Lessons From Mass-Testing for Coronavirus Disease 2019 in Long-Term Care Facilities for the Elderly in San Francisco.

Coronavirus disease 2019 can cause significant mortality in the elderly in long-term care facilities (LTCF). We describe 4 LTCF outbreaks where mass testing identified a high proportion of asymptomatic infections (4%-41% in healthcare workers and 20%-75% in residents), indicating that symptom-based screening alone is insufficient for monitoring for COVID-19 transmission.

Timely intervention and control of a novel coronavirus (COVID-19) outbreak at a large skilled nursing facility-San Francisco, California, 2020.

OBJECTIVE: To describe epidemiologic and genomic characteristics of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in a large skilled-nursing facility (SNF), and the strategies that controlled transmission. DESIGN, SETTING, AND PARTICIPANTS: This cohort study was conducted during March 22-May 4, 2020, among all staff and residents at a 780-bed SNF in San Francisco, California. METHODS: Contact tracing and symptom screening guided targeted testing of staff and residents; respiratory specimens were also collected through serial point prevalence surveys (PPSs) in units with confirmed cases. Cases were confirmed by real-time reverse transcription-polymerase chain reaction testing for SARS-CoV-2, and whole-genome sequencing (WGS) was used to characterize viral isolate lineages and relatedness. Infection prevention and control (IPC) interventions included restricting from work any staff who had close contact with a confirmed case; restricting movement between units; implementing surgical face masking facility-wide; and the use of recommended PPE (ie, isolation gown, gloves, N95 respirator and eye protection) for clinical interactions in units with confirmed cases. RESULTS: Of 725 staff and residents tested through targeted testing and serial PPSs, 21 (3%) were SARS-CoV-2 positive: 16 (76%) staff and 5 (24%) residents. Fifteen cases (71%) were linked to a single unit. Targeted testing identified 17 cases (81%), and PPSs identified 4 cases (19%). Most cases (71%) were identified before IPC interventions could be implemented. WGS was performed on SARS-CoV-2 isolates from 4 staff and 4 residents: 5 were of Santa Clara County lineage and the 3 others were distinct lineages. CONCLUSIONS: Early implementation of targeted testing, serial PPSs, and multimodal IPC interventions limited SARS-CoV-2 transmission within the SNF.

Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology of SARS-CoV-2 in Northern California from late January to mid-March 2020, using samples from 36 patients spanning nine counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least seven different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington state, with lack of a predominant lineage and limited transmission among communities. Lineages associated with outbreak clusters in two counties were defined by a single base substitution in the viral genome. These findings support contact tracing, social distancing, and travel restrictions to contain the spread of SARS-CoV-2 in California and other states.

Emergence of Neisseria gonorrhoeae Strains Harboring a Novel Combination of Azithromycin-Attenuating Mutations.

The nimbleness of Neisseria gonorrhoeae to evade the effect of antibiotics has perpetuated the fight against antibiotic-resistant gonorrhea for more than 80 years. The ability to develop resistance to antibiotics is attributable to its indiscriminate nature in accepting and integrating exogenous DNA into its genome. Here, we provide data demonstrating a novel combination of the 23S rRNA A2059G mutation with a mosaic-multiple transferable resistance (mosaic-mtr) locus haplotype in 14 N. gonorrhoeae isolates with high-level azithromycin MICs (≥256 µg/ml), a combination that may confer more fitness than in previously identified isolates with high-level azithromycin resistance. To our knowledge, this is the first description of N. gonorrhoeae strains harboring this novel combination of resistance determinants. These strains were isolated at two independent jurisdictions participating in the Gonococcal Isolate Surveillance Project (GISP) and in the Strengthening the U.S. Response to Resistant Gonorrhea (SURRG) project. The data suggest that the genome of N. gonorrhoeae continues to shuffle its genetic material. These findings further illuminate the genomic plasticity of N. gonorrhoeae, which allows this pathogen to develop mutations to escape the inhibitory effects of antibiotics.

A multisite implementation of a real-time polymerase chain reaction assay to predict ciprofloxacin susceptibility in Neisseria gonorrhoeae.

