Comparison of traditional microbiological culture and 16S polymerase chain reaction analyses for identification of preoperative airway colonization for patients undergoing lung resection

Howitt, Samuel H.; Blackshaw, Diana; Fontaine, Eustace; Hassan, Ibrahim A.; Malagon, Ignacio

doi:10.1016/j.jcrc.2018.04.013

Cited by 3 publications

(2 citation statements)

References 15 publications

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“…In 7 of the cases where different www.nature.com/scientificreports www.nature.com/scientificreports/ predominant organisms were identified, NGS16S identified anaerobes (Table 5), consistent with the fact that anaerobes are not routinely cultured for this specimen type. Prevotella and Veillonella were frequently recovered (14/20 samples, Table 3) and represented the most abundant CRC in 6/20 samples (Table 5), consistent with previous studies 14,[25][26][27] . Anaerobes were the predominant organism in approximately one third of the samples overall (Table 5).…”

Section: Discussionsupporting

confidence: 89%

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

Cummings

Hoogestraat

Rassoulian-Barrett

et al. 2020

Sci Rep

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Optimal clinical decision-making depends on identification of clinically relevant organisms present in a sample. Standard microbiological culture may fail to identify unusual or fastidious organisms and can misrepresent relative abundance of sample constituents. culture-independent methods have improved our ability to deconvolute polymicrobial patient samples. We used next-generation 16S rRNA gene sequencing (NGS16S) to determine how often cultivatable organisms in complex polymicrobial samples are not reported by standard culture. Twenty consecutive bronchoalveolar lavage (BAL) samples were plated to standard and additional media; bacteria were identified by NGS16S analysis of DNA extracted directly from samples or from washed culture plates. 96% of organisms identified were cultivable, but only 21% were reported by standard culture, indicating that standard work-up provides an incomplete assessment of microbial constituents. Direct NGS16S correlated well with standard culture, identifying the same predominant organism in 50% of samples. When predominant organisms differed, NGS16S most often detected anaerobes, whose growth is unsupported by standard culture conditions for this specimen. NGS16S identified more organisms per sample and allowed identification of fastidious organisms, while culture was better at capturing organisms when bacterial load was low, and allowed incidental recovery of non-bacterial pathogens. Molecular and culture-based methods together detect more organisms than either method alone.

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Section: Discussionsupporting

confidence: 89%

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

Cummings

Hoogestraat

Rassoulian-Barrett

et al. 2020

Sci Rep

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“…Howitt compared traditional microbiological cultures and 16S polymerase chain reaction analyses for the identification of preoperative airway colonization in patients undergoing lung resection. The results showed that 16S PCR analyses identify colonizing bacteria in a similar proportion of preoperative BAL samples as traditional cultures [36]. An approach based on Illumina HiSeq 16S rRNA amplicon was used by Xia et al [11], with results showing that Lactococcus lactis JCM5805 was below the detection level after the cessation of probiotics for 5 days, and they inferred that this strain could not colonize the gut; rather, the evaluation of colonization based on the 16S rRNA amplicon technology that they used is limited, for two reasons.…”

Section: Monitored Relative Abundance Changes By High-throughput Sequ...mentioning

confidence: 93%

Lacticaseibacillus casei ATCC 393 Cannot Colonize the Gastrointestinal Tract of Crucian Carp

Hong-yu

Wang

et al. 2021

Microorganisms

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Lactic acid bacteria (LAB) are commonly applied to fish as a means of growth promotion and disease prevention. However, evidence regarding whether LAB colonize the gastrointestinal (GI) tract of fish remains sparse and controversial. Here, we investigated whether Lacticaseibacillus casei ATCC 393 (Lc) can colonize the GI tract of crucian carp. Sterile feed irradiated with 60Co was used to eliminate the influence of microbes, and 100% rearing water was renewed at 5-day intervals to reduce the fecal–oral circulation of microbes. The experiment lasted 47 days and was divided into three stages: the baseline period (21 days), the administration period (7 days: day −6 to 0) and the post-administration period (day 1 to 19). Control groups were fed a sterile basal diet during the whole experimental period, whereas treatment groups were fed with a mixed diet containing Lc (1 × 107 cfu/g) and spore of Geobacillus stearothermophilus (Gs, 1 × 107 cfu/g) during the administration period and a sterile basal diet during the baseline and post-administration periods. An improved and highly sensitive selective culture method (SCM) was employed in combination with a transit marker (a Gs spore) to monitor the elimination of Lc in the GI tract. The results showed that Lc (<2 cfu/gastrointestine) could not be detected in any of the fish sampled from the treatment group 7 days after the cessation of the mixed diet, whereas Gs could still be detected in seven out of nine fish at day 11 and could not be detected at all at day 15. Therefore, the elimination speed of Lc was faster than that of the transit marker. Furthermore, high-throughput sequencing analysis combined with SCM was used to reconfirm the elimination kinetics of Lc in the GI tract. The results show that the Lc in the crucian carp GI tract, despite being retained at low relative abundance from day 7 (0.11% ± 0.03%) to 21, was not viable. The experiments indicate that Lc ATCC 393 cannot colonize the GI tract of crucian carp, and the improved selective culture in combination with a transit marker represents a good method for studying LAB colonization of fish.

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Species-specific genomic sequences for classification of bacteria

Paul

Raj

Murali

et al. 2020

Computers in Biology and Medicine

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Comparison of traditional microbiological culture and 16S polymerase chain reaction analyses for identification of preoperative airway colonization for patients undergoing lung resection

Cited by 3 publications

References 15 publications

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

Lacticaseibacillus casei ATCC 393 Cannot Colonize the Gastrointestinal Tract of Crucian Carp

Species-specific genomic sequences for classification of bacteria

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