICU) patients is considered a risk factor for infections, and poses as a source of spreading these strains in hospital facilities. This study aimed to perform the genetic characterization of ESBL-producing K. pneumoniae isolates recovered from surveillance swabs in an ICU in northeastern Brazil. Methods: the isolates were recovered between 2018-2019 from the nasal, axillary, and rectal sites of 24 patients admitted to the ICU. Bacterial identification was performed by traditional biochemical tests. Antimicrobial susceptibility was assessed by disk diffusion, and ESBL phenotype was detected by double-disc synergy test. Polymerase chain reaction (PCR) for blaCTX-M, blaSHV, and blaTEM genes, PFGE, and MLST were carried out in representative isolates. Results: a total of 27 isolates were recovered from 18 patients (75%). The ESBL production was detected in 85% of isolates. Resistance to ciprofloxacin, sulfamethoxazole/trimethoprim and most of the β-lactams tested was recurrent, except for carbapenems. The blaSHV, blaTEM, and blaCTX-M genes were found in high frequency, and the CTX-M-(1, 2 and 9) groups were identified. Seven sequence types (ST11, ST14, ST17, ST395, ST709, ST855, and ST3827) were described, most of them considered high-risk. Conclusion: these findings emphasize the potential threat of well-established high-risk clones in an ICU, and highlight the importance of monitoring these clones to prevent infections.Justificación y objetivos: la colonización por Klebsiella pneumoniae productora de β-lactamasas de espectro extendido (BLEE) en pacientes de Unidades de Cuidados Intensivos (UCI) se considera un factor de riesgo para infecciones, y se presenta como una fuente de propagación de estas cepas en instalaciones hospitalarias. Este estudio tuvo como objetivo realizar la caracterización genética de aislamientos de K. pneumoniae productores de BLEE recuperados de hisopos de vigilancia en una UCI en el noreste de Brasil. Métodos: los aislamientos se recuperaron entre 2018-2019 de sitios nasales, axilares y rectales de 24 pacientes ingresados en la UCI. La identificación bacteriana se realizó mediante pruebas bioquímicas tradicionales. La susceptibilidad antimicrobiana se evaluó mediante difusión en disco, y el fenotipo BLEE se detectó mediante la prueba de sinergia de doble-disco. La polymerase chain reaction (PCR) para los genes blaCTX-M, blaSHV y blaTEM, PFGE y MLST se llevaron a cabo en aislamientos representativos. Resultados: se recuperaron 27 aislamientos de 18 pacientes (75%). La producción de ESBL se detectó en 85% de los aislamientos. La resistencia a ciprofloxacino, sulfametoxazol/trimetoprima y a la mayoría de los β-lactámicos evaluados fue recurrente, excepto a los carbapenémicos. Los genes blaSHV, blaTEM y blaCTX-M se encontraron en alta frecuencia, y se identificaron los grupos CTX-M-(1, 2 y 9). Se describieron siete sequence types (ST11, ST14, ST17, ST395, ST709, ST855 y ST3827), la mayoría consideradas de alto riesgo. Conclusión: estos hallazgos enfatizan la amenaza potencial de los clones de alto riesgo bien establecidos en una UCI, y resaltan la importancia de monitorear estos clones para prevenir infecciones.Justificativa e objetivos: a colonização por Klebsiella pneumoniae produtora de β-lactamase de espectro estendido (ESBL) em pacientes de Unidade de Terapia Intensiva (UTI) é considerada um fator de risco para infecções, e representa uma fonte de disseminação dessas cepas em instalações hospitalares. Este estudo objetivou realizar a caracterização genética de isolados de K. pneumoniae produtores de ESBL recuperados de swabs de vigilância em uma UTI no Nordeste do Brasil. Métodos: os isolados foram recuperados entre 2018-2019 dos sítios nasal, axilar e retal de 24 pacientes internados na UTI. A identificação bacteriana foi realizada por testes bioquímicos tradicionais. A suscetibilidade antimicrobiana foi avaliada por disco-difusão, e o fenótipo ESBL foi detectado pelo teste de sinergia de duplo-disco. Polymerase chain reaction (PCR) para os genes blaCTX-M, blaSHV e blaTEM, PFGE e MLST foram realizados em isolados representativos. Resultados: foram recuperados 27 isolados de 18 pacientes (75%). A produção de ESBL foi detectada em 85% dos isolados. A resistência à ciprofloxacina, sulfametoxazol/trimetoprima e à maioria dos β-lactâmicos testados foi recorrente, exceto para os carbapenêmicos. Os genes blaSHV, blaTEM e blaCTX-M foram encontrados em alta frequência, e os grupos CTX-M-(1, 2 e 9) foram identificados. Sete sequence types (ST11, ST14, ST17, ST395, ST709, ST855 e ST3827) foram descritos, a maioria deles considerados de alto risco. Conclusão: esses achados enfatizam a ameaça potencial de clones de alto risco bem estabelecidos em uma UTI, e destacam a importância do monitoramento desses clones para prevenir infecções