There are no commercially available Food and Drug Administration-cleared rapid tests for Neisseria gonorrhoeae antimicrobial susceptibility testing. This study evaluated the performance of a laboratory-developed real-time polymerase chain reaction assay for genotyping the gyrA gene to determine antimicrobial susceptibility to ciprofloxacin. Validation and clinical performance of the gyrA assay were evaluated across 3 geographic locations (Los Angeles, San Francisco, Philadelphia). Following validation, clinical specimens were collected in Aptima Combo2® CT/NG transport medium from asymptomatic persons who tested positive for Neisseria gonorrhoeae and evaluated for assay percent reportable (i.e., proportion of N. gonorrhoeae-positive specimens that yielded a gyrA genotype). The percentage of gyrA genotyping results differed by laboratory and specimen type. The proportion of specimens that were reportable was best for urine/genital specimens (genotyped = 76.4% (95% confidence interval, 69.9-82%)) followed by rectal (genotyped = 67.2% (95% confidence interval, 63.4-70.6%)) and then pharyngeal specimens (genotyped = 36.1%, (95% confidence interval, 31.9-40.5%)). Overall, asymptomatic patients with N. gonorrhoeae yielded an interpretable genotype 57.2% (784/1370) of the time, of which 480 were wild-type gyrA, resulting in 61% (480/784) being potentially treatable with ciprofloxacin.

Differential response of Porphyromonas gingivalis to varying levels and duration of hydrogen peroxide-induced oxidative stress.

Porphyromonas gingivalis, an anaerobic oral pathogen implicated in adult periodontitis, can exist in an environment of oxidative stress. To evaluate its adaptation to this environment, we have assessed the response of P. gingivalis W83 to varying levels and durations of hydrogen peroxide (H(2)O(2))-induced stress. When P. gingivalis was initially exposed to a subinhibitory concentration of H(2)O(2) (0.1 mM), an adaptive response to higher concentrations could be induced. Transcriptome analysis demonstrated that oxidative stress can modulate several functional classes of genes depending on the severity and duration of the exposure. A 10 min exposure to H(2)O(2) revealed increased expression of genes involved in DNA damage and repair, while after 15 min, genes involved in protein fate, protein folding and stabilization were upregulated. Approximately 9 and 2.8% of the P. gingivalis genome displayed altered expression in response to H(2)O(2) exposure at 10 and 15 min, respectively. Substantially more genes were upregulated (109 at 10 min; 47 at 15 min) than downregulated (76 at 10 min; 11 at 15 min) by twofold or higher in response to H(2)O(2) exposure. The majority of these modulated genes were hypothetical or of unknown function. One of those genes (pg1372) with DNA-binding properties that was upregulated during prolonged oxidative stress was inactivated by allelic exchange mutagenesis. The isogenic mutant P. gingivalis FLL363 (pg1372 : : ermF) showed increased sensitivity to H(2)O(2) compared with the parent strain. Collectively, our data indicate the adaptive ability of P. gingivalis to oxidative stress and further underscore the complex nature of its resistance strategy under those conditions.

False-negative rapid diagnostic tests for malaria and deletion of the histidine-rich repeat region of the hrp2 gene.

We identified 480 persons with positive thick smears for asexual Plasmodium falciparum parasites, of whom 454 had positive rapid diagnostic tests (RDTs) for the histidine-rich protein 2 (HRP2) product of the hrp2 gene and 26 had negative tests. Polymerase chain reaction (PCR) amplification for the histidine-rich repeat region of that gene was negative in one-half (10/22) of false-negative specimens available, consistent with spontaneous deletion. False-negative RDTs were found only in persons with asymptomatic infections, and multiplicities of infection (MOIs) were lower in persons with false-negative RDTs (both P < 0.001). These results show that parasites that fail to produce HRP2 can cause patent bloodstream infections and false-negative RDT results. The importance of these observations is likely to increase as malaria control improves, because lower MOIs are associated with false-negative RDTs and false-negative RDTs are more frequent in persons with asymptomatic infections. These findings suggest that the use of HRP2-based RDTs should be reconsidered.

Mouse chromosome 9 quantitative trait loci for soft tissue regeneration: congenic analysis and fine mapping.

Development of gene therapies for wound healing will depend on the identification of the genes involved in wound healing and tissue regeneration. Previous quantitative trait loci (QTL) studies in mice using the ear punch model have shown that major QTL exist on chromosome (Chr) 9 for soft tissue regeneration. In this study, we have developed a congenic line that contains the Chr 9 QTL chromosomal region from super healer MRL/MpJ in the genomic background of poor-healing SJL/J. The phenotypic effect of this QTL was confirmed in male mice, where the congenic line has shown significant healing improvement over SJL. Fine mapping of the Chr 9 QTL region with 23 markers at an average distance of 4.2 Mb using a total of 1,564 MRL/MpJ x SJL/J F(2) mice revealed the presence of at least three QTL peaks, implying that three separate loci may contribute to the phenotypic effect of this QTL. Based on the 2-LOD intervals, the total QTL region was confined to a combined length of no more than 28.2 Mb. Application of a Bayesian shrinkage estimation indicated that a major locus was located in a region of just 1.3 Mb.

New quantitative trait loci that regulate wound healing in an intercross progeny from DBA/1J and 129 x 1/SvJ inbred strains of mice.

Wound healing/regeneration mouse models are few, and studies performed have mainly utilized crosses between MRL/MPJ (a good healer) and SJL/J (a poor healer) or MRL/lpr (a good healer) and C57BL/6J (a poor healer). Wound healing is a complex trait with many genes involved in the expression of the phenotype. Based on data from previous studies that common and additional quantitative trait loci (QTL) were identified using different crosses of inbred strains of mice for various complex traits, we hypothesized that a new cross would identify common and additional QTL, unique modes of inheritance, and interacting loci, which are responsible for variation in susceptibility to fast wound healing. In this study, we crossed DBA/1J (DBA, a good healer) and 129/SvJ (129, a poor healer) and performed a genome-wide scan using 492 (DBA x 129) F2 mice and 98 markers to identify QTL that regulate wound healing/regeneration. Four QTL on chromosomes 1, 4, 12, and 18 were identified which contributed toward wound healing in F2 mice and accounted for 17.1% of the phenotypic variation in ear punch healing. Surprisingly, locus interactions contributed to 55.7% of the phenotype variation in ear punch healing. In conclusion, we have identified novel QTL and shown that minor interacting loci contribute significantly to wound healing in DBA x 129 mice cross.

Identification of quantitative trait loci that regulate obesity and serum lipid levels in MRL/MpJ x SJL/J inbred mice.

The total body fat mass and serum concentration of total cholesterol, HDL cholesterol, and triglyceride (TG) differ between standard diet-fed female inbred mouse strains MRL/MpJ (MRL) and SJL/J (SJL) by 38-120% (P < 0.01). To investigate genetic regulation of obesity and serum lipid levels, we performed a genome-wide linkage analysis in 621 MRLx SJL F2 female mice. Fat mass was affected by two significant loci, D11Mit36 [43.7 cM, logarithm of the odds ratio (LOD) 11.2] and D16Mit51 (50.3 cM, LOD 3.9), and one suggestive locus at D7Mit44 (50 cM, LOD 2.4). TG levels were affected by two novel loci at D1Mit43 (76 cM, LOD 3.8) and D12Mit201 (26 cM, LOD 4.1), and two suggestive loci on chromosomes 5 and 17. HDL and cholesterol concentrations were influenced by significant loci on chromosomes 1, 3, 5, 7, and 17 that were in the regions identified earlier for other strains of mice, except for a suggestive locus on chromosome 14 that was specific to the MRL x SJL cross. In summary, linkage analysis in MRL x SJL F2 mice disclosed novel loci affecting TG, HDL, and fat mass, a measure of obesity. Knowledge of the genes in these quantitative trait loci will enhance our understanding of obesity and lipid metabolism.

A critical evaluation of the effect of population size and phenotypic measurement on QTL detection and localization using a large F2 murine mapping population

Population size and phenotypic measurement are two key factors determining the detection power of quantitative trait loci (QTL) mapping. We evaluated how these two controllable factors quantitatively affect the detection of QTL and their localization using a large F2 murine mapping population and found that three main points emerged from this study. One finding was that the sensitivity of QTL detection significantly decreased as the population size decreased. The decrease in the percentage logarithm of the odd score (LOD score, which is a statistical measure of the likelihood of two loci being lied near each other on a chromosome) can be estimated using the formula 1 - n/N, where n is the smaller and N the larger population size. This empirical formula has several practical implications in QTL mapping. We also found that a population size of 300 seems to be a threshold for the detection of QTL and their localization, which challenges the small population sizes commonly-used in published studies, in excess of 60 percent of which cite population sizes <300. In addition, it seems that the precision of phenotypic measurement has a limited capacity to affect detection power, which means that quantitative traits that cannot be measured precisely can also be used in QTL mapping for the detection of major QTL.

Mapping the dominant wound healing and soft tissue regeneration QTL in MRL x CAST.