A Possible Outbreak by Serratia Marcescens: Genetic Relatedness between Clinical and Environmental Strains

Serratia marcescens (SM) is a Gram-negative bacterium that is frequently found in the environment. Since 1913, when its pathogenicity was first demonstrated, the number of infections caused by SM has increased. There is ample evidence that SM causes nosocomial infections in immunocompromised or critically ill patients admitted to the intensive care units (ICUs), but also in newborns admitted to neonatal ICUs (NICUs). In this study, we evaluated the possible genetic correlation by PFGE between clinical and environmental SM strains from NICU and ICU and compared the genetic profile of clinical strains with strains isolated from patients admitted to other wards of the same hospital. We found distinct clonally related groups of SM strains circulating among different wards of a large university hospital. In particular, the clonal relationship between clinical and environmental strains in NICU and ICU 1 was highlighted. The identification of clonal relationships between clinical and environmental strains in the wards allowed identification of the epidemic and rapid implementation of adequate measures to stop the spread of SM

Origin and distribution of different retrotransposons in different taxa

Novel genome analysis technologies enable genomic studies of transposable elements (TEs) in different organisms. Population studies of human genome show thousands of individual TE insertions. These insertions are important source of natural human genetic variation. Researchers are beginning to develop population genomic data sets for evaluating the phenotypic impact of human TE polymorphisms. Because of the evidences of horizontal transfer of retrotransposons between different species genome, in this study we aimed to detect barley retrotransposons (Nikita and BAGY2) in the human genome. Inter retrotransposon amplified polymorphism polymerase chain reaction (IRAP PCR) were used to measure the distribution of Nikita and BAGY2 retroelements in the human genome. Analyses reveals that Nikita and BAGY2 are present in the human genome and show different distribution in the genome. The polymorphism ratios of retroelements suggest that Nikita and BAGY2 have been active retrotransposons in the human genome

High-risk clones of ESBL-producing Klebsiella pneumoniae colonizing ICU patients in Natal, northeastern Brazil

Background and objectives: colonization by extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae in Intensive Care Unit (ICU) patients is considered a risk factor for infections, and poses as a source of spreading these strains in hospital facilities. This study aimed to perform the genetic characterization of ESBL-producing K. pneumoniae isolates recovered from surveillance swabs in an ICU in northeastern Brazil. Methods: the isolates were recovered between 2018-2019 from the nasal, axillary, and rectal sites of 24 patients admitted to the ICU. Bacterial identification was performed by traditional biochemical tests. Antimicrobial susceptibility was assessed by disk diffusion, and ESBL phenotype was detected by double-disc synergy test. Polymerase chain reaction (PCR) for blaCTX-M, blaSHV, and blaTEM genes, PFGE, and MLST were carried out in representative isolates. Results: a total of 27 isolates were recovered from 18 patients (75%). The ESBL production was detected in 85% of isolates. Resistance to ciprofloxacin, sulfamethoxazole/trimethoprim and most of the β-lactams tested was recurrent, except for carbapenems. The blaSHV, blaTEM, and blaCTX-M genes were found in high frequency, and the CTX-M-(1, 2 and 9) groups were identified. Seven sequence types (ST11, ST14, ST17, ST395, ST709, ST855, and ST3827) were described, most of them considered high-risk. Conclusion: these findings emphasize the potential threat of well-established high-risk clones in an ICU, and highlight the importance of monitoring these clones to prevent infections

Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children

The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (blaCTX-M-65) and i-pAmpC (blaDHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with blaCTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a blaSHV gene. All isolates presented D87Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR blaCTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR blaCTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level

Multidrug-resistant and clonal dispersion of enterotoxigenic Escherichia coli from ready-to-eat meat products in Duhok province, Iraq

This research evaluated the effluent proportion of E. coli and ETEC in RTE meat products, characterized the isolated strains' clonal relatedness, and determined their antibiotic resistance. 130 RTE products were gathered from various restaurants and street fast food vendors in Duhok and Zakho Province. The Isolates of E. coli identified by culture methods were confirmed as ETEC by multiplex PCR of the identified virulence genes. ERIC-PCR was applied to establish the clonal relationships between strains. The disk diffusion method performed the susceptibility of antibiotics on the isolated ETEC. Out of 130 examined samples, 39 (30%) isolates of E. coli and 16 (12.3%) ETEC were detected. Pan-fried burgers were revealed to be the most frequent contaminated sample type, with both E. coli and ETEC 50% and 23.3%, respectively (P≤0.05). A high clonal dispersion (12 genotypes) was observed among the isolated ETEC strains. A strong genetic linkage was discovered between a few isolates retrieved from the same sample type and within the strains from the same geographic source area. A high antibiotic resistance rate was observed with total resistance to Amoxicillin/clavulanate, Clarithromycin, Doxycycline, Erythromycin, and Clindamycin. Isolates from burger samples showed a higher resistance rate when compared with the other sample types (P≤0.05). Multi-drug resistance was noticed in all ETEC isolates. RTE meat products sold in our area have a high rate of clonally heterogeneous carrying multi-drug resistant ETEC and may constitute a significant public health risk