We have used a mouse ear punch model and the QTL (quantitative trait loci) mapping technique to identify genes that are responsible for soft tissue regeneration. In the early studies, we have identified several QTL and have shown that the inheritance of ear healing was additive in one cross (MRL x SJL), and recessive in another cross (DBA x 129). Because CAST mice are genetically distinct and have a different genetic background, CAST would facilitate the identification of common and novel QTL when crossed with common inbred lines. We made a cross between super healer MRL and poor healer CAST and collected ear punch phenotype and marker genotype data from F(2). Ear punch healing exhibited a dominant mode of inheritance in this cross. There were three main QTL on Chromosomes 4, 9, and 17, and two suggestive QTL on Chromosomes 1 (new) and 7. Taken together, these QTL accounted for about 29% of total F2 variance of MRL x CAST. Compared with another study using the same cross, we found a totally different set of QTL. Two QTL interactions were identified by a full QTL model: Chromosomes 4 x 17 and 9 x 17; the latter reached to a statistical level at p < 0.05. These interactions explained about 4% of the F2 phenotypic variance. We conclude that soft tissue regeneration is controlled by multiple genes and locus vs. locus interactions.

Bayesian shrinkage estimation of quantitative trait loci parameters.

Mapping multiple QTL is a typical problem of variable selection in an oversaturated model because the potential number of QTL can be substantially larger than the sample size. Currently, model selection is still the most effective approach to mapping multiple QTL, although further research is needed. An alternative approach to analyzing an oversaturated model is the shrinkage estimation in which all candidate variables are included in the model but their estimated effects are forced to shrink toward zero. In contrast to the usual shrinkage estimation where all model effects are shrunk by the same factor, we develop a Bayesian method that allows the shrinkage factor to vary across different effects. The new shrinkage method forces marker intervals that contain no QTL to have estimated effects close to zero whereas intervals containing notable QTL have estimated effects subject to virtually no shrinkage. We demonstrate the method using both simulated and real data for QTL mapping. A simulation experiment with 500 backcross (BC) individuals showed that the method can localize closely linked QTL and QTL with effects as small as 1% of the phenotypic variance of the trait. The method was also used to map QTL responsible for wound healing in a family of a (MRL/MPJ x SJL/J) cross with 633 F(2) mice derived from two inbred lines.

Isolation of wound healing/regeneration genes using restrictive fragment differential display-PCR in MRL/MPJ and C57BL/6 mice.

Wound healing in mammals can take several weeks to months and the process is always accompanied by scar formation. Wound healing mechanisms that mimic regeneration are not found in most mature mammalian tissues. However, the MRL/MPJ (MRL) mouse has the unique capacity to regenerate ear hole wound completely in less than a month. To identify genes involved in wound healing without a scar, we chose to use restriction fragment differential display-PCR to isolate genes differentially expressed in the MRL (good healer) mouse and the C57BL/6 (poor healer) mouse at different stages of wound healing. We identified 36 genes that were differentially expressed in the regenerating tissue of good and poor healer strains of which several genes are also genetically linked to wound healing and thus are potential candidate genes for scarless wound healing.

Mapping quantitative trait loci that influence serum insulin-like growth factor binding protein-5 levels in F2 mice (MRL/MpJ X SJL/J).

Recent studies using twins and inbred strains of mice reveal evidence for genetic mechanisms contributing to variation in circulating levels of IGF-I, IGF-II, and IGF binding protein (IGFBP)-3. To examine the hypothesis that serum IGFBP-5 levels have a strong heritable component, we intercrossed two inbred strains of mice, MRL/MpJ and SJL, which exhibit 79% difference in serum IGFBP-5 levels (554 +/- 68 vs. 309 +/- 51 ng/ml respectively, P < 0.001). A genome-wide scan was carried out using 137 polymorphic markers in 633 F2 female mice. Serum IGFBP-5 levels in the F2 progeny showed a normal distribution with an estimated heritability of 74%. Whole genome-wide scans for cosegregation of genetic marker data with high or low serum IGFBP-5 levels revealed six different quantitative trait loci (QTL) in chromosomes 1, 9 (two), 10, and 11 (two), which together explained 24% of F2 variance. Chromosome 11 QTL exhibited the highest LOD score (7.5). Based on the past findings that IGFBP-5 is an important bone formation stimulator, we predicted IGFBP-5 to contribute to bone mineral density variation in F2 mice. Accordingly, we found two of the six IGFBP-5 QTLs (Chrs 1 and 11) identified for serum IGFBP-5 phenotype also showed significant association with total body bone mineral density phenotype (measured by dual energy x-ray absorptiometry) in the F2 mice.

Quantitative trait loci (QTL) for lean body mass and body length in MRL/MPJ and SJL/J F(2) mice.

Studies on the genetic mechanisms involved in the regulation of lean body mass (LBM) in mammals are minimal, although LBM is associated with a competent immune system and an overall good (healthy) body functional status. In this study, we performed a high-density genome-wide scan using 633 (MRL/MPJ x SJL/J) F(2) intercross to identify the quantitative trait loci (QTL) involved in the regulation of LBM. We hypothesized that additional QTL can be identified using a different mouse cross (MRL/SJL cross). Ten QTL were identified for LBM on chromosomes (chrs) 2, 6, 7, 9,13 and 14. Of those ten, QTL on chrs 6, 7 and 14 were exclusive to LBM, while QTL on chrs 4 and 11 were exclusively body length. LBM QTL on chrs 2 and 9 overlap with those of size. Altogether, the ten LBM QTL explained 41.2% of phenotypic variance in F(2) mice. Five significantly interacting loci that may be involved in the regulation of LBM were identified and accounted for 24.4% of phenotypic variance explained by the QTL. Five epistatic interactions, contributing 22.9% of phenotypic variance, were identified for body length. Interacting loci on chr 2 may influence LBM by regulating body length. Therefore, epistatic interactions as well as single QTL effects play an important role in the regulation of LBM.

Quantitative trait loci that harbor genes regulating muscle size in (MRL/MPJ x SJL/J) F(2) mice.

The genetic mechanisms that determine muscle size have not been elucidated, even though it is a key musculoskeletal parameter that reflects muscle strength. In this study, we performed a high-density genome-wide scan using 633 (MRL/MPJ x SJL/J) F(2) intercross 7-week-old mice to identify quantitative trait loci (QTL) involved in the determination of muscle size. Significant QTL were identified for muscle size and body length. Muscle size (adjusted by body length) QTL were identified on chromosomes 7, 9, 11, 14 (two QTL) and 17, which together explained 19.2% of phenotypic variance in F(2)mice, while body length QTL were located on chromosome 2 (two QTL), 9, 11 and 17 which accounted for 28.3% of phenotypic variance in F(2) mice. Three significant epistatic interactions between different QTL positions from muscle size and body length were identified ( P <0.01) on chromosomes 2, 9, 14 and 17, which explained 16.1% of the variance in F(2) mice.

Genetic dissection of femur breaking strength in a large population (MRL/MpJ x SJL/J) of F2 Mice: single QTL effects, epistasis, and pleiotropy.

Bone breaking strength is an ultimate measurement of the risk of fracture. For a practical reason, bone mineral density (BMD) has been commonly used for predicting the risk instead. To identify genetic loci influencing femur-breaking strength (FBS), which was measured by three-point bending using an Instron DynaMight Low-Force Testing System, the whole-genome scan was carried out using 119 polymorphic markers in 633 (MRLxSJL) F2 female mice. We identified six significant quantitative trait loci (QTL) affecting bone breaking strength on chromosomes 1, 2, 8, 9, 10, and 17, which together explained 23% of F2 variance. Of those, the QTL on chromosomes 2, 8, and 10 seem to be unique to bone breaking strength, whereas the remaining three QTL are concordant with femur BMD QTL. Genetic analysis suggests that, of these six FBS QTL, three influence BMD, two influence bone quality, and one influences bone size. We detected multiple significant epistatic interactions for FBS, which accounts for half (14.6%) of F2 variance compared with significant single QTL effects. We found evidence that pleiotropic effect might represent a common genetic mechanism to coordinately regulate bone-related phenotypes. Pleiotropic analysis also suggests that our current threshold level for significant QTL may be too high to detect biologically significant QTL with small effect. Together with epistatic interactions, these undetected small QTL could explain 30% of genetic variance that remains unaccounted for in this study (heritability estimate for FBS is 68%). Our findings in single QTL effects, epistasis, and pleiotropy demonstrate that partially overlapped but distinct combinations of genetic loci in MRL/MpJ and SJL/J inbred strains of mice regulate bone strength and bone density. Identification of the genes unique to FBS may have an impact on prediction of osteoporosis in human.

Chromosomal regions harboring genes for the work to femur failure in mice.

The work to failure is defined as the maximum energy bone can absorb before breaking, and therefore is a direct test of the risk of fracture. To determine the genetic loci influencing work to failure, we have performed a high density genome-wide scan in 633 (MRL x SJL) F(2) female mice. Five loci ( P<0.005) with significant effects on work to failure were found on chromosomes 2, 7, 8, 9, and X, which collectively explained around 20% variance of work to femur failure in F(2) mice. Of those, only the QTL on chromosome 9 was concordant with bone mineral density (BMD) QTLs. Eight significant interactions ( P<0.01) between marker loci were identified, which accounted for an equivalent amount of F(2) variance (23%) to combined single QTL effects. Our results demonstrate that most of the genetic loci regulating work to failure are different from those for BMD in the 7-week-old female mice. If this is also true in humans, this finding will challenge the predictive value of BMD for the risk of fracture.